[Bio-Linux] Bowtie 2 and Galaxy
Tim Booth
tbooth at ceh.ac.uk
Wed May 8 04:54:25 EDT 2013
Hi Eamonn,
Oh dear - I just tried running the basic example/test dataset on tophat2
via the command line on my machine and I got the same error, so the
installation is totally broken. I'm not sure which update caused that
(it worked before - honest!) but hopefully it will be a simple fix.
I'll look into it right now.
Cheers,
TIM
On Wed, 2013-05-08 at 07:54 +0100, Mallon, Eamonn B. (Dr.) wrote:
> Hi Tim,
> I really appreciate you getting back to me so quickly and generally
> for all the work you've done on BioLinux.
>
> I tried your suggestion. Bowtie2 now works but neither tophat nor
> tophat2 do. See error report below. Version 2.1.0 of bowtie2 is
> installed
>
> Thanks
> Eamonn
>
>
> Dataset 73: Tophat2 on data 4 and data 6: deletions
> Tool execution generated the following error message:
>
> Error in tophat:
>
> [2013-05-08 07:47:45] Beginning TopHat run (v2.0.7)
> -----------------------------------------------
> [2013-05-08 07:47:45] Checking for Bowtie
> Error: TopHat requires Bowtie 2.0.5 or later
>
> The tool produced the following additional output:
>
> Settings:
> Output files: "/tmp/tmphaTcDz/dataset_6.*.bt2"
> Line rate: 6 (line is 64 bytes)
> Lines per side: 1 (side is 64 bytes)
> Offset rate: 4 (one in 16)
> FTable chars: 10
> Strings: unpacked
> Max bucket size: default
> Max bucket size, sqrt multiplier: default
> Max bucket size, len divisor: 4
> Difference-cover sample period: 1024
> Endianness: little
> Actual local endianness: little
> Sanity checking: disabled
> Assertions: disabled
> Random seed: 0
> Sizeofs: void*:8, int:4, long:8, size_t:8
> Input files DNA, FASTA:
> /usr/lib/galaxy-server/database/files/000/dataset_6.dat
> Reading reference sizes
> Time reading reference sizes: 00:00:00
> Calculating joined length
> Writing header
> Reserving space for joined string
> Joining reference sequences
> Time to join reference sequences: 00:00:00
> bmax according to bmaxDivN setting: 12804
> Using parameters --bmax 9603 --dcv 1024
> Doing ahead-of-time memory usage test
> TopHat v2.0.7
> Passed! Constructing with these parameters: --bmax 9603 --dcv 1024
> Constructing suffix-array element generator
> Building DifferenceCoverSample
> Building sPrime
> Building sPrimeOrder
> V-Sorting samples
> V-Sorting samples time: 00:00:00
> Allocating rank array
> Ranking v-sort output
> Ranking v-sort output time: 00:00:00
> Invoking Larsson-Sadakane on ranks
> Invoking Larsson-Sadakane on ranks time: 00:00:00
> Sanity-checking and returning
> Building samples
> Reserving space for 12 sample suffixes
> Generating random suffixes
> QSorting 12 sample offsets, eliminating duplicates
> QSorting sample offsets, eliminating duplicates time: 00:00:00
> Multikey QSorting 12 samples
> (Using difference cover)
> Multikey QSorting samples time: 00:00:00
> Calculating bucket sizes
> Binary sorting into buckets
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Binary sorting into buckets time: 00:00:00
> Splitting and merging
> Splitting and merging time: 00:00:00
> Split 2, merged 7; iterating...
> Binary sorting into buckets
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Binary sorting into buckets time: 00:00:00
> Splitting and merging
> Splitting and merging time: 00:00:00
> Split 2, merged 1; iterating...
