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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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RSEM rsem-parse-alignments problem #83

Closed reedliu closed 6 years ago

reedliu commented 6 years ago

Hi RSEM expert, Recently I met a problem with the RSEM . The errors are as follows: rsem-parse-alignments /home/u1239/workspace/rna-seq/Quantification/../Assembly/trinity_out_dir/Trinity.fasta.RSEM RSEM.temp/RSEM RSEM.stat/RSEM bowtie2.bam 3 -tag XM open: No such file or directory Cannot open 3! It may not exist. "rsem-parse-alignments /home/u1239/workspace/rna-seq/Quantification/../Assembly/trinity_out_dir/Trinity.fasta.RSEM RSEM.temp/RSEM RSEM.stat/RSEM bowtie2.bam 3 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline! Error, cmd: rsem-calculate-expression --paired-end -p 24 --no-bam-output --bam bowtie2.bam /home/u1239/workspace/rna-seq/Quantification/../Assembly/trinity_out_dir/Trinity.fasta.RSEM RSEM died with ret: 65280 at /home/u1239/Biosoft/Trinity-v2.5.1/util/align_and_estimate_abundance.pl line 778.

bli25wisc commented 6 years ago

@reedliu , that's weird. Could you update RSEM to v1.3.0 and try it again?

golharam commented 4 years ago

Hi all - I'm see this issue with v1.3.2.tar.gz. Need to run 'make'. I thought binaries were included but I guess not.