search

HTGenomeAnalysisUnit / SCE-VCF

Sample Contamination Estimate from VCF
MIT License
17 stars 0 forks source link

Computed contamination values for 0 sample(s #1

Open npatel-ah opened 2 weeks ago

npatel-ah commented 2 weeks ago

Hello,

I am trying to run the tool on a multiple sample VCF with over 200 samples. However, I am keep getting no output. Please see my command and log

./sceVCF test.vcf.gz -f LAD -o out -d 5,100 -q 5 -s Samples.txt [14:40:19-202] - INFO: SCE-VCF v0.1.2 [14:40:19-202] - ARG: Input VCF: @["test.vcf.gz"] [14:40:19-202] - ARG: Output: out [14:40:19-202] - ARG: AD field: LAD [14:40:19-202] - ARG: AF field: AF [14:40:19-202] - ARG: Is refAF: false [14:40:19-202] - ARG: REF AF limits: 0.1,0.9 [14:40:19-202] - ARG: Het AB limit: 0.25,0.75 [14:40:19-202] - ARG: Min GQ: 5 [14:40:19-202] - ARG: DP limit: 5,100 [14:40:19-202] - ARG: Samples Samples.txt [14:40:19-202] - INFO: Reading samples list from file: Samples.txt [14:40:19-203] - INFO: Imported 283 sampless [14:40:19-204] - INFO: Variant processing started [14:40:19-204] - INFO: Processing file test.vcf.gz [14:40:21-961] - INFO: 50000 variants processed. Last batch: 50000 in 2 seconds and 756 milliseconds [14:40:24-757] - INFO: 100000 variants processed. Last batch: 50000 in 2 seconds and 796 milliseconds [14:40:27-546] - INFO: 150000 variants processed. Last batch: 50000 in 2 seconds and 788 milliseconds [14:40:30-294] - INFO: 200000 variants processed. Last batch: 50000 in 2 seconds and 748 milliseconds [14:40:32-997] - INFO: 250000 variants processed. Last batch: 50000 in 2 seconds and 702 milliseconds [14:40:35-821] - INFO: 300000 variants processed. Last batch: 50000 in 2 seconds and 824 milliseconds [14:40:38-647] - INFO: 350000 variants processed. Last batch: 50000 in 2 seconds and 825 milliseconds [14:40:41-412] - INFO: 400000 variants processed. Last batch: 50000 in 2 seconds and 765 milliseconds [14:40:44-192] - INFO: 450000 variants processed. Last batch: 50000 in 2 seconds and 779 milliseconds [14:40:46-909] - INFO: 500000 variants processed. Last batch: 50000 in 2 seconds and 714 milliseconds [14:40:52-318] - INFO: 600000 variants processed. Last batch: 100000 in 5 seconds and 408 milliseconds [14:40:57-501] - INFO: 700000 variants processed. Last batch: 100000 in 5 seconds and 183 milliseconds [14:41:02-886] - INFO: 800000 variants processed. Last batch: 100000 in 5 seconds and 384 milliseconds [14:41:08-117] - INFO: 900000 variants processed. Last batch: 100000 in 5 seconds and 230 milliseconds [14:41:13-174] - INFO: 999851 variants processed, 0 vars ignored: 0 multiallelic, 0 indels, 0 outside ref AF limits, 0 missing AF tag [14:41:13-174] - INFO: Computing contamination values [14:41:13-174] - INFO: Computed contamination values for 0 sample(s) in 53 seconds and 964 milliseconds

raonyguimaraes commented 1 week ago

Hi there, Im getting the same:

[12:04:00-830] - INFO: SCE-VCF v0.1.2 [12:04:00-832] - ARG: Input VCF: @["sample.h.vcf.gz"] [12:04:00-832] - ARG: Output: stdout [12:04:00-832] - ARG: AD field: AD [12:04:00-832] - ARG: AF field: AF [12:04:00-832] - ARG: Is refAF: false [12:04:00-832] - ARG: REF AF limits: 0.1,0.9 [12:04:00-832] - ARG: Het AB limit: 0.25,0.75 [12:04:00-832] - ARG: Min GQ: 20 [12:04:00-832] - ARG: DP limit: 20,100 [12:04:00-832] - ARG: Samples xxxSAMPLENAMExxx [12:04:00-832] - INFO: Reading samples list from comma-separated string [12:04:00-832] - INFO: Imported 1 sampless

SAMPLE HQ_HOM HQ_HOM_RATE HQ_HET HQ_HET_RATE CHARR MEAN_REF_AB_HOM_ALT HETEROZYGOSITY_RATE INCONSISTENT_AB_HET_RATE

[12:04:00-856] - INFO: Variant processing started [12:01:06-366] - INFO: 369120692 variants processed, 339343248 vars ignored: 6216433 multiallelic, 333126815 indels, 0 outside ref AF limits, 0 missing AF tag [12:01:06-370] - INFO: Computing contamination values [12:01:06-370] - INFO: Computed contamination values for 0 sample(s) in 13 minutes, 32 seconds, and 914 milliseconds

What should I do?