Converting PLINK to EIGENSTRAT error using convertf (no valid snps)

Xue-yd commented 5 years ago

Hi, I'm trying to convert a set of PLINK files to EIGENSTRAT, but I have this error:

/data/users/xueyingdi/software/EIG-7.2.1/bin/convertf -p transfer.conf 
parameter file: transfer.conf
genotypename: sylvaticum.ped
snpname: sylvaticum.map
indivname: sylvaticum.ped 
outputformat: EIGENSTRAT
genotypeoutname: sylvaticum.eigenstratgeno
snpoutname: sylvaticum.snp
indivoutname: sylvaticum.ind
familynames: NO
warning (mapfile): bad chrom: 0 Chr01:1074      0       1074
warning (mapfile): bad chrom: 0 Chr01:1194      0       1194
warning (mapfile): bad chrom: 0 Chr01:1644      0       1644
warning (mapfile): bad chrom: 0 Chr01:1645      0       1645
warning (mapfile): bad chrom: 0 Chr01:1825      0       1825
warning (mapfile): bad chrom: 0 Chr01:2917      0       2917
warning (mapfile): bad chrom: 0 Chr01:3190      0       3190
warning (mapfile): bad chrom: 0 Chr01:3193      0       3193
warning (mapfile): bad chrom: 0 Chr01:3219      0       3219
warning (mapfile): bad chrom: 0 Chr01:3248      0       3248
genetic distance set from physical distance
PLINK input. No check on SNP order
snp order check fail; snp list not ordered: sylvaticum.map (processing continues)   99     0    12 
zzz 0 392203
snp order check fail; snp list not ordered: sylvaticum.map (processing continues)   99     0    16 
zzz 1 392204
snp order check fail; snp list not ordered: sylvaticum.map (processing continues)   99     0    30 
zzz 2 392205
snp order check fail; snp list not ordered: sylvaticum.map (processing continues)   99     0    36 
zzz 3 391687
snp order check fail; snp list not ordered: sylvaticum.map (processing continues)   99     0    38 
zzz 4 393019
snp order check fail; snp list not ordered: sylvaticum.map (processing continues)   99     0    40 
zzz 5 392591
snp order check fail; snp list not ordered: sylvaticum.map (processing continues)   99     0    44 
zzz 6 392592
snp order check fail; snp list not ordered: sylvaticum.map (processing continues)   99     1    52 
zzz 7 392206
snp order check fail; snp list not ordered: sylvaticum.map (processing continues)   99     1    57 
zzz 8 392684
fatalx:
no valid snps
Aborted (core dumped)

Why it's saying that I have no valid SNPs?

I think it's because: I don't have the chromosomes names and I don't have the genetic distances (in cMorgan)

Is there a way that I can fix that? This is part of my .map file:

Chr01   1       1       1
Chr01   2       4       2
Chr01   5       5       5
Chr01   6       8       9
Chr01   9       11      10
Chr01   12      13      12
Chr01   14      17      13
Chr01   18      21      14
Chr01   22      22      13
Chr01   23      24      14
Chr01   25      26      10
Chr01   27      27      14
Chr01   28      28      15
Chr01   29      29      14
Chr01   30      32      15
Chr01   33      33      17
Chr01   34      35      20
Chr01   36      41      19
Chr01   42      47      20
Chr01   48      51      21
Chr01   52      52      22
Chr01   53      54      23
Chr01   55      57      22
Chr01   58      61      23
Chr01   62      62      24

Thanks in advance.

bumblenick commented 5 years ago

It thinks that you have a chromosome labeled 0. Please check you .map file carefully

Nick

On Thu, Jul 25, 2019 at 3:33 AM YindyXue notifications@github.com wrote:

Hi, I'm trying to convert a set of PLINK files to EIGENSTRAT, but I have this error:

