warning: bad chrom

[NicMAlexandre]

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

[bumblenick]

Chromosomes are supposed to be small integers. Chr1 -> 1 etc and all should be well Nick

…

On Tue, Mar 8, 2022 at 6:16 PM nicolasalexandre21 ***@***.***> wrote: *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 — Reply to this email directly, view it on GitHub <#89>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AEE77B7G6OTV7ZX5YTGYUQTU67NVLANCNFSM5QH2QGQA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[NicMAlexandre]

Thank you! This answers my question.

…

On Tue, Mar 8, 2022 at 4:17 PM bumblenick ***@***.***> wrote: Chromosomes are supposed to be small integers. Chr1 -> 1 etc and all should be well Nick On Tue, Mar 8, 2022 at 6:16 PM nicolasalexandre21 ***@***.***> wrote: > *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 > > — > Reply to this email directly, view it on GitHub > <#89>, or unsubscribe > < https://github.com/notifications/unsubscribe-auth/AEE77B7G6OTV7ZX5YTGYUQTU67NVLANCNFSM5QH2QGQA > > . > Triage notifications on the go with GitHub Mobile for iOS > < https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675 > > or Android > < https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub >. > > You are receiving this because you are subscribed to this thread.Message > ID: ***@***.***> > — Reply to this email directly, view it on GitHub <#89 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AFB6336YPOMPZ733WTWRFHLU67UZ7ANCNFSM5QH2QGQA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub>. You are receiving this because you authored the thread.Message ID: ***@***.***>

-- Best, Nicolas Alexandre PhD Candidate, Integrative Biology Whiteman Lab University of California - Berkeley ***@***.*** ***@***.***>