I can not get any output file using v0.6.0b1 version

vep command: ~/VEP/ensembl-vep/vep --assembly GRCh38 --cache --dir_plugins /home/yubau/.vep/Plugins --everything --fasta /home/yubau/.vep/homo_sapiens/99_GRCh38 --force_overwrite --fork 48 --format vcf --input_file HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vcf --offline --output_file HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep.vcf --symbol --terms SO --tsl --vcf

vcf using VEP annotated file (head -n 1000) (Total 4,773,130 line when run charger): HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep_1000.txt

install: mkdir CharGer_test_python38 cd CharGer_test_python38 conda create --name CharGer_python_38 python=3.8 conda activate CharGer_python_38 pip install pysam

(CharGer_python_38) [yubau@cmuh-i2 CharGer]$ conda list # packages in environment at /home/yubau/anaconda2/envs/CharGer_python_38: # # Name Version Build Channel _libgcc_mutex 0.1 main attrs 19.3.0 pypi_0 pypi ca-certificates 2020.1.1 0 certifi 2019.11.28 py38_0 charger 0.6.0b1 pypi_0 pypi cyvcf2 0.11.6 pypi_0 pypi ld_impl_linux-64 2.33.1 h53a641e_7 libedit 3.1.20181209 hc058e9b_0 libffi 3.2.1 hd88cf55_4 libgcc-ng 9.1.0 hdf63c60_0 libstdcxx-ng 9.1.0 hdf63c60_0 loguru 0.4.1 pypi_0 pypi ncurses 6.2 he6710b0_0 numpy 1.18.1 pypi_0 pypi openssl 1.1.1d h7b6447c_4 pip 20.0.2 py38_1 pysam 0.15.4 pypi_0 pypi python 3.8.1 h0371630_1 readline 7.0 h7b6447c_5 setuptools 45.2.0 py38_0 sqlite 3.31.1 h7b6447c_0 tk 8.6.8 hbc83047_0 wheel 0.34.2 py38_0 xz 5.2.4 h14c3975_4 zlib 1.2.11 h7b6447c_3

(CharGer_python_38) [yubau@cmuh-i2 CharGer]$ pip install --pre -i https://pypi.org/simple/ --extra-index-url https://test.pypi.org/simple/ charger

command:

(CharGer_python_38) [yubau@cmuh-i2 CharGer]$ charger --input HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep.vcf --output HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep.charger.tsv INFO | Running CharGer v0.6.0b1 with parameters: --input HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep.vcf --output HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep.charger.tsv

