szpiech
commented
2 years ago 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
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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