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warning: bad chrom

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Assessment

Difficulty
4/5
Estimated time
3-5 days
Newbie friendliness
30/100
Issue type
Bug
Clarity
Needs clarification
Activity status
Stale
Tech stack
c
Domain
data, tooling

Research direction

Start by comparing the chromosome and position fields in Merged.snp, including the rejected Sca100 entry, with the input format expected by smartpca. Check smartpca.params.txt and the Merged.geno/Merged.ind headers for consistency; done means identifying the cause of the bad-chromosome warnings and fatal error, with a reproducible correction or clear input-format guidance.

Written by the indexing model from the issue text.

Description

I have the following error:

parameter file: smartpca.params.txt

THE INPUT PARAMETERS

##PARAMETER NAME: VALUE
genotypename: Merged.geno
snpname: Merged.snp
indivname: Merged.ind
evecoutname: Merged.pca.evec.txt
evaloutname: Merged.pca.eval.txt
poplistname: pop.txt
lsqproject: YES
numoutevec: 10
numthreads: 12
numoutliter: 0

smartpca version: 16000

norm used

lsqproject used
warning: bad chrom: Chr1:24 Chr1 0.0 24 A G
warning: bad chrom: Chr1:25 Chr1 0.0 25 G A
warning: bad chrom: Chr1:55 Chr1 0.0 55 G A
warning: bad chrom: Chr1:59 Chr1 0.0 59 A C
warning: bad chrom: Chr1:86 Chr1 0.0 86 A G
warning: bad chrom: Chr1:111 Chr1 0.0 111 G A
warning: bad chrom: Chr1:116 Chr1 0.0 116 A C
warning: bad chrom: Chr1:123 Chr1 0.0 123 G T
warning: bad chrom: Chr1:143 Chr1 0.0 143 G C
warning: bad chrom: Chr1:151 Chr1 0.0 151 T C
fatalx:
bad chrom: Sca100
/var/spool/slurmd/job11595754/slurm_script: line 14: 48503 Aborted smartpca -p smartpca.params.txt

The following are the heads of my .geno, .snp, and .ind files:

Merged.geno:

000000000000292220222222222200002002222292229
222222222022292922222222222222022222222292229
222222222292292222222222222222222222222222202
222222222222292222292222222222222222202222222
222222222222222222000002222222222222222222222
222222222222222222222222222222222222222022222
222222222222222222202222222222222222222222222
222222222222222222222222222222222222222222202
222222222222202222222222222222222222222222222
222222222222202022222222220222222222222222222

Merged.ind

AL-5_28-1_S10_L001-1 U BTH
AL-5_29-4_S9_L001-1 U BTH
AL2_7_7_10_S15_L002-1 U BTH
AL2_7_7_1_S14_L002-1 U BTH
AL2_7_7_20_S26_L002-1 U BTH
AL2_7_7_2_S25_L002-1 U BTH
AL2_7_7_5_S29_L002-1 U BTH
AL3_7_3_10_S34_L002-1 U BTH
AL4_7_9_2_S46_L002-1 U BTH
AL5_7_10_12_S49_L002-1 U BTH

Merged.snp

Chr1:24 Chr1 0.0 24 A G
Chr1:25 Chr1 0.0 25 G A
Chr1:55 Chr1 0.0 55 G A
Chr1:59 Chr1 0.0 59 A C
Chr1:86 Chr1 0.0 86 A G
Chr1:111 Chr1 0.0 111 G A
Chr1:116 Chr1 0.0 116 A C
Chr1:123 Chr1 0.0 123 G T
Chr1:143 Chr1 0.0 143 G C
Chr1:151 Chr1 0.0 151 T C

Dominant language
C
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