Selscan load loci after running and after the process killed

[farhan-lab]

Hi, Szpiech,

I try to run the following command to to calculate iHS

**./selscan-master/src/selscan --ihs --vcf ../SNP.dom.phased.mfa.recode.vcf --map mfa_out_temp.map --out mfa --threads 64
selscan v2.0.0
Opening ../SNP.dom.phased.mfa.recode.vcf...
Loading -6 haplotypes and 806822 loci...
Killed

Here is how my input file vcf and map are:

head ../SNP.dom.phased.mfa.recode.vcf

##fileformat=VCFv4.2
##filedate=20220426
##source="beagle.21Jan17.6cc.jar (version 4.1)"
#CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BNT1443_1_sorted BNT1444_1_sorted BNT1445_1_sorted BNT1446_1_sorted BNT1447_1_sorted BNT1448_1_sorted BNT1449_1_sorted BNT1450_1_sorted BNT1451_1_sorted BNT1452_1_sorted BNT1453_1_sorted BNT1454_1_sorted BNT1455_1_sorted BNT1456_1_sorted MFRC01_1_sorted MFRC02_1_sorted MFRC04_1_sorted MFRC06_1_sorted MFRC07_1_sorted MFRC08_1_sorted MFRC09_1_sorted MFRC11_1_sorted MFRC13_1_sorted MFRC1329_1_sorted MFRC1330_1_sorted MFRC1331_1_sorted MFRC1332_1_sorted MFRC1336_1_sorted MFRC1337_1_sorted MFRC1339_1_sorted MFRC1340_1_sorted MFRC1341_1_sorted MFRC15_1_sorted MFRC16_1_sorted MFRC18_1_sorted MFRC19_1_sorted MFRC20_1_sorted MFRC21_1_sorted MFRC22_1_sorted MFRC23_1_sorted MFRC24_1_sorted MFRC25_1_sorted MFRC26_1_sorted MFRC27_1_sorted MFRC29_1_sorted MFRC30_1_sorted MFRC31_1_sorted MFRC32_1_sorted MFRC33_1_sorted WPN1295_1_sorted WPN1296_1_sorted WPN1297_1_sorted WPN1298_1_sorted WPN1299_1_sorted WPN1300_1_sorted WWM01_1_sorted WWM08_1_sorted WWM12_1_sorted WWM14_1_sorted WWM15_1_sorted WWM19_1_sorted WWM20_1_sorted WWM21_1_sorted WWM23_1_sorted WWM24_1_sorted WWM25_1_sorted WWM28_1_sorted WWM30_1_sorted WWM31_1_sorted WWM32_1_sortedWWM33_1_sorted WWM36_1_sorted WWM37_1_sorted WWM38_1_sorted WWM40_1_sorted WWM41_1_sorted WWM43_1_sorted WWM44_1_sorted WWM45_1_sorted WWM46_1_sorted WWM47_1_sorted WWM48_1_sorted WWM49_1_sorted WWM50_1_sorted WWM51_1_sortedWWM52_1_sorted
NW_005093516.1 6 259794:79:- G A 0
NW_005099967.1 6 262702:120:- A G 0
NW_005098139.1 9 262555:89:- T C 0
NW_005093516.1 10 259794:75:- T G 0
NW_005093516.1 11 259794:74:- C A 0
NW_005099044.1 14 262636:71:- A T 0

head mfa_out_temp.map

NW_005100299.1 262963:69:- 7204 7204
NW_005100299.1 262963:63:- 7210 7210
NW_005100299.1 262963:58:- 7215 7215
NW_005100299.1 262963:57:- 7216 7216
NW_005100299.1 262963:55:- 7218 7218
NW_005100299.1 262963:39:- 7234 7234
NW_005100299.1 262963:36:- 7237 7237
NW_005100299.1 262963:32:- 7241 7241
NW_005100299.1 262963:23:- 7250 7250
NW_005100299.1 262963:22:- 7251 7251

Could you please suggest me how can I run the selscan with success.
Many thanks,
Best regards,
Farhan

[szpiech]

Hello, Is the only error message you get that the process was killed? There may be something weird with your input files, as selscan seems to think there are -6 haplotypes. This snippet of a vcf file you sent certainly looks strange.

