Question: Trinity transcript_abundance.pl error using RSEM
0
gravatar for dimitrischat
11 months ago by
dimitrischat120
dimitrischat120 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 • 408 views
ADD COMMENTlink written 11 months ago by dimitrischat120
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1544 users visited in the last hour
_