[Next-Generation Sequencing Book]

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[ Ticket #1117 ] blprotein - Jalview can't load input file
Date:
02/28/11 17:02
Submitted by:
B_Fristensky 		Assigned to:
B_Fristensky
Category:
bioLegato 		Priority:
3
Ticket group:
Bug 		Resolution:
Resolved
Summary:
blprotein - Jalview can't load input file
Original submission:
Linux-intel, Feb. 22 Development version

cd $tutorials/bioLegato/phylogeny/distance
blprotein
File --> Open chitIII.pro.tcoffee.gde
Select All
Alignment --> Jalview

Jalview launches, but gives the message:

Couldn't load file bioxxxxxxxxx.tmp.fsa
Problem opening file bioxxxxxxxx.tmp.fsa: FILE CANNOT BE OPENED FOR READING
Formats currently supported are BLC, CLUSTAL.MSF, PileUp,PIR,PFAM,STH, PDF, AND JnetFile.

File looks like a perfectly good fasta file.
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Followups
Comment Date By
Fixed bldna and blprotein.

Jalview -open requires a fully-qualified path, even if the input file is in the current working directory.
The command is therefore

Jalview -open $PWD/in1.fsa

This was mentioned in the comment lines for jalview.item, but somehow, the $PWD got taken out. It has been restored.

02/28/11 17:44 B_Fristensky
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Ticket change history
Field Old value Date By
status_id Open 03/13/11 19:15 B_Fristensky
close_date 12/31/69 19:00 03/13/11 19:15 B_Fristensky
resolution_id Not Resolved 02/28/11 17:44 B_Fristensky
status_id Pending 02/28/11 17:02 B_Fristensky
priority 5 02/28/11 17:02 B_Fristensky
assigned_to unset 02/28/11 17:02 B_Fristensky
resolution_id Unset 02/28/11 17:02 B_Fristensky

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