SimonHegele
commented
1 month ago The .gtf-file GCF_037355615.1 drosophila genome assembly was processed perfectly fine. The first annotation I used apparently didn't include the ORFs. Sorry to have bothered you.
Hello,
I tried using sqanti-sim.py classif with the .gtf-file for the GCF_000002985.6 c. elegans assembly (https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000002985.6/). Is this a problem of SQANTI-SIM or of the file I used? If it is the file, could you provide one that works for SQANTI-SIM?
Thanks!
Error: exonFrames field is being added, but I found a gene (NM_078464.8) with CDS but no valid frames. This can happen if program is invoked with -genePredExt but no valid frames are given in the file. If the 8th field of GFF/GTF file is always a placeholder, then don't use -genePredExt. 30536 errors Traceback (most recent call last): File "/root/SQANTI-SIM/sqanti-sim.py", line 539, in
res = classif(input)
^^^^^^^^^^^^^^
File "/root/SQANTI-SIM/sqanti-sim.py", line 64, in classif
trans_info = classify_gtf.classify_gtf(args)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/SQANTI-SIM/src/classify_gtf.py", line 1313, in classify_gtf
trans_by_chr = gtf_parser(args.gtf)
^^^^^^^^^^^^^^^^^^^^
File "/root/SQANTI-SIM/src/classify_gtf.py", line 194, in gtf_parser
if subprocess.check_call(cmd, shell=True) != 0:
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/root/miniconda3/envs/SQANTI-SIM.env/lib/python3.11/subprocess.py", line 413, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '/root/SQANTI-SIM/src/SQANTI3/utilities/gtfToGenePred ../elegans/ncbi_dataset/GCF_000002985.6/genomic.gtf ../elegans/ncbi_dataset/GCF_000002985.6/genomic.genePred -genePredExt -allErrors -ignoreGroupsWithoutExons' returned non-zero exit status 255.