[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $sbst_model = 'HKY85' will be changed to 'TN93' ...

[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $resfreq = 'e' will be changed to '0.25,0.25,0.25,0.25' ...

[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $gaprate = '0.025' will be changed to 'Dawgx0.71251' ...

[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $gapext = '0.75' will be changed to '0.3957' ...

[INFO 'classify_msa_errors_via_mblks.2val.pl'] The argument $if_insopen_forever = '0' will be changed to '1' ...


<<<<<<< Program name: classify_msa_errors_via_mblks.2val.pl (path: /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/Scripts/classify_msa_errors_via_mblks.2val.pl) >>>>>>>>

Current working directory: /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/class_0001/lclid_0000005 .

Binary programs:
     (for tree inference)  /Users/kezawa3/Bioinformatics/PhyML/Compiled/bin/phyml ,
Source control file (for PhyML): Not used .
Source file of substitution model (for PhyML): Not used .

Sequence type: Nucleotide .

Input files:
     (Tree)      /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/dawg_inp0000005.txt .

    (anchor MSA) /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/refaln.0000005.aln .

   (simulation parameters} /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/dawg_inp0000005.txt,
   (reference MSA)         /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/refaln.0000005.aln,
   (reconstructed MSA)     /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/recaln.0000005.aln,
   (list of segments)      /Users/kezawa3/Ezawa_works_UH/Main_Project/Secondary_Projects/ANALYSES/MSA_Prcd_Errors3/Contrast_Analyses/Classify_Errors/Erroneous_Regions/Validation/TEST_Outputs/Test_MAFFT/Temporary/class_0001/equiv_rgs_brief.0000005.txt .

Directory for interim output files for tree inference: Interim/Infer_tree .

Interim output list of candidate trees:  {topoutdir}/tree_whole_full.txt .
Temporary directories for PAML (obsolete):  {top_tmpdir}/s{seg_id}/g{indx_gpattern}/t{indx_tree}/,
   where {top_tmpdir} = Interim/Tmp/Ref for the reference MSA,
                      = Interim/Tmp/Rec for the reconstructed MSA.

Summary outputs:
   (1st Round) tbl_summ_class_msa_errors.1.txt ,
   (2nd Round) tbl_summ_class_msa_errors.2.txt .

Directory for the log files: {log_dir} = LogFiles .

Log files:
   (for candidate tree enumeration) {log_dir}/log_tree_whole_full.txt .

   (for analyzing the reference & reconstructed MSAs for each segment) {log_dir}log_seg_anal.{seg_id}.txt .

* All the temporary outputs will be removed .

Parameters for tree inference (via PhyML):

   Substitution model:  TN93 .
   (Model for PhyML: HKY85 .)

   #{Substitution rate categories}: 1 .
   Gamma shape parameter for the rate variation across sites: 0 .
   Tree topology search method: NNI .
   Option on what to do with the residue frequencies: 0.25,0.25,0.25,0.25 .


   Transition/transversion ratios:
        (for A <-> G) 1 ,
        (for T <-> C) 1 ,
       (average (to be used for PhyML (if applicable))) 1 .



Options for PhyML shared by both tree inference and column-wise likelihood calculation:

   $OPTIONS_SHARED = ' -d nt -c 1 ' .


Levels of tests for debugging or behavior tests:

   $TEST_LEVEL_VAL    =  1 ,

   $TEST_LEVEL        =  0 ,
   $TEST_LEVEL2       =  0 ,
   $TEST_LEVEL_newtype   = 0 ,
   $TEST_LEVEL_cipc   = 0 ,
   $TEST_LEVEL_cipc2   = 0 ,
   $TEST_LEVEL_umlp   = 0 ,
   $DBG_LEVEL_EXPHYML =  0 ,
   $FLG_RMV_TMPOUT    =  1 .


Parameters in the Perl package 'MyMalnComparison.pm':

$MyMalnComparison::TEST_LEVEL_lc  = 0 .


Parameters in the Perl package 'MyTreeMap_indels_spt_odr.pm':

$MyTreeMap_indels_spt_odr::UPPER_BOUND_ANAL_LEN_GBCLS = 150 ,
$MyTreeMap_indels_spt_odr::UPPER_BOUND_ANAL_GAPLEN = 120 .