> Binary sorting into buckets
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Binary sorting into buckets time: 00:00:00
> Splitting and merging
> Splitting and merging time: 00:00:00
> Avg bucket size: 6401.5 (target: 9602)
> Converting suffix-array elements to index image
> Allocating ftab, absorbFtab
> Entering Ebwt loop
> Getting block 1 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 7826
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 7827
> Getting block 2 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 8958
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 8959
> Getting block 3 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 926
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 927
> Getting block 4 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 9019
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 9020
> Getting block 5 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 9538
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 9539
> Getting block 6 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 1983
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 1984
> Getting block 7 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 7919
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 7920
> Getting block 8 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 5043
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 5044
> Exited Ebwt loop
> fchr[A]: 0
> fchr[C]: 12811
> fchr[G]: 25322
> fchr[T]: 37448
> fchr[$]: 51219
> Exiting Ebwt::buildToDisk()
> Returning from initFromVector
> Wrote 4211664 bytes to primary EBWT file: /tmp/tmphaTcDz/dataset_6.1.bt2
> Wrote 12812 bytes to secondary EBWT file: /tmp/tmphaTcDz/dataset_6.2.bt2
> Re-opening _in1 and _in2 as input streams
> Returning from Ebwt constructor
> Headers:
> len: 51219
> bwtLen: 51220
> sz: 12805
> bwtSz: 12805
> lineRate: 6
> offRate: 4
> offMask: 0xfffffff0
> ftabChars: 10
> eftabLen: 20
> eftabSz: 80
> ftabLen: 1048577
> ftabSz: 4194308
> offsLen: 3202
> offsSz: 12808
> lineSz: 64
> sideSz: 64
> sideBwtSz: 48
> sideBwtLen: 192
> numSides: 267
> numLines: 267
> ebwtTotLen: 17088
> ebwtTotSz: 17088
> color: 0
> reverse: 0
> Total time for call to driver() for forward index: 00:00:00
> Reading reference sizes
> Time reading reference sizes: 00:00:00
> Calculating joined length
> Writing header
> Reserving space for joined string
> Joining reference sequences
> Time to join reference sequences: 00:00:00
> Time to reverse reference sequence: 00:00:00
> bmax according to bmaxDivN setting: 12804
> Using parameters --bmax 9603 --dcv 1024
> Doing ahead-of-time memory usage test
> Passed! Constructing with these parameters: --bmax 9603 --dcv 1024
> Constructing suffix-array element generator
> Building DifferenceCoverSample
> Building sPrime
> Building sPrimeOrder
> V-Sorting samples
> V-Sorting samples time: 00:00:00
> Allocating rank array
> Ranking v-sort output
> Ranking v-sort output time: 00:00:00
> Invoking Larsson-Sadakane on ranks
> Invoking Larsson-Sadakane on ranks time: 00:00:00
> Sanity-checking and returning
> Building samples
> Reserving space for 12 sample suffixes
> Generating random suffixes
> QSorting 12 sample offsets, eliminating duplicates
> QSorting sample offsets, eliminating duplicates time: 00:00:00
> Multikey QSorting 12 samples
> (Using difference cover)
> Multikey QSorting samples time: 00:00:00
> Calculating bucket sizes
> Binary sorting into buckets
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Binary sorting into buckets time: 00:00:00
> Splitting and merging
> Splitting and merging time: 00:00:00
> Split 2, merged 7; iterating...
> Binary sorting into buckets
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Binary sorting into buckets time: 00:00:00
> Splitting and merging
> Splitting and merging time: 00:00:00
> Split 2, merged 1; iterating...
