Some issue about the software
Nobody has claimed this yet.
Assessment
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Newbie friendliness
- 25/100
Research direction
Start by reproducing the qpDstat crash with Dsta_par and the referenced 66inds_SNP.eigenstratgeno, 66inds_SNP.snp, 66inds_SNP.ind, and list_pop1 inputs. Inspect qpDstat's chromosome parsing around the reported scaffold_0 warnings; done means identifying the malformed-input or parsing condition that causes the segmentation fault and confirming the command completes safely.
Written by the indexing model from the issue text.
Description
I meet some problem when I used qpDstat.
Some of my genotype data:
292229222299999999999999999999999999999999999999101919999999999999
999229229999299999292999292929992199090092222929222929222229922229
999229229991299999222229291209991222222222222229222222222222222229
999229229992229229222299222229992229222221111019222222222222222222
999229229992229229222222222229992229222222222229222220191112222222
SNP data:
scaffold_0:25599 0 0 25599 C T
scaffold_0:26840 0 0 26840 C T
scaffold_0:27901 0 0 27901 C A
scaffold_0:27953 0 0 27953 T A
scaffold_0:27992 0 0 27992 G A
individual data:
GSA1 U GSA
GSA2 U GSA
GSA3 U GSA
GSA4 U GSA
GSA5 U GSA
GSA6 U GSA
GSA7 U GSA
GSA8 U GSA
GSA9 U GSA
Besides, my genotype data have 786 scaffolds. When I run the commond qpDstat -p Dsta_par, it tells some problems:
qpDstat: parameter file: Dsta_par
THE INPUT PARAMETERS
##PARAMETER NAME: VALUE
genotypename: 66inds_SNP.eigenstratgeno
snpname: 66inds_SNP.snp
indivname: 66inds_SNP.ind
popfilename: list_pop1
qpDstat version: 755
warning: bad chrom: scaffold_0:14883 0 0 14883 C T
warning: bad chrom: scaffold_0:15074 0 0 15074 G T
warning: bad chrom: scaffold_0:15222 0 0 15222 C T
warning: bad chrom: scaffold_0:25526 0 0 25526 C T
warning: bad chrom: scaffold_0:25579 0 0 25579 C T
warning: bad chrom: scaffold_0:25599 0 0 25599 C T
warning: bad chrom: scaffold_0:26840 0 0 26840 C T
warning: bad chrom: scaffold_0:27901 0 0 27901 C A
warning: bad chrom: scaffold_0:27953 0 0 27953 T A
warning: bad chrom: scaffold_0:27992 0 0 27992 G A
Segmentation fault (core dumped)
Please tell me what's wrong with my data?
Thank you very much.
- Dominant language
- C
- Stars
- 236
- Forks
- 76
- PR merge metrics
- No merged PRs in 30d
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