<<<<< Now, read in the list of segments >>>>>


#{segments} = 33

Seg_ID	Start_in_Ref	End_in_ref	Start_in_Rec	End_in_Rec	Diagnosis

0	0	0	0	0	IDENTICAL
1	14	25	14	25	CLEARLY_DIFFERENT
2	41	86	41	78	CLEARLY_DIFFERENT
3	105	153	97	141	CLEARLY_DIFFERENT
4	157	167	145	153	CLEARLY_DIFFERENT
5	175	198	161	181	CLEARLY_DIFFERENT
6	210	218	193	201	CLEARLY_DIFFERENT
7	221	223	204	206	CLEARLY_DIFFERENT
8	228	246	211	229	CLEARLY_DIFFERENT
9	253	255	236	238	CLEARLY_DIFFERENT
10	259	266	242	249	CLEARLY_DIFFERENT
11	274	282	257	265	CLEARLY_DIFFERENT
12	286	328	269	310	CLEARLY_DIFFERENT
13	360	367	342	349	CLEARLY_DIFFERENT
14	394	503	376	437	CLEARLY_DIFFERENT
15	508	672	442	532	CLEARLY_DIFFERENT
16	681	686	541	545	CLEARLY_DIFFERENT
17	701	809	560	666	CLEARLY_DIFFERENT
18	825	859	682	716	CLEARLY_DIFFERENT
19	860	864	717	721	CLEARLY_DIFFERENT
20	905	924	762	779	CLEARLY_DIFFERENT
21	937	941	792	796	CLEARLY_DIFFERENT
22	949	990	804	840	CLEARLY_DIFFERENT
23	1002	1110	852	957	CLEARLY_DIFFERENT
24	1177	1242	1024	1072	CLEARLY_DIFFERENT
25	1296	1439	1126	1267	CLEARLY_DIFFERENT
26	1454	1456	1282	1284	CLEARLY_DIFFERENT
27	1463	1475	1291	1303	CLEARLY_DIFFERENT
28	1489	1563	1317	1384	CLEARLY_DIFFERENT
29	1573	1588	1394	1409	CLEARLY_DIFFERENT
30	1592	1609	1413	1425	CLEARLY_DIFFERENT
31	1616	1623	1432	1438	CLEARLY_DIFFERENT
32	1626	1759	1441	1572	CLEARLY_DIFFERENT



<<<<< Now, read in the reference MSA >>>>>

#{sequences in MSA} =  15 .
#{columns in MSA}   = 1759 .


<<<<< Now, read in the reconstructed MSA >>>>>

#{columns in MSA} = 1572 .


<<<<< Now, read in the core alignment (to be fed into tree reconstruction, if necessary) >>>>>

#{columns in MSA} = 1759 .


<<<<< Now, give nominal frequencies to the residues >>>>>



<< Residue frequencies estimated from the core alignment >>

Residue	Frequency

A	0.2500000
C	0.2500000
G	0.2500000
T	0.2500000



<<<<< Reading-in the Input Tree >>>>>


<<<<< Now, create an interim file recording the input trees >>>>>


<<<<< Now, calculate the Akaike weights of the candidate trees and necessary inputs  >>>>>


<<<<< Now, Output candidate trees, their Akaike weights, and their attributes  >>>>>

< The 0 th candidate tree (topnode ID: 29; Log_Akaike_weight = 0) >

Sum (-log(Pv)) = NA
log (Prob(MSA|Tree)_ML) = NA
#{free parameters} = NA
AIC = 0
BIC = 0

( seq0020{28}:0.1529, ( seq0018{26}:0.1741, ( ( seq0015{23}:0.1492, ( seq0013{20}:0.1827, seq0014{21}:0.1659 ){22}:0.0049 ){24}:0.0297, ( ( seq0008{16}:0.0865, seq0009{17}:0.1286 ){18}:0.0335, ( ( seq0005{10}:0.0368, ( seq0006{11}:0.0286, seq0007{12}:0.0362 ){13}:0.0065 ){14}:0.0368, ( ( seq0000{1}:0.0054, seq0001{2}:0.0081 ){3}:0.0232, ( seq0002{4}:0.0189, ( seq0003{5}:0.0124, seq0004{6}:0.0108 ){7}:0.0070 ){8}:0.0270 ){9}:0.0205 ){15}:0.0703 ){19}:0.0383 ){25}:0.0314 ){27}:0.0130 ){29};

Branch_ID	length	P-value	parent_node_ID

1	0.0054	NA	3
2	0.0081	NA	3
3	0.0232	NA	9
4	0.0189	NA	8
5	0.0124	NA	7
6	0.0108	NA	7
7	0.0070	NA	8
8	0.0270	NA	9
9	0.0205	NA	15
10	0.0368	NA	14
11	0.0286	NA	13
12	0.0362	NA	13
13	0.0065	NA	14
14	0.0368	NA	15
15	0.0703	NA	19
16	0.0865	NA	18
17	0.1286	NA	18
18	0.0335	NA	19
19	0.0383	NA	25
20	0.1827	NA	22
21	0.1659	NA	22
22	0.0049	NA	24
23	0.1492	NA	24
24	0.0297	NA	25
25	0.0314	NA	27
26	0.1741	NA	27
27	0.0130	NA	29
28	0.1529	NA	29



 ... Confirmed that all interior nodes of this tree have 2 child nodes each ...


 ... The subroutine 'make_node2abs_depth' Ended ...


 ... The subroutine 'make_node2ct_exoffs' Ended ...

