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:
For reference, when it works, I get:
Has anyone gotten these errors before? I'd appreciate any suggestions!
Thanks!!
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.
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)
Thanks!!
Comment