…

-Zachary Le jeu. 28 avr. 2022 à 12:44 AM, farhan-lab ***@***.***> a écrit :

Hi, Szpiech, I try to run the following command to to calculate iHS *./selscan-master/src/selscan --ihs --vcf ../SNP.dom.phased.mfa.recode.vcf --map mfa_out_temp.map --out mfa --threads 64 selscan v2.0.0* Opening ../SNP.dom.phased.mfa.recode.vcf... Loading -6 haplotypes and 806822 loci... Killed Here is how my input file vcf and map are: *head ../SNP.dom.phased.mfa.recode.vcf* ##fileformat=VCFv4.2 ##filedate=20220426 ##source="beagle.21Jan17.6cc.jar (version 4.1)" #CHROM POS ID REF ALT QUAL FILTER INFO FORMAT BNT1443_1_sorted BNT1444_1_sorted BNT1445_1_sorted BNT1446_1_sorted BNT1447_1_sorted BNT1448_1_sorted BNT1449_1_sorted BNT1450_1_sorted BNT1451_1_sorted BNT1452_1_sorted BNT1453_1_sorted BNT1454_1_sorted BNT1455_1_sorted BNT1456_1_sorted MFRC01_1_sorted MFRC02_1_sorted MFRC04_1_sorted MFRC06_1_sorted MFRC07_1_sorted MFRC08_1_sorted MFRC09_1_sorted MFRC11_1_sorted MFRC13_1_sorted MFRC1329_1_sorted MFRC1330_1_sorted MFRC1331_1_sorted MFRC1332_1_sorted MFRC1336_1_sorted MFRC1337_1_sorted MFRC1339_1_sorted MFRC1340_1_sorted MFRC1341_1_sorted MFRC15_1_sorted MFRC16_1_sorted MFRC18_1_sorted MFRC19_1_sorted MFRC20_1_sorted MFRC21_1_sorted MFRC22_1_sorted MFRC23_1_sorted MFRC24_1_sorted MFRC25_1_sorted MFRC26_1_sorted MFRC27_1_sorted MFRC29_1_sorted MFRC30_1_sorted MFRC31_1_sorted MFRC32_1_sorted MFRC33_1_sorted WPN1295_1_sorted WPN1296_1_sorted WPN1297_1_sorted WPN1298_1_sorted WPN1299_1_sorted WPN1300_1_sorted WWM01_1_sorted WWM08_1_sorted WWM12_1_sorted WWM14_1_sorted WWM15_1_sorted WWM19_1_sorted WWM20_1_sorted WWM21_1_sorted WWM23_1_sorted WWM24_1_sorted WWM25_1_sorted WWM28_1_sorted WWM30_1_sorted WWM31_1_sorted WWM32_1_sortedWWM33_1_sorted WWM36_1_sorted WWM37_1_sorted WWM38_1_sorted WWM40_1_sorted WWM41_1_sorted WWM43_1_sorted WWM44_1_sorted WWM45_1_sorted WWM46_1_sorted WWM47_1_sorted WWM48_1_sorted WWM49_1_sorted WWM50_1_sorted WWM51_1_sortedWWM52_1_sorted NW_005093516.1 6 259794:79:- G A 0 NW_005099967.1 6 262702:120:- A G 0 NW_005098139.1 9 262555:89:- T C 0 NW_005093516.1 10 259794:75:- T G 0 NW_005093516.1 11 259794:74:- C A 0 NW_005099044.1 14 262636:71:- A T 0 *head mfa_out_temp.map* NW_005100299.1 262963:69:- 7204 7204 NW_005100299.1 262963:63:- 7210 7210 NW_005100299.1 262963:58:- 7215 7215 NW_005100299.1 262963:57:- 7216 7216 NW_005100299.1 262963:55:- 7218 7218 NW_005100299.1 262963:39:- 7234 7234 NW_005100299.1 262963:36:- 7237 7237 NW_005100299.1 262963:32:- 7241 7241 NW_005100299.1 262963:23:- 7250 7250 NW_005100299.1 262963:22:- 7251 7251 Could you please suggest m how can I run the selscan with success. Many thanks, Best regards, Farhan — Reply to this email directly, view it on GitHub <#81>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABAKRQWPRA37LRCXWDN2DVLVHIJRRANCNFSM5UREDUSA> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[farhan-lab]

Yes, the error was due to my input file (VCF wrong format). Many thanks, I can run the selscan with success now :)