Node_ID	Depth	#{exteior_offsprings}

1	8	1
2	8	1
3	7	2
4	8	1
5	9	1
6	9	1
7	8	2
8	7	3
9	6	5
10	7	1
11	8	1
12	8	1
13	7	2
14	6	3
15	5	8
16	6	1
17	6	1
18	5	2
19	4	10
20	6	1
21	6	1
22	5	2
23	5	1
24	4	3
25	3	13
26	3	1
27	2	14
28	2	1
29	1	15



Seq_indx	Seqname	Node_ID

0	seq0000	1
1	seq0001	2
2	seq0002	4
3	seq0003	5
4	seq0004	6
5	seq0005	10
6	seq0006	11
7	seq0007	12
8	seq0008	16
9	seq0009	17
10	seq0013	20
11	seq0014	21
12	seq0015	23
13	seq0018	26
14	seq0020	28






<<<<<<< The Main Analyses: Classify the MSA Errors in each Erroneous Segments by comparing Reference & Reconstructed segmental MSAs. >>>>>>>

<<<<<< Segment ID: 1  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (11, 11)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 1 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 1) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 11 ,
#{columns in new reconstructed MSA} = 11 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10

seq0000   	    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    0    0    0    -
seq0009   	    -    -    -    3    3    3    3    0    0    0    -
seq0013   	    0    0    0    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10

seq0000   	    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    -    1    1    1
seq0009   	    -    -    -    -    1    1    1    1    1    1    1
seq0013   	    0    0    0    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	1	0	1	1	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift	1	17:4:6:X	17:0:2:X
2nd(reconstructed)	Complex(???)	100	18:10:10:X/17:0:2:X	17:0:3:X


{Total penalty} = 101 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 11 ,
#{columns in new reconstructed MSA} = 11 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10

seq0000   	    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    -    1    1    1
seq0009   	    0    0    0    0    -    -    -    -    1    1    1
seq0013   	    0    0    0    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10

seq0000   	    0    0    0    0    0    0    0    0    0    0    0
seq0001   	    0    0    0    0    0    0    0    0    0    0    0
seq0002   	    0    0    0    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    0    0    0    -    0    0    0
seq0009   	    -    -    -    -    4    4    4    4    0    0    0
seq0013   	    0    0    0    0    0    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	1	1	0	1	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift	1	18:10:10:X	18:7:7:X
2nd(reconstructed)	Inter-branch-transfer(rec>ref)(??)	7	17:4:6:X	17:0:3:X/16:7:7:X


{Total penalty} = 8 .





 --- Finished analysis for the segment 1 ! ---

<<<<<< Segment ID: 2  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (45, 37)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 18) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 2 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 4) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 4 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (0 -> 4) canNOT be undone completely because of the failure type, $if_success = -11: No such file or directory !

{ The 1 th Path: (refernce ->) 4 -(intermediate)-> 0 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (4 -> 0) canNOT be undone completely because of the failure type, $if_success = -3: No such file or directory !


< The 2 th pair : (6, 11) >

{ The 0 th Path: (refernce ->) 6 -(intermediate)-> 11 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (6 -> 11) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !

{ The 1 th Path: (refernce ->) 11 -(intermediate)-> 6 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (11 -> 6) canNOT be undone completely because of the failure type, $if_success = -2: No such file or directory !


 --- Finished analysis for the segment 2 ! ---

<<<<<< Segment ID: 3  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (48, 44)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 9) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 3 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (5, 6) >

{ The 0 th Path: (refernce ->) 5 -(intermediate)-> 6 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (5 -> 6) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !

{ The 1 th Path: (refernce ->) 6 -(intermediate)-> 5 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (6 -> 5) canNOT be undone completely because of the failure type, $if_success = -11: No such file or directory !


< The 2 th pair : (7, 1) >

{ The 0 th Path: (refernce ->) 7 -(intermediate)-> 1 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (7 -> 1) canNOT be undone completely because of the failure type, $if_success = -8: No such file or directory !

{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 7 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (1 -> 7) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !


 --- Finished analysis for the segment 3 ! ---

<<<<<< Segment ID: 4  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (10, 8)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 4 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 1) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 10 ,
#{columns in new reconstructed MSA} = 8 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9

seq0000   	    0    -    -    -    -    -   -1   -1    -    -
seq0001   	    0    -    -    -    -    -   -1   -1    -    -
seq0002   	    0    -    -    -    -    -   -1   -1    -    -
seq0003   	    0    -    -    -    -    -   -1   -1    -    -
seq0004   	    0    -    -    -    -    -   -1   -1    -    -
seq0005   	    0    -    -    -    -    -   -1   -1    -    -
seq0006   	    0   -1   -1   -1   -1   -1   -1   -1    -    -
seq0007   	    0    -    -    -    -    -   -1   -1    -    -
seq0008   	    0    -    -    -    -    -   -1   -1    -    -
seq0009   	    -    -    -    -    -    -   -1   -1    -    -
seq0013   	    0    -    -    -    -    -   -1   -1    -    -
seq0014   	    0    -    -    -    -    -   -1   -1    -    -
seq0015   	    0    -    -    -    -    -   -1   -1    -    -
seq0018   	    0    0    -    -    -    -    -    0    0    0
seq0020   	    0    -    -    -    -    -   -1   -1    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7

