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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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3 -tag XM" failed! when running rsem-calculate-expression #168

Open deb0612 opened 3 years ago

deb0612 commented 3 years ago

Dear sir, When I ran "rsem-calculate-expression --paired-end --alignments -p 8input.bam" gencodev22 ./out. I got error message

rsem-parse-alignments ../bowtie2/hg38 ./rsem-out.temp/rsem-out ./rsem-out.stat/rsem-out /NGS_Storage/Debbie/RNA-seq/variant_calling_20210602/RNA-leukemia002A-906.para.bam 3 -tag XM Read A00355:209:H3KTLDSX2:2:2606:24677:17425: The adjacent two lines do not represent the two mates of a paired-end read! (RSEM assumes the two mates of a paired-end read should be adjacent) "rsem-parse-alignments ../bowtie2/hg38 ./rsem-out.temp/rsem-out ./rsem-out.stat/rsem-out /NGS_Storage/Debbie/RNA-seq/variant_calling_20210602/RNA-leukemia002A-906.para.bam 3 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!

I tried different bams, all got the same result.

see-the-sun commented 1 year ago

I have the same problem. Have you solved it?