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vastgroup / vast-tools

A toolset for profiling alternative splicing events in RNA-Seq data.
MIT License
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3'-bias file open error #40

Closed UBrau closed 9 years ago

UBrau commented 9 years ago

There appears to be a problem file I/O since introduction of the 3'-bias analysis.

Sample output:

Tue May 19 12:59:16 2015

==> vast-tools.o18985318 ==> Run command : /home/blencowe/blencowe1/ulrich/AS_PIPE_S_dev/vast-tools align --sp Mmu --dbdir /home/blencowe/blencowe1/ulrich/AS_PIPE_S_dev/ -c 2 -o vast/ --expr raw/combined/N2A_siMbnl1_plus_2_R1.fq.gz raw/combined/N2A_siMbnl1_plus_2_R2.fq.gz ==> Execution host : node27.ccbr.utoronto.ca [vast align]: Setting output directory to vast/ [vast align]: Setting tmp directory.. [vast align]: Set tmp directory to /home/blencowe/blencowe1/shared/Ulrich/RNAseq.Hong.CGR8.N2A.150401/combi/vast/tmp! [vast align]: Mapping reads against mRNA sequences [vast align]: Calculating cRPKMs '# reads processed: 74874493 '# reads with at least one reported alignment: 50092377 (66.90%) '# reads that failed to align: 19401424 (25.91%) '# reads with alignments suppressed due to -m: 5380692 (7.19%) Reported 50092377 alignments to 1 output stream(s) Can't open expr_out/N2A_siMbnl1_plus_2_R1: No such file or directory at /home/blencowe/blencowe1/ulrich/AS_PIPE_S_dev/bin/expr_RPKM.pl line 35, <> line 50115044. [vast align]: Trimming fastq sequences to 50 nt sequences [vast trim]: Total processed reads: 74874493 [vast trim]: Total valid fwd reads: 74874493 [vast trim]: Total valid rev reads: 74874493 [vast align]: Doing genome substraction [ ABBREVIATED ]

It seems to be happening here: verbPrint "Calculating cRPKMs\n"; sysErrMsg "$cmd | $binPath/expr_RPKM.pl - $dbDir/EXPRESSION/$species"."_mRNA-$le.eff expr_out/$root > expr_out/$root.cRPKM";

The cRPKM table that is produced seems OK, but the full content of the .3bias file in this example was this: N2A_siMbnl1_plus_2_R1 500nt 15.30 18.22 19.94 22.07 24.46 5908 N2A_siMbnl1_plus_2_R1 1000nt 15.24 17.88 20.04 22.34 24.50 1643

kcha commented 9 years ago

@mirimia, can you take a look at this?

mirimia commented 9 years ago

It's a harmless (and expected) error. I'll try to find out a way to avoid it...

mirimia commented 9 years ago

(I'll leave the issue open so I remember it)

mirimia commented 9 years ago

Just added a fix for this.