Closed miyakokodama closed 4 years ago
Hi Miyako, apologies for the delay. I'll get to this over the weekend.
Hey Miyako,
Thanks for using DegNorm. Looks like an issue with your .gtf file. Please make sure that the attribute
field of the .gtf file contains either a gene_id
or gene_name
attribute (see example). If experiencing further issues, please post the first few lines of your .gtf.
Hi, thanks for your reply! Found out that there were a few rows with just transcript_id
but not gene_id
and gene_name
in the attribute.
Supplied these as unknown
, degnorm seems to be just running fine now. Thanks so much for your help!
Hi
I am currently running DegNorm (version 0.1.4) on .bam files that have been aligned to a genome using STAR (I have 414 samples).
I am getting the following error message:
DegNorm (12/03/2019 12:53:35) ---- creating index file for /home/projects/S_373_Aligned_REAL.sortedByCoord.out.bam -- 414 / 414 DegNorm (12/03/2019 01:10:14) ---- SAMPLE S_373_Aligned_REAL.sortedByCoord.out -- sample contains single-end reads DegNorm (12/03/2019 01:10:15) ---- Begin genome annotation file processing... DegNorm (12/03/2019 01:10:15) ---- Loading genome annotation file /home/projects/GCF_000233375.1_ICSASG_v2_genomic.gtf... Traceback (most recent call last): File "/services/tools/anaconda3/4.0.0/bin/degnorm", line 8, in
sys.exit(main())
File "/services/tools/anaconda3/4.0.0/lib/python3.5/site-packages/degnorm/main.py", line 84, in main
exon_df = gap.run()
File "/services/tools/anaconda3/4.0.0/lib/python3.5/site-packages/degnorm/gene_processing.py", line 107, in run
exon_df = self.load()
File "/services/tools/anaconda3/4.0.0/lib/python3.5/site-packages/degnorm/gene_processing.py", line 35, in load
exon_df = self.loader.get_data()
File "/services/tools/anaconda3/4.0.0/lib/python3.5/site-packages/degnorm/loaders.py", line 147, in get_data
df['gene'] = df.attribute.apply(lambda x: self._attribute_to_gene(x, exprs=find_me))
File "/services/tools/anaconda3/4.0.0/lib/python3.5/site-packages/pandas/core/series.py", line 4045, in apply
mapped = lib.map_infer(values, f, convert=convert_dtype)
File "pandas/_libs/lib.pyx", line 2228, in pandas._libs.lib.map_infer
File "/services/tools/anaconda3/4.0.0/lib/python3.5/site-packages/degnorm/loaders.py", line 147, in
df['gene'] = df.attribute.apply(lambda x: self._attribute_to_gene(x, exprs=find_me))
File "/services/tools/anaconda3/4.0.0/lib/python3.5/site-packages/degnorm/loaders.py", line 106, in _attribute_to_gene
gene_matches = list(filter(exprs[expr_idx].match, splt))
IndexError: list index out of range
Is this an issue with my .gtf file, or .bam file containing single-end reads?
Any help you could provide would be greatly appreciated.
Thanks! Miyako