rsem-prepare-reference error

[mroodgar]

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

[bli25wisc]

Hi @mroodgar , sorry for my late reply. Do you still have this issue?

[DrJones85]

Hi @bli25wisc ,

I am getting this same error. My code differs slightly in that I am asking for a bowtie reference. But the error is the same and it occurs after a bunch of files are created.

Command executed (paths have been shortened make it easier to read)

rsem-prepare-reference --gtf ~/Genome_Files/GTF_files/FANTOM_CAT.lv2_permissive.gtf --bowtie ~/Genome_files/hg19_files/hg19.fa hg19_FANTOM

End of output and error message (same paths have been shortened make it easier to read)

Parsed 200000 lines
Parsed 400000 lines
Parsed 600000 lines
Parsed 800000 lines
Parsed 1000000 lines
Parsed 1200000 lines
Parsed 1400000 lines
Parsed 1600000 lines
Parsed 1800000 lines
Parsed 2000000 lines
Parsed 2200000 lines
Parsed 2400000 lines
Parsed 2600000 lines
Parsed 2800000 lines
Parsed 3000000 lines
Parsed 3200000 lines
Parsed 3400000 lines
Parsed 3600000 lines
Parsed 3800000 lines
Parsed 4000000 lines
Parsed 4200000 lines
Parsed 4400000 lines
Parsed 4600000 lines
Parsed 4800000 lines
Parsed 5000000 lines
Parsing gtf File is done!
~/Genome_Files/hg19_files/hg19.fa is processed!
712715 transcripts are extracted and 0 transcripts are omitted.
Extracting sequences is done!
Group File is generated!
Transcript Information File is generated!
Chromosome List File is generated!
"rsem-extract-reference-transcripts hg19_FANTOM 0 ~/Genome_Files/GTF_files/FANTOM_CAT.lv2_permissive.gtf 0 ~/Genome_Files/hg19_files/hg19.fa" failed! Plase check if you provide correct parameters/options for the pipeline!```

[ghost]

Hi @mroodgar were you able to resolve your issue? I am getting the same error and was wondering if you could help me resolve it?

Thanks in advance!