----screen info start------------------------------------------------------------------------------------- INFO | Validate the given config DEBUG | Given config: CharGerConfig(input=PosixPath('HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep.vcf'), output=PosixPath('HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep.charger.tsv'), hotspot3d_cluster=None, pathogenic_variant=None, override_variant_info=False, include_vcf_details=False, clinvar_table=None, rare_threshold=0.0005, common_threshold=0.005, acmg_module_scores={'PVS1': 8, 'PS1': 7, 'PS2': 4, 'PS3': 4, 'PS4': 4, 'PM1': 2, 'PM2': 2, 'PM3': 2, 'PM4': 2, 'PM5': 2, 'PM6': 2, 'PP1': 1, 'PP2': 1, 'PP3': 1, 'PP4': 1, 'PP5': 1, 'BP1': -1, 'BP2': -1, 'BP3': -1, 'BP4': -1, 'BP5': -1, 'BP6': -1, 'BP7': -1, 'BS1': -4, 'BS2': -4, 'BS3': -4, 'BS4': -4, 'BA1': -8}, charger_module_scores={'PSC1': 4, 'PMC1': 2, 'PPC1': 1, 'PPC2': 1, 'BMC1': -2, 'BSC1': -6}, min_pathogenic_score=9, min_likely_pathogenic_score=5, max_likely_benign_score=-4, max_benign_score=-8, disease_specific=False, inheritance_gene_table=None, PP2_gene_list=None, BP1_gene_list=None) INFO | Read input VCF from HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep.vcf DEBUG | VEP version 99 with CSQ format [66 fields]: Allele,Consequence,IMPACT,SYMBOL,Gene,Feature_type,Feature,BIOTYPE,EXON,INTRON,HGVSc,HGVSp,cDNA_position,CDS_position,Protein_position,Amino_acids,Codons,Existing_variation,DISTANCE,STRAND,FLAGS,VARIANT_CLASS,SYMBOL_SOURCE,HGNC_ID,CANONICAL,MANE,TSL,APPRIS,CCDS,ENSP,SWISSPROT,TREMBL,UNIPARC,GENE_PHENO,SIFT,PolyPhen,DOMAINS,miRNA,HGVS_OFFSET,AF,AFR_AF,AMR_AF,EAS_AF,EUR_AF,SAS_AF,AA_AF,EA_AF,gnomAD_AF,gnomAD_AFR_AF,gnomAD_AMR_AF,gnomAD_ASJ_AF,gnomAD_EAS_AF,gnomAD_FIN_AF,gnomAD_NFE_AF,gnomAD_OTH_AF,gnomAD_SAS_AF,MAX_AF,MAX_AF_POPS,CLIN_SIG,SOMATIC,PHENO,PUBMED,MOTIF_NAME,MOTIF_POS,HIGH_INF_POS,MOTIF_SCORE_CHANGE SUCCESS | Read total 4,772,905 variants from the input VCF WARNING | Inheritance gene table is not provided, CharGer cannot make ACMG PVS1/PM4 calls or CharGer PSC1/PPC1 calls. Disable all these modules WARNING | CharGer cannot make PP2 calls without the given gene list. Disable PP2 module WARNING | CharGer cannot make BP1 calls without the given gene list. Disable BP1 module INFO | Skip matching ClinVar INFO | Run all ACMG modules INFO | Skipped PVS1 module INFO | Skipped PM4 module INFO | Run all CharGer modules INFO | Skipped PSC1 module INFO | Running PMC1 module INFO | Skipped PPC1 module INFO | Running PPC2 module ----screen info end-------------------------------------------------------------------------------------

(CharGer_python_38) [yubau@cmuh-i2 CharGer]$ ls CHANGES.rst demo.vcf demo.vep.vcf_summary.html HCC297_S7_hg38.GATK.HaplotypeCaller.variants.vep.vcf poetry.lock README.md setup.cfg tests tox.ini clinvar_20200210.vep.vcf demo.vep.vcf docs LICENSE.txt pyproject.toml scripts src tox_conda.ini

(CharGer_python_38) [yubau@cmuh-i2 CharGer]$ python -V Python 3.8.1 (CharGer_python_38) [yubau@cmuh-i2 CharGer]$ which python ~/anaconda2/envs/CharGer_python_38/bin/python (CharGer_python_38) [yubau@cmuh-i2 CharGer]$ which pip ~/anaconda2/envs/CharGer_python_38/bin/pip (CharGer_python_38) [yubau@cmuh-i2 CharGer]$ pip --version pip 20.0.2 from /home/yubau/anaconda2/envs/CharGer_python_38/lib/python3.8/site-packages/pip (python 3.8) (CharGer_python_38) [yubau@cmuh-i2 CharGer]$ charger --version CharGer v0.6.0b1 (CharGer_python_38) [yubau@cmuh-i2 CharGer]$ which charger ~/anaconda2/envs/CharGer_python_38/bin/charger

I can not get any output file using v0.6.0b1 version

I used VEP to annotate 0.5.4 version demo.vcf file and run charger v0.6.0b1, than can not get any output file

Can you upload a demo.vcf for charger v0.6.0b1 thanks!

yubau, from taiwan

ding-lab / CharGer

I can not get any output file using v0.6.0b1 version #41