Question: Trinity transcript_abundance.pl error using RSEM
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gravatar for dimitrischat
7 weeks ago by
dimitrischat110
dimitrischat110 wrote:

when i try to run transcript_abundance.pl using RSEM

./align_and_estimate_abundance.pl --seqType fq --single '..x.fastq' --transcripts '.../Trinity.fasta' --output_dir '/..output' --est_method RSEM --aln_method bowtie2 --trinity_mode --prep_reference

it runs good up until :

samtools sort -n -@ 1 -m 1G -o bowtie2.bam.for_rsem.tmp.bam bowtie2.bam

[bam_sort_core] merging from 114 files and 1 in-memory blocks...

rsem-scan-for-paired-end-reads 1 bowtie2.bam.for_rsem.tmp.bam bowtie2.bam.for_rsem.bam
..................................................................................................
Finished!

Conversion is completed. bowtie2.bam.for_rsem.bam will be checked by 'rsem-sam-validator'.
rsem-sam-validator bowtie2.bam.for_rsem.bam
...................................................................................................................................................................................................................................................................................................................................................................................................................................................
The input file is valid!

then this error:

CMD: rsem-calculate-expression     -p 4 --fragment-length-mean 200 --fragment-length-sd 80   --no-bam-output --bam bowtie2.bam.for_rsem.bam /Trinity_trimmed.fasta.RSEM RSEM 
rsem-parse-alignments /trinity_trimmed/Trinity_trimmed.fasta.RSEM RSEM.temp/RSEM RSEM.stat/RSEM bowtie2.bam.for_rsem.bam 1 -tag XM
Cannot open /trinity_trimmed/Trinity_trimmed.fasta.RSEM.grp! It may not exist.
"rsem-parse-alignments /home/app/Trinity_trimmed.fasta.RSEM RSEM.temp/RSEM RSEM.stat/RSEM bowtie2.bam.for_rsem.bam 1 -tag XM" failed! Plase check if you provide correct parameters/options for the pipeline!
Error, cmd: rsem-calculate-expression     -p 4 --fragment-length-mean 200 --fragment-length-sd 80   --no-bam-output --bam bowtie2.bam.for_rsem.bam /Trinity_trimmed.fasta.RSEM RSEM  died with ret: 65280 at ./align_and_estimate_abundance.pl line 729.
rna-seq assembly • 87 views
ADD COMMENTlink written 7 weeks ago by dimitrischat110
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