/data/users/xueyingdi/software/EIG-7.2.1/bin/convertf -p transfer.conf parameter file: transfer.conf genotypename: sylvaticum.ped snpname: sylvaticum.map indivname: sylvaticum.ped outputformat: EIGENSTRAT genotypeoutname: sylvaticum.eigenstratgeno snpoutname: sylvaticum.snp indivoutname: sylvaticum.ind familynames: NO warning (mapfile): bad chrom: 0 Chr01:1074 0 1074 warning (mapfile): bad chrom: 0 Chr01:1194 0 1194 warning (mapfile): bad chrom: 0 Chr01:1644 0 1644 warning (mapfile): bad chrom: 0 Chr01:1645 0 1645 warning (mapfile): bad chrom: 0 Chr01:1825 0 1825 warning (mapfile): bad chrom: 0 Chr01:2917 0 2917 warning (mapfile): bad chrom: 0 Chr01:3190 0 3190 warning (mapfile): bad chrom: 0 Chr01:3193 0 3193 warning (mapfile): bad chrom: 0 Chr01:3219 0 3219 warning (mapfile): bad chrom: 0 Chr01:3248 0 3248 genetic distance set from physical distance PLINK input. No check on SNP order snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 12 zzz 0 392203 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 16 zzz 1 392204 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 30 zzz 2 392205 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 36 zzz 3 391687 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 38 zzz 4 393019 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 40 zzz 5 392591 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 44 zzz 6 392592 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 1 52 zzz 7 392206 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 1 57 zzz 8 392684 fatalx: no valid snps Aborted (core dumped)

Why it's saying that I have no valid SNPs?

I think it's because: I don't have the chromosomes names and I don't have the genetic distances (in cMorgan)

Is there a way that I can fix that? This is part of my .map file:

Chr01 1 1 1 Chr01 2 4 2 Chr01 5 5 5 Chr01 6 8 9 Chr01 9 11 10 Chr01 12 13 12 Chr01 14 17 13 Chr01 18 21 14 Chr01 22 22 13 Chr01 23 24 14 Chr01 25 26 10 Chr01 27 27 14 Chr01 28 28 15 Chr01 29 29 14 Chr01 30 32 15 Chr01 33 33 17 Chr01 34 35 20 Chr01 36 41 19 Chr01 42 47 20 Chr01 48 51 21 Chr01 52 52 22 Chr01 53 54 23 Chr01 55 57 22 Chr01 58 61 23 Chr01 62 62 24

Thanks in advance.

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bumblenick commented 5 years ago

Sorry: I didn't read your whole message. Set chromosome names to small positive integers and genetic distances to 0. I also think it's bad style to use integers as snp names -- though the software should run

N

On Thu, Jul 25, 2019 at 10:25 AM Nick Patterson nickp@broadinstitute.org wrote:

It thinks that you have a chromosome labeled 0. Please check you .map file carefully

Nick

On Thu, Jul 25, 2019 at 3:33 AM YindyXue notifications@github.com wrote:

Hi, I'm trying to convert a set of PLINK files to EIGENSTRAT, but I have this error:

/data/users/xueyingdi/software/EIG-7.2.1/bin/convertf -p transfer.conf parameter file: transfer.conf genotypename: sylvaticum.ped snpname: sylvaticum.map indivname: sylvaticum.ped outputformat: EIGENSTRAT genotypeoutname: sylvaticum.eigenstratgeno snpoutname: sylvaticum.snp indivoutname: sylvaticum.ind familynames: NO warning (mapfile): bad chrom: 0 Chr01:1074 0 1074 warning (mapfile): bad chrom: 0 Chr01:1194 0 1194 warning (mapfile): bad chrom: 0 Chr01:1644 0 1644 warning (mapfile): bad chrom: 0 Chr01:1645 0 1645 warning (mapfile): bad chrom: 0 Chr01:1825 0 1825 warning (mapfile): bad chrom: 0 Chr01:2917 0 2917 warning (mapfile): bad chrom: 0 Chr01:3190 0 3190 warning (mapfile): bad chrom: 0 Chr01:3193 0 3193 warning (mapfile): bad chrom: 0 Chr01:3219 0 3219 warning (mapfile): bad chrom: 0 Chr01:3248 0 3248 genetic distance set from physical distance PLINK input. No check on SNP order snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 12 zzz 0 392203 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 16 zzz 1 392204 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 30 zzz 2 392205 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 36 zzz 3 391687 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 38 zzz 4 393019 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 40 zzz 5 392591 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 44 zzz 6 392592 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 1 52 zzz 7 392206 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 1 57 zzz 8 392684 fatalx: no valid snps Aborted (core dumped)

Why it's saying that I have no valid SNPs?

