Joyjoyjoyc
commented
2 months ago hi@suhuanhou, I got the same problem, did you figure it out? thanks!!
Open suhuanhou opened 1 year ago
Joyjoyjoyc
commented
2 months ago hi@suhuanhou, I got the same problem, did you figure it out? thanks!!
freebayes -f /share/home/shh/download/refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa -iXu -C 2 -q 20 -n 3 -E 1 -m 30 --min-coverage 6 ${souporcell_out}minitagged_sorted.bam
fileformat=VCFv4.1
fileDate=20230612
source=freeBayes v0.9.21
reference=/share/home/shh/download/refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa
phasing=none
commandline="freebayes -f /share/home/shh/download/refdata-cellranger-GRCh38-3.0.0/fasta/genome.fa -iXu -C 2 -q 20 -n 3 -E 1 -m 30 --min-coverage 6 /share/home/shh/download/souporcell_out/minitagged_sorted.bam"
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CHROM POS ID REF ALT QUAL FILTER INFO FORMAT unknown
1 16495 . G C 2.17973 . AB=0.25;ABP=7.35324;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=8;DPB=8;DPRA=0;EPP=7.35324;EPPR=16.0391;GTI=0;LEN=1;MEANALT=1;MQM=50;MQMR=41.3333;NS=1;NUMALT=1;ODDS=0.427928;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=222;RO=6;RPL=2;RPP=7.35324;RPPR=16.0391;RPR=0;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=6;SRP=16.0391;SRR=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:8:6:222:2:74:-4.58141,0,-16.6279 1 135040 . T C 768.691 . AB=0.7;ABP=20.3821;AC=1;AF=0.5;AN=2;AO=35;CIGAR=1X;DP=50;DPB=50;DPRA=0;EPP=20.9405;EPPR=10.1038;GTI=0;LEN=1;MEANALT=1;MQM=53.5714;MQMR=54.9333;NS=1;NUMALT=1;ODDS=53.1878;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=1271;QR=555;RO=15;RPL=26;RPP=20.9405;RPPR=10.1038;RPR=9;RUN=1;SAF=35;SAP=79.0118;SAR=0;SRF=15;SRP=35.5824;SRR=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:50:15:555:35:1271:-97.4787,0,-35.0744 1 139366 . C T 15.4215 . AB=0.285714;ABP=8.59409;AC=1;AF=0.5;AN=2;AO=4;CIGAR=1X;DP=14;DPB=14;DPRA=0;EPP=11.6962;EPPR=24.725;GTI=0;LEN=1;MEANALT=1;MQM=58;MQMR=37.5;NS=1;NUMALT=1;ODDS=3.5218;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=136;QR=370;RO=10;RPL=4;RPP=11.6962;RPPR=24.725;RPR=0;RUN=1;SAF=4;SAP=11.6962;SAR=0;SRF=10;SRP=24.725;SRR=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:14:10:370:4:136:-8.35585,0,-26.0761 1 191016 . A G 8.42038 . AB=0.333333;ABP=4.45795;AC=1;AF=0.5;AN=2;AO=2;CIGAR=1X;DP=6;DPB=6;DPRA=0;EPP=7.35324;EPPR=5.18177;GTI=0;LEN=1;MEANALT=1;MQM=55;MQMR=57.25;NS=1;NUMALT=1;ODDS=1.78353;PAIRED=0;PAIREDR=0;PAO=0;PQA=0;PQR=0;PRO=0;QA=74;QR=148;RO=4;RPL=0;RPP=7.35324;RPPR=5.18177;RPR=2;RUN=1;SAF=2;SAP=7.35324;SAR=0;SRF=4;SRP=11.6962;SRR=0;TYPE=snp GT:DP:RO:QR:AO:QA:GL 0/1:6:4:148:2:74:-5.21085,0,-11.8675 Aborted (core dumped)
How can this problem be solved? Thank you for answering!