seq0000   	    0    -    -    -    -    -    0    0
seq0001   	    0    -    -    -    -    -    0    0
seq0002   	    0    -    -    -    -    -    0    0
seq0003   	    0    -    -    -    -    -    0    0
seq0004   	    0    -    -    -    -    -    0    0
seq0005   	    0    -    -    -    -    -    0    0
seq0006   	    0    0    0    0    0    0    0    0
seq0007   	    0    -    -    -    -    -    0    0
seq0008   	    0    -    -    -    -    -    0    0
seq0009   	    -    -    -    -    -    -    0    0
seq0013   	    0    -    -    -    -    -    0    0
seq0014   	    0    -    -    -    -    -    0    0
seq0015   	    0    -    -    -    -    -    0    0
seq0018   	    0    0    -    -    -   -2   -2   -2
seq0020   	    0    -    -    -    -    -    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	1	0	5
2nd(reconstructed)	2	0	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Incomplete-Collapse-of-Independent-Insertions(+slide(?))(+5)(?)	16	26:9:9:-/11:2:6:-	27:1:1:-/24:1:1:X/18:1:1:X/9:1:1:X/10:1:1:X/12:1:1:X/11:2:5:-
2nd(reconstructed)	Complex(???)	100	26:6:6:X/26:8:9:-	None


{Total penalty} = 116 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 9 ,
#{columns in new reconstructed MSA} = 8 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8

seq0000   	    0    -    -    -    -    -    -    0    0
seq0001   	    0    -    -    -    -    -    -    0    0
seq0002   	    0    -    -    -    -    -    -    0    0
seq0003   	    0    -    -    -    -    -    -    0    0
seq0004   	    0    -    -    -    -    -    -    0    0
seq0005   	    0    -    -    -    -    -    -    0    0
seq0006   	    0    -    0    0    0    0    0    0    0
seq0007   	    0    -    -    -    -    -    -    0    0
seq0008   	    0    -    -    -    -    -    -    0    0
seq0009   	    -    -    -    -    -    -    -    0    0
seq0013   	    0    -    -    -    -    -    -    0    0
seq0014   	    0    -    -    -    -    -    -    0    0
seq0015   	    0    -    -    -    -    -    -    0    0
seq0018   	    0    0    -    -    -   -2   -2   -2    -
seq0020   	    0    -    -    -    -    -    -    0    0



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7

seq0000   	    0    -    -    -    -    -   -1   -1
seq0001   	    0    -    -    -    -    -   -1   -1
seq0002   	    0    -    -    -    -    -   -1   -1
seq0003   	    0    -    -    -    -    -   -1   -1
seq0004   	    0    -    -    -    -    -   -1   -1
seq0005   	    0    -    -    -    -    -   -1   -1
seq0006   	    0   -1   -1   -1   -1   -1   -1   -1
seq0007   	    0    -    -    -    -    -   -1   -1
seq0008   	    0    -    -    -    -    -   -1   -1
seq0009   	    -    -    -    -    -    -   -1   -1
seq0013   	    0    -    -    -    -    -   -1   -1
seq0014   	    0    -    -    -    -    -   -1   -1
seq0015   	    0    -    -    -    -    -   -1   -1
seq0018   	    0    0    -    -    -    0    0    0
seq0020   	    0    -    -    -    -    -   -1   -1





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	1	0	0
2nd(reconstructed)	1	1	0	1	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	26:9:9:-	26:8:8:X/27:5:6:-
2nd(reconstructed)	Complex(???)	100	11:2:4:-	11:2:4:-/12:1:5:X


{Total penalty} = 200 .





 --- Finished analysis for the segment 4 ! ---

<<<<<< Segment ID: 5  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (23, 20)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 15) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 5 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (1, 4) >

{ The 0 th Path: (refernce ->) 1 -(intermediate)-> 4 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 22 ,
#{columns in new reconstructed MSA} = 20 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20   21

seq0000   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -2   -2    -    -
seq0001   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -2   -2    -    -
seq0002   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0    0    0
seq0003   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0    0    0
seq0004   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0    0    0
seq0005   	   -1   -2   -2   -2    -    -    0    0    0    0    0    0    0   -1   -1   -1   -1    -    -    0    0    0
seq0006   	   -1   -2   -2   -2    -    -    0    0    0    0    0    0    0   -1    -    -    -    -    -   -2    -    -
seq0007   	   -1   -2   -2   -2    -    -    0    0    0    0    0    0    0   -1   -1   -1   -1    -    -    0    0    0
seq0008   	   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3    -    -
seq0009   	    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0    0    0
seq0013   	   -1   -2   -2   -2   -2    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0    0    0
seq0014   	   -1   -2   -2   -2   -2    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0    0    0
seq0015   	   -1   -2   -2   -2   -2    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0    0    0
seq0018   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -    0    0    0
seq0020   	   -1    -    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19

seq0000   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    -    -    0    0
seq0001   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    -    -    0    0
seq0002   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0003   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0004   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0005   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0006   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0007   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0013   	    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0014   	    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0015   	    0    0    0    0    0    -    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0018   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -2   -2   -2
seq0020   	    0   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 4) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	1	0	0	0
2nd(reconstructed)	1	0	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	26:2:2:-/28:18:18:-	26:17:18:X
2nd(reconstructed)	Complex(???)	100	27:1:2:-	None