I think it's because: I don't have the chromosomes names and I don't have the genetic distances (in cMorgan)

Is there a way that I can fix that? This is part of my .map file:

Chr01 1 1 1 Chr01 2 4 2 Chr01 5 5 5 Chr01 6 8 9 Chr01 9 11 10 Chr01 12 13 12 Chr01 14 17 13 Chr01 18 21 14 Chr01 22 22 13 Chr01 23 24 14 Chr01 25 26 10 Chr01 27 27 14 Chr01 28 28 15 Chr01 29 29 14 Chr01 30 32 15 Chr01 33 33 17 Chr01 34 35 20 Chr01 36 41 19 Chr01 42 47 20 Chr01 48 51 21 Chr01 52 52 22 Chr01 53 54 23 Chr01 55 57 22 Chr01 58 61 23 Chr01 62 62 24

Thanks in advance.

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Xue-yd commented 5 years ago

Thank you so much. I have set chromosome names to small positive integers. And it runs very well. I can't thank you any more.

------------------ 原始邮件 ------------------ 发件人: "bumblenick"notifications@github.com; 发送时间: 2019年7月25日(星期四) 晚上10:27 收件人: "DReichLab/EIG"EIG@noreply.github.com; 抄送: "遇见"1771012116@qq.com;"Author"author@noreply.github.com; 主题: Re: [DReichLab/EIG] Converting PLINK to EIGENSTRAT error usingconvertf (no valid snps) (#37)

Sorry: I didn't read your whole message. Set chromosome names to small positive integers and genetic distances to 0. I also think it's bad style to use integers as snp names -- though the software should run

N

On Thu, Jul 25, 2019 at 10:25 AM Nick Patterson nickp@broadinstitute.org wrote:

It thinks that you have a chromosome labeled 0. Please check you .map file carefully

Nick

On Thu, Jul 25, 2019 at 3:33 AM YindyXue notifications@github.com wrote:

Hi, I'm trying to convert a set of PLINK files to EIGENSTRAT, but I have this error:

/data/users/xueyingdi/software/EIG-7.2.1/bin/convertf -p transfer.conf parameter file: transfer.conf genotypename: sylvaticum.ped snpname: sylvaticum.map indivname: sylvaticum.ped outputformat: EIGENSTRAT genotypeoutname: sylvaticum.eigenstratgeno snpoutname: sylvaticum.snp indivoutname: sylvaticum.ind familynames: NO warning (mapfile): bad chrom: 0 Chr01:1074 0 1074 warning (mapfile): bad chrom: 0 Chr01:1194 0 1194 warning (mapfile): bad chrom: 0 Chr01:1644 0 1644 warning (mapfile): bad chrom: 0 Chr01:1645 0 1645 warning (mapfile): bad chrom: 0 Chr01:1825 0 1825 warning (mapfile): bad chrom: 0 Chr01:2917 0 2917 warning (mapfile): bad chrom: 0 Chr01:3190 0 3190 warning (mapfile): bad chrom: 0 Chr01:3193 0 3193 warning (mapfile): bad chrom: 0 Chr01:3219 0 3219 warning (mapfile): bad chrom: 0 Chr01:3248 0 3248 genetic distance set from physical distance PLINK input. No check on SNP order snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 12 zzz 0 392203 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 16 zzz 1 392204 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 30 zzz 2 392205 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 36 zzz 3 391687 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 38 zzz 4 393019 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 40 zzz 5 392591 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 0 44 zzz 6 392592 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 1 52 zzz 7 392206 snp order check fail; snp list not ordered: sylvaticum.map (processing continues) 99 1 57 zzz 8 392684 fatalx: no valid snps Aborted (core dumped)

Why it's saying that I have no valid SNPs?

I think it's because: I don't have the chromosomes names and I don't have the genetic distances (in cMorgan)

Is there a way that I can fix that? This is part of my .map file:

Chr01 1 1 1 Chr01 2 4 2 Chr01 5 5 5 Chr01 6 8 9 Chr01 9 11 10 Chr01 12 13 12 Chr01 14 17 13 Chr01 18 21 14 Chr01 22 22 13 Chr01 23 24 14 Chr01 25 26 10 Chr01 27 27 14 Chr01 28 28 15 Chr01 29 29 14 Chr01 30 32 15 Chr01 33 33 17 Chr01 34 35 20 Chr01 36 41 19 Chr01 42 47 20 Chr01 48 51 21 Chr01 52 52 22 Chr01 53 54 23 Chr01 55 57 22 Chr01 58 61 23 Chr01 62 62 24

Thanks in advance.

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Converting PLINK to EIGENSTRAT error using convertf (no valid snps) #37