warning: bad chrom

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

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.