Error in LASSI or saltiLASSI

[DuttaAnik]

Hi Zachary,

I have successfully ran the LASSI on one scaffold and 9 population using the following code: lassip --vcf Scaffold_1__2_contigs__length_78070536.vcf --calc-spec --hapstats --lassi --winsize 200 --winstep 20 --out Chr_1 --pop Pop.info.txt

However, when I want to move on to the next step using the --spectra. I get an error like this: lassip --spectra *.spectra.gz --lassi --out pop_Chr1

Error:

Loading Chr_1.P_1958.lassip.hap.spectra.gz with 1 pops and K = 10
Loading Chr_1.P_1963.lassip.hap.spectra.gz with 1 pops and K = 10
ERROR: Not all files have the same set of populations.
terminate called after throwing an instance of 'int'
Aborted (core dumped)

Can you please tell me how to correct this? In one population I have 10 individuals and in another I have 12. The rest seven populations comprise 11 individuals each.

[jaavedm]

I'm also facing an issue with "terminate called after throwing an instance of 'int'" at the spectra step

I obtained 1000g-AFR-chr*.AFR.lassip.hap.stats.gz files for all autosomes using the command: lassip --threads 4 --vcf 1000g.AFR.chr${CHROM}.vcf.gz --hapstats --salti --winsize 117 --winstep 12 --out 1000g-AFR-chr${CHROM} --pop ./AFR_individuals.txt

This ran fine. In the next step, I run the command:

> lassip --spectra 1000g-AFR-chr* --salti --out 1000g-AFR-chraut
lassip v1.1.1
ERROR: Must provide valid spectra files.
terminate called after throwing an instance of 'int'
Aborted (core dumped)

Can you help.

[szpiech]

Hi Jaaved,

If you wish to compute the —salti statistic, you will need to use the —calc-spec flag in the first command you issue. This will create the haplotype spectra (.spectra.gz files) to be used for the salti statistic.

Let me know if you have any trouble.

Zachary

Le jeu. 11 août 2022 à 7:16 PM, Jaaved Mohammed @.***> a écrit :

I'm also facing an issue with "terminate called after throwing an instance of 'int'" at the spectra step

I obtained 1000g-AFR-chr*.AFR.lassip.hap.stats.gz files for all autosomes using the command: lassip --threads 4 --vcf 1000g.AFR.chr${CHROM}.vcf.gz --hapstats --salti --winsize 117 --winstep 12 --out 1000g-AFR-chr${CHROM} --pop ./AFR_individuals.txt

This ran fine. In the next step, I run the command:

lassip --spectra 1000g-AFR-chr* --salti --out 1000g-AFR-chraut lassip v1.1.1 ERROR: Must provide valid spectra files. terminate called after throwing an instance of 'int' Aborted (core dumped)

Can you help.

— Reply to this email directly, view it on GitHub https://github.com/szpiech/lassip/issues/3#issuecomment-1212582583, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQVIW4HLKGHHE4C5HWLVYWCVPANCNFSM5ZIVSCCQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[jaavedm]

Thank you. I've corrected my mistake and now the program runs to completion without any problems.

[szpiech]

Hello,

This sounds like there are .spectra.gz files being included that include extra/different populations than the others. Are you accidentally including files you don’t mean to by using the wildcard *?

Zachary

Le lun. 20 juin 2022 à 7:59 AM, Anik Dutta @.***> a écrit :

Hi Zachary,

I have successfully ran the LASSI on one scaffold and 9 population using the following code: lassip --vcf Scaffold_1__2_contigs__length_78070536.vcf --calc-spec --hapstats --lassi --winsize 200 --winstep 20 --out Chr_1 --pop Pop.info.txt

However, when I want to move on to the next step using the --spectra. I get an error like this: lassip --spectra *.spectra.gz --lassi --out pop_Chr1

Error:

Loading Chr_1.P_1958.lassip.hap.spectra.gz with 1 pops and K = 10 Loading Chr_1.P_1963.lassip.hap.spectra.gz with 1 pops and K = 10 ERROR: Not all files have the same set of populations. terminate called after throwing an instance of 'int' Aborted (core dumped)

Can you please tell me how to correct this? In one population I have 10 individuals and in another I have 12. The rest seven populations comprise 11 individuals each.

— Reply to this email directly, view it on GitHub https://github.com/szpiech/lassip/issues/3, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQUNMPQBBPB7OSK4X43VQBMKJANCNFSM5ZIVSCCQ . You are receiving this because you are subscribed to this thread.Message ID: @.***>

[yangwukaidi]

Hi, I found --salti to be very time-consuming. How long did everyone take?

[szpiech]

As I mentioned in the other thread, if you increase winstep this will help with runtime.

Zachary

Le jeu. 30 nov. 2023 à 3:55 PM, yangwukaidi @.***> a écrit :

Hi, I found --salti to be very time-consuming. How long did everyone take?

— Reply to this email directly, view it on GitHub https://github.com/szpiech/lassip/issues/3#issuecomment-1833940897, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQU6GK3CQCJ74LDRFKDYHCM6FAVCNFSM5ZIVSCC2U5DIOJSWCZC7NNSXTN2JONZXKZKDN5WW2ZLOOQ5TCOBTGM4TIMBYHE3Q . You are receiving this because you commented.Message ID: @.***>

[drsancho]

hello, i m having problem with the tag --pop. i m using downloaded genotypic data with only snp id. how to generate the population id to it. i was trying to use the .nosex file for the population id , but its not working. so kindly help me with it

[szpiech]

Hello,

Well you just need to create a flat text file formatted as

indID1 pop1 indID2 pop1 indID3 pop2 ...

and so on. If you want to analyze all samples in your VCF together as they are in the same population, you would list them all and associate them with the same pop code. I'm not sure of a tool that will do this for you.

-Zachary

On Tue, Jul 2, 2024 at 5:07 AM drsancho @.***> wrote:

hello, i m having problem with the tag --pop. i m using downloaded genotypic data with only snp id. how to generate the population id to it. i was trying to use the .nosex file for the population id , but its not working. so kindly help me with it

— Reply to this email directly, view it on GitHub https://github.com/szpiech/lassip/issues/3#issuecomment-2202415337, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABAKRQUTYFK6BVIFJTMOI4DZKJUW5AVCNFSM6AAAAABKHDOGC2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEMBSGQYTKMZTG4 . You are receiving this because you commented.Message ID: @.***>

[drsancho]

okay sir. thank you. it ran