Two mates are aligned to two different transcripts

[albustruong]

Hi,

I was running this test:

!/bin/bash

rsem-calculate-expression \
    --bowtie2 --phred33-quals \
    --paired-end \
    --p 6 --output-genome-bam --sort-bam-by-coordinate \
    sub1-Ca13mCh-LGC9389_L1_1_cleaned.fq.gz \
    sub1-Ca13mCh-LGC9389_L1_2_cleaned.fq.gz \
    human \
    sub1-Ca13mCh-LGC9389_L1_PE_quals \
    2>&1 | tee sub1-Ca13mCh-LGC9389_L1_log.txt

But there was this error:

rsem-tbam2gbam human sub1-Ca13mCh-LGC9389_L1_PE_quals.transcript.bam sub1-Ca13mCh-LGC9389_L1_PE_quals.genome.bam A00599:555:HCFC7DSXC:1:2429:4345:28933's two mates are aligned to two different transcripts! Start converting: "rsem-tbam2gbam human sub1-Ca13mCh-LGC9389_L1_PE_quals.transcript.bam sub1-Ca13mCh-LGC9389_L1_PE_quals.genome.bam" failed! Plase check if you provide correct parameters/options for the pipeline!

sub1-Ca13mCh-LGC9389_L1_log.txt

Please help me and see the attached log for full information.

Thanks so much!!!

[albustruong]

Update: we have found the solution. We got this error using rsem installed from Bioconda. After we reinstall it from here, it is fine.