run with gnomAD converted VCF fails
dsantesmasses opened this issue · 0 comments
dsantesmasses commented
Describe the bug
Hi!
I am trying to run CRISPRme with a converted gnomAD VCF but the run fails. I am using v2.1.0 by conda.
The Genome folder contains chr22 only, and the VCFs folder contains the corresponding VCF for chr22 converted using the gnomAD-converter. A run without VCFs finished without errors.
To Reproduce
The full command line is the following
crisprme.py complete-search --genome Genomes/hg38_chr22 --guide sg1617.txt --pam PAMs/20bp-NGG-SpCas9.txt --annotation Annotations/encode+gencode.hg38.bed --gene_annotation Annotations/gencode.protein_coding.bed --mm 6 --output sg1617_gnomad_chr22_top --thread 12 --vcf list_vcf_gnomad_chr22.txt --samplesID list_samplesID_gnomad.txt
I get the following error message
$ cat Results/sg1617_gnomad_chr22_top/log_error_no_check.txt
Traceback (most recent call last):
File "./process_summaries.py", line 136, in <module>
dict_samples[sample][3] += 1
KeyError: 'raw'
Traceback (most recent call last):
File "./process_summaries.py", line 136, in <module>
dict_samples[sample][3] += 1
KeyError: 'raw'
Traceback (most recent call last):
File "./process_summaries.py", line 136, in <module>
dict_samples[sample][3] += 1
KeyError: 'raw'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CFD.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CRISTA.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_fewest.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CFD.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CRISTA.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_fewest.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CFD.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CRISTA.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_fewest.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CFD.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CRISTA.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_fewest.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CFD.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CRISTA.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_fewest.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CFD.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CRISTA.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_fewest.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CFD.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_CRISTA.txt'
Traceback (most recent call last):
File "/home/ubuntu/miniconda3/envs/crisprme/opt/crisprme/PostProcess/populations_distribution.py", line 87, in <module>
with open(sys.argv[1]) as summary:
FileNotFoundError: [Errno 2] No such file or directory: '/data2/crisprme_test/Results/sg1617_gnomad_chr22_top/.sg1617_gnomad_chr22_top.PopulationDistribution_fewest.txt'