Hello everyone,
I'm working with the trinity pipeline to eventually generate gene expression data from an RNA sequencing project. I have successfully made my transcriptome and now I am using bowtie (through the alignReads.pl) script in the trinity pipeline. I made it most of the way through alignment 1/12 but received an error converting from SAM--BAM:
Error, cmd: /programs/trinityrnaseq_r2012-10-05/util/../trinity-plugins/rsem/convert-sam-for-rsem JUL10SF2_aln.nameSorted.PropMapPairsForRSEM.pre.bam JUL10SF2_aln.nameSorted.PropMapPairsForRSEM -T . died with ret 65280 at /programs/trinityrnaseq_r2012-10-05/util/alignReads.pl line 720
main:rocess_cmd('/programs/trinityrnaseq_r2012-10-05/util/../trinity-plugins/r...') called at /programs/trinityrnaseq_r2012-10-05/util/alignReads.pl line 738
main::make_RSEM_bam('JUL10SF2_aln.nameSorted.PropMapPairsForRSEM.pre.bam') called at /programs/trinityrnaseq_r2012-10-05/util/alignReads.pl line 695
Anyone have any thoughts? I also posted to the trinity mailing list.
Tx,
I'm working with the trinity pipeline to eventually generate gene expression data from an RNA sequencing project. I have successfully made my transcriptome and now I am using bowtie (through the alignReads.pl) script in the trinity pipeline. I made it most of the way through alignment 1/12 but received an error converting from SAM--BAM:
Error, cmd: /programs/trinityrnaseq_r2012-10-05/util/../trinity-plugins/rsem/convert-sam-for-rsem JUL10SF2_aln.nameSorted.PropMapPairsForRSEM.pre.bam JUL10SF2_aln.nameSorted.PropMapPairsForRSEM -T . died with ret 65280 at /programs/trinityrnaseq_r2012-10-05/util/alignReads.pl line 720
main:rocess_cmd('/programs/trinityrnaseq_r2012-10-05/util/../trinity-plugins/r...') called at /programs/trinityrnaseq_r2012-10-05/util/alignReads.pl line 738
main::make_RSEM_bam('JUL10SF2_aln.nameSorted.PropMapPairsForRSEM.pre.bam') called at /programs/trinityrnaseq_r2012-10-05/util/alignReads.pl line 695
Anyone have any thoughts? I also posted to the trinity mailing list.
Tx,