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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-calculate-expression error #14

Closed qwangmsk closed 9 years ago

qwangmsk commented 9 years ago

Hi RSEM expert:

When running this command: "rsem-calculate-expression --bam --estimate-rspd --no-bam-output --paired-end Aligned.toTranscriptome.out.bam ./rsem-out Quant", I received an error (see error message below). I wonder what rsem-out.grp is? Could you please give me a hint how to fix it?

Many thanks, Qingguo

rsem-parse-alignments ./rsem-out Quant.temp/Quant Quant.stat/Quant b Aligned.toTranscriptome.out.bam -t 3 -tag XM Cannot open ./rsem-out.grp! It may not exist. "rsem-parse-alignments ./rsem-out Quant.temp/Quant Quant.stat/Quant b Aligned.toTranscriptome.out.bam -t 3 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!

mbernste commented 9 years ago

Hi, I'm not an expert of the RSEM package, but I have run into this problem before. Instead of pointing to the reference "./rsem-out", change it to "./rsem-out/RSEMref". It seems that the the calculate-expression program expects "RSEMref" to be appended to the reference's prefix. That fixed it for me.

Matt

qwangmsk commented 9 years ago

Hi Matt, this fixed this error! Thanks for your kind help.

Qingguo

reedliu commented 6 years ago

Hi I met this problem with rsem-parse-alignments, can you give me some advice? Thanks!

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.

mroodgar commented 6 years ago

Hi there, I am trying to run "rsem-prepare-reference" using the options below:

rsem-prepare-reference --gtf /PATH_to_gtf_file.gtf --star --star-path /PATH_to STAR -p 8 /PATH_to_Genome.fa ./RSEMref

But I get error below:

"rsem-extract-reference-transcripts ./RSEMref 0 /PATH_to_gtf_file.gtf None 0 /PATH_to_Genome.fa" failed! Plase check if you provide correct parameters/options for the pipeline!

Has anyone faced the same error or know how to fix this?

Thanks,

Morteza