bcftools related error encountered while executing karyoscan #4
Description
Hi
I am trying to execute karyoscan and I ran into some errors and I am writing this email to seek help from your side.
So, I have installed all the dependencies (like bcftools , bedtools etc) required to execute karyoscan and prepared the config file as suggested on the github page
And then I executed karyoscan, see the output given below (Notice the message Both INFO/DP and FORMAT/DP exist, which one do you want? ):
bioinfo@bioinfo-pc:~/karyoscan$ date && time ./ks_driver.sh config.txt 0
Thu Nov 28 10:45:19 IST 2019
Reading configuration file....
Calculating r_i, gamma_i (read coverage chromosomal summary) values for all samples in /home/bioinfo/karyoscan/test_rdcov_input.tsv file...
Parsing VCF files to identify het allele balance metrics and ROH segments...
Processing B90127145 /home/bioinfo/karyoscan/sample.vcf.gz
Both INFO/DP and FORMAT/DP exist, which one do you want?
Failed to open -: unknown file type
Number of target samples: 1
Number of --estimate-AF samples: 0
Number of sites in the buffer/overlap: unlimited
[E::_regions_match_alleles] Compressed and indexed targets file is required
Error in aggregate.data.frame(mf[1L], mf[-1L], FUN = FUN, ...) :
no rows to aggregate
Calls: aggregate -> aggregate.formula -> aggregate.data.frame
In addition: Warning messages:
1: In is.na(df$runmed) :
is.na() applied to non-(list or vector) of type 'NULL'
2: In is.na(df$runmed) :
is.na() applied to non-(list or vector) of type 'NULL'
Execution halted
Completed stage 1 (gammai matrix calculation and VCF parsing)...
Performing cohort-wide regression modelling on read-coverage (gamma_i) and chromosomal het allele balance (ChromHetAB)...
There were 50 or more warnings (use warnings() to see the first 50)
Error in `contrasts<-`(`*tmp*`, value = contr.funs[1 + isOF[nn]]) :
contrasts can be applied only to factors with 2 or more levels
Calls: lm ... model.matrix -> model.matrix.default -> contrasts<-
In addition: There were 44 warnings (use warnings() to see them)
Execution halted
Completed stage 2 (gamma_i and ChromHetAB regression)...
Aggregating signals from all metrics...
Parsing /home/bioinfo/karyoscan/test_output/coverage_anomalies.txt file...
awk: cmd. line:1: fatal: cannot open file `/home/bioinfo/karyoscan/test_output/coverage_anomalies.txt' for reading (No such file or directory)
Parsing /home/bioinfo/karyoscan/test_output/chrom_ab_anomalies.txt file...
awk: cmd. line:4: fatal: cannot open file `/home/bioinfo/karyoscan/test_output/chrom_ab_anomalies.txt' for reading (No such file or directory)
Parsing /home/bioinfo/karyoscan/test_output/all_local_ab.txt file...
awk: fatal: cannot open file `/home/bioinfo/karyoscan/test_output/all_local_ab.txt' for reading (No such file or directory)
Parsing /home/bioinfo/karyoscan/test_output/all_roh.txt file (this will take the longest)...
awk: fatal: cannot open file `/home/bioinfo/karyoscan/test_output/all_roh.txt' for reading (No such file or directory)
Parsed all files, merging output
Done
Scoring anomalies...
Completed stage 3 (signal aggregation and event scoring)...
Done, all output placed in /home/bioinfo/karyoscan/test_output
The highlighted message is thrown from bcftools (I am pretty sure about that) and I indeed have DP in INFO and the FORMAT columns in my vcf file, please see below:
| INFO | FORMAT |
|---|---|
| AC=2;AF=1.00;AN=2;CNN_1D=3.482;DP=40;ExcessHet=3.0103;FS=0.000;MLEAC=2;MLEAF=1.00;MQ=60.00;QD=27.30;SOR=1.292 | GT:AD:DP:GQ:PL |
What additional information do you require from my side. Looking forward to hear from you soon.