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deweylab / RSEM

RSEM: accurate quantification of gene and isoform expression from RNA-Seq data
http://deweylab.biostat.wisc.edu/rsem/
GNU General Public License v3.0
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Error while using RSEM in trinity pipeline #138

Open bioinfonext opened 4 years ago

bioinfonext commented 4 years ago

Hello,

I am getting error while running RSEM in trinity data, could you please suggest what could be the reason:

command: /opt/apps/trinity/2.8.5/util/align_and_estimate_abundance.pl --transcripts Trinity.fasta --est_method RSEM --aln_method bowtie2 --prep_reference --trinity_mode --samples_file sample.file.txt --seqType fq

24.01% overall alignment rate [bam_sort_core] merging from 0 files and 4 in-memory blocks... CMD: touch bowtie2.bam.ok CMD: convert-sam-for-rsem bowtie2.bam bowtie2.bam.for_rsem bash: convert-sam-for-rsem: command not found Error, cmd: convert-sam-for-rsem bowtie2.bam bowtie2.bam.for_rsem died with ret: 32512 at /opt/apps/trinity/2.8.5/util/align_and_estimate_abundance.pl line 733.

thanks