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Old 04-24-2015, 11:25 AM   #1
colibri14
Junior Member
 
Location: New York

Join Date: Nov 2014
Posts: 1
Default Trinity error in both.fa

Hi!

I am using Trinity (r2014-07-17) for de novo assembly of RNA-seq data (100bp PE). I have 12 samples and 9 of them have successfully completed, however 3 fail early on in the program.

For these samples, the error message I get is:
HTML Code:
Monday, April 13, 2015: 15:18:53	CMD: mkdir -p /brashear/mlim/Trinityfiles/trinityResults/CGML001B/chrysalis
CMD finished (0 seconds)
Converting input files. (in parallel)Monday, April 13, 2015: 15:18:54	CMD: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001B_trinity_left.fq >> left.fa 2> /brashear/mlim/Trinityfiles/CGML001B_trinity_left.fq.readcount 
Monday, April 13, 2015: 15:18:54	CMD: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001B_trinity_right.fq >> right.fa 2> /brashear/mlim/Trinityfiles/CGML001B_trinity_right.fq.readcount 
CMD finished (62 seconds)
Thread 1 terminated abnormally: Error, cmd: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001B_trinity_left.fq >> left.fa 2> /brashear/mlim/Trinityfiles/CGML001B_trinity_left.fq.readcount  died with ret 256 at /usr/local/packages/trinity/r2014-07-17/Trinity line 1990.
Use of uninitialized value in array dereference at /usr/local/packages/trinity/r2014-07-17/Trinity line 1171.
Error prepping sequences. at /usr/local/packages/trinity/r2014-07-17/Trinity line 1175.
For reference, when it works, I get:
HTML Code:
Wednesday, April 8, 2015: 18:40:33	CMD: mkdir -p /brashear/mlim/Trinityfiles/trinityResults/CGML001A/chrysalis
CMD finished (0 seconds)
Converting input files. (in parallel)Wednesday, April 8, 2015: 18:40:33	CMD: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001A_trinity_left.fq >> left.fa 2> /brashear/mlim/Trinityfiles/CGML001A_trinity_left.fq.readcount 
Wednesday, April 8, 2015: 18:40:33	CMD: /usr/local/packages/trinity/r2014-07-17/trinity-plugins/fastool/fastool --illumina-trinity --to-fasta /brashear/mlim/Trinityfiles/CGML001A_trinity_right.fq >> right.fa 2> /brashear/mlim/Trinityfiles/CGML001A_trinity_right.fq.readcount 
CMD finished (47 seconds)
CMD finished (49 seconds)
Done converting input files.Wednesday, April 8, 2015: 18:41:22	CMD: cat left.fa right.fa > both.fa
CMD finished (21 seconds)
Has anyone gotten these errors before? I'd appreciate any suggestions!
Thanks!!
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Old 07-19-2015, 10:09 AM   #2
enelkinsan
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Location: NZ

Join Date: May 2012
Posts: 14
Default

This loos like input problem. Check if your fastq files for 3 fails are in correct format.
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