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 4 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 21 ,
#{columns in new reconstructed MSA} = 20 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19   20

seq0000   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -2   -2    -
seq0001   	   -1   -2   -2   -2    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -    -   -2   -2    -
seq0002   	   -1   -2   -2   -2    -    -    -    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0003   	   -1   -2   -2   -2    -    -    -    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0004   	   -1   -2   -2   -2    -    -    -    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0005   	   -1   -2   -2   -2    -    -    0    0    0    0    0    0    0   -1   -1   -1   -1    -   -1   -1   -1
seq0006   	   -1   -2   -2   -2    -    -    0    0    0    0    0    0    0   -1    -    -    -    -    -   -2    -
seq0007   	   -1   -2   -2   -2    -    -    0    0    0    0    0    0    0   -1   -1   -1   -1    -   -1   -1   -1
seq0008   	   -1   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -2   -3   -3   -3   -3    -
seq0009   	    0    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1    -   -1   -1   -1
seq0013   	   -1   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0014   	   -1   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0015   	   -1   -2   -2   -2   -2    -    -    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0018   	    -    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0020   	   -1    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18   19

seq0000   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    -    -    0    0
seq0001   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    -    -    0    0
seq0002   	    0    0    0    0    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0003   	    0    0    0    0    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0004   	    0    0    0    0    -    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0005   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0006   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    -    -    -    -    -    0
seq0007   	    0    0    0    0    -    -    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0008   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1
seq0013   	    0    0    0    0    0    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0014   	    0    0    0    0    0    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0015   	    0    0    0    0    0    -   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0018   	   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1
seq0020   	    0   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1   -1





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (4 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	1	0	0	0
2nd(reconstructed)	1	0	1	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	28:18:18:-/26:2:2:-	27:1:1:-
2nd(reconstructed)	Complex(???)	100	26:0:0:X/27:1:1:-	None


{Total penalty} = 200 .





 --- Finished analysis for the segment 5 ! ---

<<<<<< Segment ID: 6  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (8, 8)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 6 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 6 ! ---

<<<<<< Segment ID: 7  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 2)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 7 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 7 ! ---

<<<<<< Segment ID: 8  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (18, 18)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 8 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 8 ! ---

<<<<<< Segment ID: 9  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 2)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 9 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 9 ! ---

<<<<<< Segment ID: 10  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (7, 7)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 10 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 10 ! ---

<<<<<< Segment ID: 11  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (8, 8)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 11 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 11 ! ---

<<<<<< Segment ID: 12  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (42, 41)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 4) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 12 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 12 ! ---

<<<<<< Segment ID: 13  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (7, 7)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 13 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 13 ! ---

<<<<<< Segment ID: 14  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (109, 61)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 19) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 14 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (4, 13) >

{ The 0 th Path: (refernce ->) 4 -(intermediate)-> 13 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (4 -> 13) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !

{ The 1 th Path: (refernce ->) 13 -(intermediate)-> 4 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (13 -> 4) canNOT be undone completely because of the failure type, $if_success = -3: No such file or directory !


< The 2 th pair : (9, 17) >

{ The 0 th Path: (refernce ->) 9 -(intermediate)-> 17 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (9 -> 17) canNOT be undone completely because of the failure type, $if_success = -2: No such file or directory !

{ The 1 th Path: (refernce ->) 17 -(intermediate)-> 9 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (17 -> 9) canNOT be undone completely because of the failure type, $if_success = -3: No such file or directory !


 --- Finished analysis for the segment 14 ! ---

<<<<<< Segment ID: 15  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (164, 90)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

[WARNING 'cal_init_psm_cands_for_twin_msas'] Found a cluster of length 159, which is LONGER THAN the upper-bound, 150... I will skip analyzing this pair of reference & reconstructed MSAs: No such file or directory !

[INFORMATION] SKIPPED the Calculation for the 15 th segment, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


<<<<<< Segment ID: 16  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (5, 4)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 16 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 16 ! ---

<<<<<< Segment ID: 17  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (108, 106)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 18) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 17 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (15, 2) >

{ The 0 th Path: (refernce ->) 15 -(intermediate)-> 2 (= reconstructed) }

[WARNING 'undo_mvd_latter_of_cblocks_pair'] An UNEXPECTED situation: The 2nd moved c-block (index: 2) has a NON-POSITIVE left-end shift (=-5) and a NON-NEGATIVE right-end shift (=0): No such file or directory !


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (15 -> 2) canNOT be undone completely because of the failure type, $if_success = -101: No such file or directory !

{ The 1 th Path: (refernce ->) 2 -(intermediate)-> 15 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (2 -> 15) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !


 --- Finished analysis for the segment 17 ! ---

<<<<<< Segment ID: 18  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (34, 34)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 5) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 18 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 18 ! ---

<<<<<< Segment ID: 19  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (4, 4)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 19 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 19 ! ---

<<<<<< Segment ID: 20  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (19, 17)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 8) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 20 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 3) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 3 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 19 ,
#{columns in new reconstructed MSA} = 17 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16   17   18

seq0000   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1    -   -2   -2    -    -
seq0001   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1    -   -2   -2    -    -
seq0002   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2    -    -
seq0003   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2    -    -
seq0004   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2    -    -
seq0005   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2    -    -
seq0006   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2    -    -
seq0007   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2    -    -
seq0008   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2    -    -
seq0009   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2    -    -
seq0013   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1    -   -1   -1    -    -
seq0014   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -1   -1    -    -
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1    -    -
seq0018   	   -1   -1   -6   -6    -    -    -    -    -    -    0    0    0    -    0    0    0    0    0
seq0020   	    0    0    0   -5   -5   -5    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2    -    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16

seq0000   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    -    0    0
seq0001   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    -    0    0
seq0002   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    -    0    0
seq0014   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	    0    0    0    0    -    -    -    -    -   -1   -1   -1   -2   -2   -2   -2   -2
seq0020   	    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 3) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	3	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	26:0:0:X	26:4:9:X
2nd(reconstructed)	Complex	100	26:4:9:X/26:17:18:-/26:13:13:X	26:4:5:X


{Total penalty} = 200 .




{ The 1 th Path: (refernce ->) 3 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 17 ,
#{columns in new reconstructed MSA} = 17 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16

seq0000   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1    -   -2   -2
seq0001   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1    -   -2   -2
seq0002   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2
seq0003   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2
seq0004   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2
seq0005   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2
seq0006   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2
seq0007   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2
seq0008   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2
seq0009   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -2   -2
seq0013   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1    -   -1   -1
seq0014   	    0    0    0   -5    -    -    -    -    -    0    0    0    0   -1   -1   -1   -1
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0   -1   -1   -1   -1
seq0018   	    -    0    0    -    -    -    -   -1   -1   -1   -1   -1   -2   -2   -2   -2   -2
seq0020   	    0    0    0   -5   -5   -5    -    -    -   -2   -2   -2   -2   -2   -2   -2   -2



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11   12   13   14   15   16

seq0000   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    -    0    0
seq0001   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    -    0    0
seq0002   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0003   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0004   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0005   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0006   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0007   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0008   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0009   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0013   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    -    0    0
seq0014   	    0    0    0    0    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0    0
seq0018   	   -1   -1   -5   -5    -    -    -    -    -    0    0    0    0    0    0    0    0
seq0020   	    0    0    0    0    0    0    -    -    -    0    0    0    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (3 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	0	1	0	1	0	0
2nd(reconstructed)	2	1	1	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Complex(???)	100	None	26:3:5:X/27:7:8:-
2nd(reconstructed)	Complex	100	26:0:0:X/26:3:5:X/27:7:8:-	26:4:5:X


{Total penalty} = 200 .





 --- Finished analysis for the segment 20 ! ---

<<<<<< Segment ID: 21  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (4, 4)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 21 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 21 ! ---

<<<<<< Segment ID: 22  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (41, 36)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 22 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 22 ! ---

<<<<<< Segment ID: 23  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (108, 105)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 3) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 23 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 23 ! ---

<<<<<< Segment ID: 24  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (65, 48)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 16) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 24 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (12, 14) >

{ The 0 th Path: (refernce ->) 12 -(intermediate)-> 14 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 0 th path (12 -> 14) canNOT be undone completely because of the failure type, $if_success = -14: No such file or directory !

{ The 1 th Path: (refernce ->) 14 -(intermediate)-> 12 (= reconstructed) }


[CAUTION 'classify_msa_errors_via_mblks.2val.pl'] Subroutine 'undo_mv_latter_of_cblock_pair' indicated that the 1 th path (14 -> 12) canNOT be undone completely because of the failure type, $if_success = -11: No such file or directory !


 --- Finished analysis for the segment 24 ! ---

<<<<<< Segment ID: 25  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (143, 141)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

[WARNING 'cal_init_psm_cands_for_twin_msas'] Found 1 gaps longer than 120. So, I will skip analyzing this pair of reference & reconstructed MSAs: No such file or directory !

[INFORMATION] SKIPPED the Calculation for the 25 th segment, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...


