error log:
[W] overlapping records at NC_051386.1:468540 for sample 0
[W] Variants that overlap on the reference allele: 7644
[I] Total VCF records: 13147524
[I] Non-reference VCF records: 13147524
[W] overlapping records at NC_051386.1:468540 for sample 0
[W] Variants that overlap on the reference allele: 7853
[I] Total VCF records: 13163970
[I] Non-reference VCF records: 13163970
2023-03-16 09:12:51,659 ERROR [Errno 7] Argument list too long
2023-03-16 09:12:51,660 ERROR Traceback (most recent call last):
2023-03-16 09:12:51,660 ERROR File "/opt/hap.py/bin/hap.py", line 540, in
2023-03-16 09:12:51,660 ERROR main()
2023-03-16 09:12:51,660 ERROR File "/opt/hap.py/bin/hap.py", line 394, in main
2023-03-16 09:12:51,660 ERROR convert_gvcf_to_vcf=convert_gvcf_query)
2023-03-16 09:12:51,660 ERROR File "/opt/hap.py/bin/pre.py", line 195, in preprocess
2023-03-16 09:12:51,660 ERROR num_threads=threads)
2023-03-16 09:12:51,660 ERROR File "/opt/hap.py/lib/python27/Tools/bcftools.py", line 266, in preprocessVCF
2023-03-16 09:12:51,660 ERROR raise ex
2023-03-16 09:12:51,660 ERROR OSError: [Errno 7] Argument list too long
Hap.py
Error running BCFTOOLS; please check your file for compatibility issues issues using vcfcheck
vcfcheck：
vcf1：
docker run --user 1019:1019 -v /home/zhaolx/gtx-run-species:/data -w /data happy:v0.3.15 /opt/hap.py/bin/ gtx_reference_data/analysis/Penaeus_monodon[W] overlapping records at NC_051386.1:468540 for sample 0
[W] Variants that overlap on the reference allele: 7644
[I] Total VCF records: 13147524
[I] Non-reference VCF records: 13147524
[I] X chromosome appears to not be haploid -- assuming this is a female sample
vcf2：
docker run --user 1019:1019 -v /home/zhaolx/gtx-run-species:/data -w /data happy:v0.3.15 /opt/hap.py/bin/vcfcheck gtx_reference_data/analysis/Penaeus_monodon/Penaeus_monodon_SRR12180364/gtx_2.2.0-pre1/Penaeus_monodon_SRR12180364.vcf.gz
[W] overlapping records at NC_051386.1:468540 for sample 0
[I] X chromosome appears to not be haploid -- assuming this is a female sample
[W] Variants that overlap on the reference allele: 7853
[I] Total VCF records: 13163970
[I] Non-reference VCF records: 13163970
my cmd: docker run --user 1019:1019 -v /home/zhaolx/gtx-run-species:/data -w /data happy:v0.3.15 /opt/hap.py/bin/hap.py gtx_reference_data/analysis/Penaeus_monodon/Penaeus_monodon_SRR12180364/gatk_4.1.8.1/Penaeus_monodon_SRR12180364.vcf.gz gtx_reference_data/analysis/Penaeus_monodon/Penaeus_monodon_SRR12180364/Penaeus_monodon_SRR12180364.vcf.gz -r gtx_reference_data/reference/Penaeus_monodon/bwa-index/GCF_015228065.1_NSTDA_Pmon_1_genomic.fna -o Penaeus_monodon_SRR12180364_gatk-4.1.8.1 --threads 10 --engine vcfeval
error log: [W] overlapping records at NC_051386.1:468540 for sample 0 [W] Variants that overlap on the reference allele: 7644 [I] Total VCF records: 13147524 [I] Non-reference VCF records: 13147524 [W] overlapping records at NC_051386.1:468540 for sample 0 [W] Variants that overlap on the reference allele: 7853 [I] Total VCF records: 13163970 [I] Non-reference VCF records: 13163970 2023-03-16 09:12:51,659 ERROR [Errno 7] Argument list too long 2023-03-16 09:12:51,660 ERROR Traceback (most recent call last): 2023-03-16 09:12:51,660 ERROR File "/opt/hap.py/bin/hap.py", line 540, in
2023-03-16 09:12:51,660 ERROR main()
2023-03-16 09:12:51,660 ERROR File "/opt/hap.py/bin/hap.py", line 394, in main
2023-03-16 09:12:51,660 ERROR convert_gvcf_to_vcf=convert_gvcf_query)
2023-03-16 09:12:51,660 ERROR File "/opt/hap.py/bin/pre.py", line 195, in preprocess
2023-03-16 09:12:51,660 ERROR num_threads=threads)
2023-03-16 09:12:51,660 ERROR File "/opt/hap.py/lib/python27/Tools/bcftools.py", line 266, in preprocessVCF
2023-03-16 09:12:51,660 ERROR raise ex
2023-03-16 09:12:51,660 ERROR OSError: [Errno 7] Argument list too long
Hap.py
Error running BCFTOOLS; please check your file for compatibility issues issues using vcfcheck
vcfcheck： vcf1： docker run --user 1019:1019 -v /home/zhaolx/gtx-run-species:/data -w /data happy:v0.3.15 /opt/hap.py/bin/ gtx_reference_data/analysis/Penaeus_monodon[W] overlapping records at NC_051386.1:468540 for sample 0 [W] Variants that overlap on the reference allele: 7644 [I] Total VCF records: 13147524 [I] Non-reference VCF records: 13147524 [I] X chromosome appears to not be haploid -- assuming this is a female sample
vcf2： docker run --user 1019:1019 -v /home/zhaolx/gtx-run-species:/data -w /data happy:v0.3.15 /opt/hap.py/bin/vcfcheck gtx_reference_data/analysis/Penaeus_monodon/Penaeus_monodon_SRR12180364/gtx_2.2.0-pre1/Penaeus_monodon_SRR12180364.vcf.gz [W] overlapping records at NC_051386.1:468540 for sample 0 [I] X chromosome appears to not be haploid -- assuming this is a female sample [W] Variants that overlap on the reference allele: 7853 [I] Total VCF records: 13163970 [I] Non-reference VCF records: 13163970
Tks