search

ylab-hi / ScanNeo

A pipeline for identifying indel derived neoantigens using RNA-Seq data
Other
29 stars 7 forks source link

Errors about parsing the VEP annotation output file (tmp_vcf) #21

Open paulhtyang opened 2 years ago

paulhtyang commented 2 years ago

I am running the latest version (v2.2) of ScanNeo and VEP (v106.1), and successfully complete the first step. However, I got some error messages by running the second step of the workflow below: Thanks, Paul

Command: ScanNeo.py anno --dir /data/ensemble -i Adipose01_R1.HISAT2-2.1.0.aligned.sorted.indel.vcf -o Adipose01_R1.HISAT2-2.1.0.aligned.sorted.indel.vcf.ann

Error messages:

Checking for 'picard': found /data/anaconda3/envs/Ensembl/bin/picard

Checking for 'vep': found /data/anaconda3/envs/Ensembl/bin/vep

Checking for 'sambamba': found /data/anaconda3/envs/Ensembl/bin/sambamba

Checking for 'bedtools': found /data/anaconda3/envs/Ensembl/bin/bedtools

Checking for 'bwa': found /data/anaconda3/envs/Ensembl/bin/bwa

Checking for 'transIndel_build_RNA.py': found /data/tools/transIndel/transIndel_build_RNA.py

Checking for 'transIndel_call.py': found /data/tools/transIndel/transIndel_call.py

Begin deal with VCF: Adipose01_R1.HISAT2-2.1.0.aligned.sorted.indel.vcf VCF add sequences [ref, alt] accomplished! vep --offline --force_overwrite --dir /data/ensemble --species homo_sapiens --assembly GRCh38 --input_file pre_vep.7219.vcf --format vcf --output_file tmp.953900885997.vcf --vcf --symbol --terms SO --af --af_gnomad --plugin Downstream --plugin Wildtype --no_stats VEP begin annotation VEP annotation finished! VEP accomplished! Traceback (most recent call last): File "/data/tools/ScanNeo/ScanNeo.py", line 1011, in main() File "/data/tools/ScanNeo/ScanNeo.py", line 930, in main cutoff=args.cutoff, File "/data/tools/ScanNeo/ScanNeo.py", line 376, in vep_caller csq_allele = alleles_dict[alt] TypeError: unhashable type: '_Substitution'

sandain commented 2 years ago

I believe I have fixed this issue. Check out PR #19 and issue #18 for more information.

paulhtyang commented 2 years ago

Thank you, Sandian,

I did updates the codes at the lines (ssue https://github.com/ylab-hi/ScanNeo/issues/18) you showed for ScanNeo.py file. Now it is working very well. Paul