Error Using RSEM Prepare Reference

Skip to first unread message

Christopher Bryan

Nov 3, 2022, 2:15:06 PM11/3/22
to RSEM Users
rsem-prepare-reference --gtf index/gencode.v23lift37.annotation.gtf \
--star  index/GRCh37.primary_assembly.genome.fa \

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
Parsing gtf File is done!
index/GRCh37.primary_assembly.genome.fa is processed!
198356 transcripts are extracted.
Extracting sequences is done!
Group File is generated!
Transcript Information File is generated!
Chromosome List File is generated!
Extracted Sequences File is generated!

rsem-preref /ref/human.transcripts.fa 1 /ref/human
Cannot open /ref/human.transcripts.fa! It may not exist.
"rsem-preref /ref/human.transcripts.fa 1 /ref/human" failed! Plase check if you provide correct parameters/options for the pipeline!

I attempted to create a reference for the tutorial dataset using the commands on Github, but I received the same message.
Reply all
Reply to author
0 new messages