<<<<<< Segment ID: 26  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (2, 2)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 1) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 26 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 26 ! ---

<<<<<< Segment ID: 27  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (12, 12)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 27 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 1) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 12 ,
#{columns in new reconstructed MSA} = 12 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11

seq0000   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0001   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0002   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0003   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0004   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0005   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0006   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0007   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0008   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0009   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0013   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0018   	    -    -    -    -    4    4    4    0    0    0    0    -
seq0020   	    -    -    -    -    4    4    4    0    0    0    0    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11

seq0000   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0001   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0002   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0003   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0004   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0005   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0006   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0007   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0008   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0009   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0013   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0018   	    -    -    -    -    -    1    1    1    1    1    1    1
seq0020   	    -    -    -    -    -    1    1    1    1    1    1    1





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	1	0	0	0	0
2nd(reconstructed)	2	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Shift	1	21:3:6:-	21:0:3:-
2nd(reconstructed)	Merge(same-type)	2	21:0:3:-/21:11:11:-	21:0:4:-


{Total penalty} = 3 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 12 ,
#{columns in new reconstructed MSA} = 12 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11

seq0000   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0001   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0002   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0003   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0004   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0005   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0006   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0007   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0008   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0009   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0013   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0018   	    0    0    0    -    -    -    -    -    1    1    1    1
seq0020   	    0    0    0    -    -    -    -    -    1    1    1    1



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5    6    7    8    9   10   11

seq0000   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0001   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0002   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0003   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0004   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0005   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0006   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0007   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0008   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0009   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0013   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0014   	    0    0    0    0    0    0    0    0    0    0    0    0
seq0015   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0018   	    -    -    -    -    -    5    5    5    0    0    0    0
seq0020   	    -    -    -    -    -    5    5    5    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	2	1	0	0	0	0
2nd(reconstructed)	1	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Merge(same-type)	2	21:3:6:-/21:11:11:-	21:3:7:-
2nd(reconstructed)	Shift	1	21:3:7:-	21:0:4:-


{Total penalty} = 3 .





 --- Finished analysis for the segment 27 ! ---

<<<<<< Segment ID: 28  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (74, 67)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 28 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 28 ! ---

<<<<<< Segment ID: 29  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (15, 15)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 29 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 29 ! ---

<<<<<< Segment ID: 30  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (17, 12)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 4) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 30 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


 --- Finished analysis for the segment 30 ! ---

<<<<<< Segment ID: 31  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (7, 6)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

<<<<< Preliminary (7'): Lump together some neighboring MINI-blocks affecting the identical set of sequences. >>>>>

<<<<< Preliminary (8): Reorganize the list of insertions/deletions in the initial candidate of parsimonious scenarios, for reference and reconstructed MSAs. >>>>>

<<<<< Preliminary (9): Identify the pairs of 'equivalent' indel events in the reference & reconstructed MSAs...  >>>>>

<<<<< (i) MAIN PROCESS (1st Round)!!!: Associate each Composite 'MINI-Block' with (an) appropriate type(s) of MSA error(s)... (#{composite blocks} = 2) >>>>>


... The MAIN PROCESS (1st Round) ENDED for the 31 th segment ...


<<<< (ii) MAIN PROCESS (2nd Round)!!: Attempt to 'hard-link' skipped composite 'MINI-Block's to non-skipped ones, and to resolve Composite 'MINI-Block's associated with 'Complex' errors... >>>>


<< ... Finally, we can now attempt to associate errors with each pair of 'soft-linked' c-blocks ... >>


< The 1 th pair : (0, 1) >

{ The 0 th Path: (refernce ->) 0 -(intermediate)-> 1 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 7 ,
#{columns in new reconstructed MSA} = 6 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5    6

seq0000   	    -    1    0    0    0    0    -
seq0001   	    -    1    0    0    0    0    -
seq0002   	    -    1    0    0    0    0    -
seq0003   	    -    1    0    0    0    0    -
seq0004   	    -    1    0    0    0    0    -
seq0005   	    -    1    0    0    0    0    -
seq0006   	    -    1    0    0    0    0    -
seq0007   	    -    1    0    0    0    0    -
seq0008   	    -    1    0    0    0    0    -
seq0009   	    -    1    0    0    0    0    -
seq0013   	    0    0    0    0    0    0    -
seq0014   	    0    -    0    0    0    0    0
seq0015   	    -    1    0    0    0    0    -
seq0018   	    -    1    0    0    0    0    -
seq0020   	    -    1    0    0    0    0    -



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5

seq0000   	    -    0    0    0    0    0
seq0001   	    -    0    0    0    0    0
seq0002   	    -    0    0    0    0    0
seq0003   	    -    0    0    0    0    0
seq0004   	    -    0    0    0    0    0
seq0005   	    -    0    0    0    0    0
seq0006   	    -    0    0    0    0    0
seq0007   	    -    0    0    0    0    0
seq0008   	    -    0    0    0    0    0
seq0009   	    -    0    0    0    0    0
seq0013   	    0    0    0    0    0    0
seq0014   	    0   -1   -1   -1   -1   -1
seq0015   	    -    0    0    0    0    0
seq0018   	    -    0    0    0    0    0
seq0020   	    -    0    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (0 -> 1) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	0	1	1	1	0	0
2nd(reconstructed)	2	0	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Neighboring-branch-Split(2del)(?)	4	20:1:1:-	22:0:0:-/21:1:1:X
2nd(reconstructed)	Purge(?)	3	21:1:1:X/21:6:6:-	None


{Total penalty} = 7 .