> Binary sorting into buckets
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Binary sorting into buckets time: 00:00:00
> Splitting and merging
> Splitting and merging time: 00:00:00
> Avg bucket size: 6401.5 (target: 9602)
> Converting suffix-array elements to index image
> Allocating ftab, absorbFtab
> Entering Ebwt loop
> Getting block 1 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 7682
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 7683
> Getting block 2 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 6747
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 6748
> Getting block 3 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 4689
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 4690
> Getting block 4 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 7452
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 7453
> Getting block 5 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 6415
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 6416
> Getting block 6 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 7731
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 7732
> Getting block 7 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 8264
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 8265
> Getting block 8 of 8
> Reserving size (9603) for bucket
> Calculating Z arrays
> Calculating Z arrays time: 00:00:00
> Entering block accumulator loop:
> 10%
> 20%
> 30%
> 40%
> 50%
> 60%
> 70%
> 80%
> 90%
> 100%
> Block accumulator loop time: 00:00:00
> Sorting block of length 2232
> (Using difference cover)
> Sorting block time: 00:00:00
> Returning block of 2233
> Exited Ebwt loop
> fchr[A]: 0
> fchr[C]: 12811
> fchr[G]: 25322
> fchr[T]: 37448
> fchr[$]: 51219
> Exiting Ebwt::buildToDisk()
> Returning from initFromVector
> Wrote 4211664 bytes to primary EBWT file: /tmp/tmphaTcDz/dataset_6.rev.1.bt2
> Wrote 12812 bytes to secondary EBWT file: /tmp/tmphaTcDz/dataset_6.rev.2.bt2
> Re-opening _in1 and _in2 as input streams
> Returning from Ebwt constructor
> Headers:
> len: 51219
> bwtLen: 51220
> sz: 12805
> bwtSz: 12805
> lineRate: 6
> offRate: 4
> offMask: 0xfffffff0
> ftabChars: 10
> eftabLen: 20
> eftabSz: 80
> ftabLen: 1048577
> ftabSz: 4194308
> offsLen: 3202
> offsSz: 12808
> lineSz: 64
> sideSz: 64
> sideBwtSz: 48
> sideBwtLen: 192
> numSides: 267
> numLines: 267
> ebwtTotLen: 17088
> ebwtTotSz: 17088
> color: 0
> reverse: 1
> Total time for backward call to driver() for mirror index: 00:00:00
> tophat2 -p 4 /tmp/tmphaTcDz/dataset_6 /usr/lib/galaxy-server/database/files/000/dataset_4.dat
>
> ________________________________________
> From: bio-linux-bounces at nebclists.nerc.ac.uk [bio-linux-bounces at nebclists.nerc.ac.uk] On Behalf Of Tim Booth [tbooth at ceh.ac.uk]
> Sent: Tuesday, May 07, 2013 3:39 PM
> To: Bio-Linux help and discussion
> Subject: Re: [Bio-Linux] Bowtie 2 and Galaxy
>
> Hi Eamonn,
>
> It seems there is an omission in the update script, so it could well be
> that you are missing bowtie2 and you just have bowtie on there. Please
> try:
>
> sudo apt-get install bowtie2 bowtie2-examples
>
> Hopefully this will be enough to get Galaxy working, but please be aware
> that the Galaxy configuration is badly in need of maintenance and it may
> still not work. If so, please send the full error message and I'll see
> what I can do.
>
> Cheers,
>
> TIM
>
> On Tue, 2013-05-07 at 15:07 +0100, Mallon, Eamonn B. (Dr.) wrote:
> > Hi
> > I've just installed biolinux 7. I tried to run top hat through galaxy
> > and I keep getting an error. It seems to be because bowtie2 doesn't
> > exist. Has anyone had a similar experience. Any tips?
> >
> >
> > Eamonn
> >
> >
> >
> >
> > Dr Eamonn Mallon
> > Lecturer in Evolutionary Biology
> > Adrian 220
> > Biology Department
> > University of Leicester
> >
> >
> > http://www2.le.ac.uk/departments/biology/people/mallon
> >
> >
>
> --
> Tim Booth <tbooth at ceh.ac.uk>
> NERC Environmental Bioinformatics Centre
>
> Centre for Ecology and Hydrology
> Maclean Bldg, Benson Lane
> Crowmarsh Gifford
> Wallingford, England
> OX10 8BB
>
> http://nebc.nerc.ac.uk
> +44 1491 69 2705
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
> _______________________________________________
> Bio-Linux mailing list
> Bio-Linux at nebclists.nerc.ac.uk
> http://nebclists.nerc.ac.uk/mailman/listinfo/bio-linux
--
Tim Booth <tbooth at ceh.ac.uk>
NERC Environmental Bioinformatics Centre
Centre for Ecology and Hydrology
Maclean Bldg, Benson Lane
Crowmarsh Gifford
Wallingford, England
OX10 8BB
http://nebc.nerc.ac.uk
+44 1491 69 2705
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