xryanglab/RiboCode

prepare_transcripts failed

manishbiotechie opened this issue · 3 comments

manishbiotechie commented

Traceback (most recent call last):
File "/home/dr/anaconda2/bin/prepare_transcripts", line 10, in
sys.exit(main())
File "/home/dr/anaconda2/lib/python2.7/site-packages/RiboCode/prepare_transcripts.py", line 388, in main
processTranscripts(args.genomeFasta,args.gtfFile,args.out_dir)
File "/home/dr/anaconda2/lib/python2.7/site-packages/RiboCode/prepare_transcripts.py", line 308, in processTranscripts
gene_dict,transcript_dict = readGTF(gtfFile)
File "/home/dr/anaconda2/lib/python2.7/site-packages/RiboCode/prepare_transcripts.py", line 187, in readGTF
gene => transcript => exon (or CDS)" % i)
RiboCode.prepare_transcripts.ParsingError: Error in line 0. The annotation in GTF file should be three-level hierarchy of gene => transcript => exon (or CDS)

I am getting this error and I am new to bioinformatics kindly resolve....

zhengtaoxiao commented

Hi, it looks like the annotations in your GTF file are not complete, it should include three-level hierarchy annotations: genes,transcripts and exons. You can add the missing annotations by using the "GTFupdate" command in RiboCode. Please refer to GTF_update.rst for more information.

Udaykage commented

I also got the same error and i use GTFupdate command and i got a error saying

Traceback (most recent call last):
File "/apps/python/3.7.2/bin/GTFupdate", line 11, in
load_entry_point('RiboCode==1.2.11', 'console_scripts', 'GTFupdate')()
File "/apps/python/3.7.2/lib/python3.7/site-packages/RiboCode/GTF_update.py", line 117, in main
gset,sourted_gset_keys = GroupGeneSubsets(args.gtfFile)
File "/apps/python/3.7.2/lib/python3.7/site-packages/RiboCode/GTF_update.py", line 50, in GroupGeneSubsets
chrom,gid,strand = i.split(":")
ValueError: too many values to unpack (expected 3)

Appreciate your help.
Thanks

L1angyan commented

I also got the same error and i use GTFupdate command and i got a error saying

Traceback (most recent call last):
File "/apps/python/3.7.2/bin/GTFupdate", line 11, in
load_entry_point('RiboCode==1.2.11', 'console_scripts', 'GTFupdate')()
File "/apps/python/3.7.2/lib/python3.7/site-packages/RiboCode/GTF_update.py", line 117, in main
gset,sourted_gset_keys = GroupGeneSubsets(args.gtfFile)
File "/apps/python/3.7.2/lib/python3.7/site-packages/RiboCode/GTF_update.py", line 50, in GroupGeneSubsets
chrom,gid,strand = i.split(":")
ValueError: too many values to unpack (expected 3)

Appreciate your help.
Thanks

I also got the same error when I updated my GTF file.

Traceback (most recent call last):
File "/public/home/yliang/miniconda3/envs/ribocode/bin/GTFupdate", line 10, in
sys.exit(main())
File "/public/home/yliang/miniconda3/envs/ribocode/lib/python2.7/site-packages/RiboCode/GTF_update.py", line 117, in main
gset,sourted_gset_keys = GroupGeneSubsets(args.gtfFile)
File "/public/home/yliang/miniconda3/envs/ribocode/lib/python2.7/site-packages/RiboCode/GTF_update.py", line 50, in GroupGeneSubsets
chrom,gid,strand = i.split(":")
ValueError: too many values to unpack