antisunny / coval-qtl Goto Github PK

Dear All,
I am executing Coval for Variant Calling in qtl analysis. First I executed
perl coval refine -r GCF_000150535.2_Papaya1.0_genomic.fna -p coval_output -s SO_6823_S_E1_csorted.bam
And I got the out_prefix.sam file.
But when I executed perl coval call-sam coval_output.sam, I got the following error

Use of uninitialized value $qualities in concatenation (.) or string at /media/ravishankar/Bannana/Desktop/01032018/Steffi/QTL/coval-call-sam.pl line 658, line 47663920.
Filtered reads: 48000000 pos = 32841
substr outside of string at /media/ravishankar/Bannana/Desktop/01032018/Steffi/QTL/coval-call-sam.pl line 655, line 48022424.
Filtered reads: 49000000 pos = 145532
Filtered reads: 50000000 pos = 288576
Filtered reads: 51000000 pos = 422081
Use of uninitialized value $qualities in concatenation (.) or string at /media/ravishankar/Bannana/Desktop/01032018/Steffi/QTL/coval-call-sam.pl line 658, line 51691314.
Filtered reads: 52000000 pos = 10072
Filtered reads: 53000000 pos = 24734
Filtered reads: 54000000 pos = 39741
Filtered reads: 55000000 pos = 56302
Filtered reads: 56000000 pos = 70897
read number = 62186801
genome size = 370418818
total genome positions covered by reads = 267801200
genome coverage = 72.2 %
average read depth = 17.6 X
average Q for all SNPs/indels with the minimum number/frequency of SNPs/indels = 33.1230170324572
Illegal division by zero at /media/ravishankar/Bannana/Desktop/01032018/Steffi/QTL/coval-call-sam.pl line 592.