{ The 1 th Path: (refernce ->) 1 -(intermediate)-> 0 (= reconstructed) }

<< Output of 'undo_mv_latter_of_cblock_pair' >>

#{columns in intermediate MSA} = 6 ,
#{columns in new reconstructed MSA} = 6 .

$baseline_shift_intm = 0 .

[[ Shifts between the reference and intermediate MSAs (mapped onto the latter)  ]]

(position)	    0    1    2    3    4    5

seq0000   	    0    -    0    0    0    0
seq0001   	    0    -    0    0    0    0
seq0002   	    0    -    0    0    0    0
seq0003   	    0    -    0    0    0    0
seq0004   	    0    -    0    0    0    0
seq0005   	    0    -    0    0    0    0
seq0006   	    0    -    0    0    0    0
seq0007   	    0    -    0    0    0    0
seq0008   	    0    -    0    0    0    0
seq0009   	    0    -    0    0    0    0
seq0013   	    0    0    0    0    0    0
seq0014   	    0   -1   -1   -1   -1   -1
seq0015   	    0    -    0    0    0    0
seq0018   	    0    -    0    0    0    0
seq0020   	    0    -    0    0    0    0



[[ Shifts between the intermediate and reconstructed MSAs (mapped onto the latter) ]]

(position)	    0    1    2    3    4    5

seq0000   	    -    1    0    0    0    0
seq0001   	    -    1    0    0    0    0
seq0002   	    -    1    0    0    0    0
seq0003   	    -    1    0    0    0    0
seq0004   	    -    1    0    0    0    0
seq0005   	    -    1    0    0    0    0
seq0006   	    -    1    0    0    0    0
seq0007   	    -    1    0    0    0    0
seq0008   	    -    1    0    0    0    0
seq0009   	    -    1    0    0    0    0
seq0013   	    0    0    0    0    0    0
seq0014   	    0    0    0    0    0    0
seq0015   	    -    1    0    0    0    0
seq0018   	    -    1    0    0    0    0
seq0020   	    -    1    0    0    0    0





[ Outputs of the subroutine 'classify_error_assoc_w_sgl_cblk' on the pairs of c-blocks (1 -> 0) ]

Subject_c-block	#{rlv_indels}_bf	#{rlv_indels}_af	#{rltd_indels}_bf	#{rltd_indels}_af	#{other_involved}_bf	#{other_involved}_af

1st(intermediate)	1	0	1	1	0	0
2nd(reconstructed)	1	1	0	0	0	0


Subject_c-block	Type	Penalty	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(before)	br1:beg1:end1:stat_ue1/br2:beg2:end2:stat_ue2/...(after)

1st(intermediate)	Neighboring-branch-Merge(2ins)(+shift)(?)	5	21:6:6:-/20:1:1:-	22:1:1:-
2nd(reconstructed)	Shift	1	22:1:1:-	22:0:0:-


{Total penalty} = 6 .





 --- Finished analysis for the segment 31 ! ---

<<<<<< Segment ID: 32  (Diagnosis: CLEARLY_DIFFERENT) >>>>>>

<<<< Prepare for segments of reference/reconstructed MSAs >>>>

(ref_len, rec_len) = (133, 131)

<<<<< Preliminary (0): Map the residue numbers onto the reference & reconstructed MSAs... >>>>>

<<<<< Preliminary (1): Map the position shifts (from reference to reconstructed) onto the Reconstructed MSA... >>>>>

<<<<< Preliminary (2): Put together the mapped position shifts into some Classes ... >>>>>

<<<<< Preliminary (3'): For each MINI-class of shifts, parsimoniously infer the branch(es) separating the affected sequences from the rest. >>>>>

<<<<< ADDITIONAL Preliminary Process (3.5'): Split mini-classes each of which consists of unnaturally remote sequences... >>>>>

<<<<< Preliminary (4'): Merge the MINI-classes of shifts. >>>>>

<<<<< Preliminary (5'): Identify 'trivial' MINI-blocks. >>>>>

<<<<< Preliminary (6): Identify gap-pattern blocks, calculate their Dollo parsimony scenarios, and the initial parsimony candidate scenario of each gapped segment in the segmental MSAs (reference & reconstructed). >>>>>

[WARNING 'cal_init_psm_cands_for_twin_msas'] Found 3 gaps longer than 120. So, I will skip analyzing this pair of reference & reconstructed MSAs: No such file or directory !

[INFORMATION] SKIPPED the Calculation for the 32 th segment, because either reference or reconstructed MSA contains (a) gap(s) or (a) gapped segment(s) that is (are) too long ...




 === All the Analyses FINISHED !! ===

#{Segments skipped} = 1 .
#{Segments whose ComplLiMMent calculations skipped} = 0 .
#{Anomalous segments} = 0 .
#{Segments used as inputs} = 0 .
#{Segments successfully processed} = 29 .
#{Segments failed to be processed} = 0 .


real	0m1.959s
user	0m1.088s
sys	0m0.499s
