MSMC error

[kentsing]

Dear @stschiff I'm new for msmc2, and when i'm trying i meet an error

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Haplotype index exceeds number of haplotypes in datafile

and also:

error in parsing command line: object.Exception@model/data.d(189): chromosomes must all be the same within one file (sorry) can one file only contain data of one scaffold/chr?

Thanks

[stschiff]

Hi,

what's not to understand about these error messages? The first one suggests that you are using an index number in the -I flag that exceeds the number of haplotypes that are actually in your file. Note that indexing here is 0-based. The second error suggests that you have put multiple chromosome into one file, which is not allowed. You need to separate chromosomes into separate files and give all those files to MSMC on the command line.

Best, Stephan

[kentsing]

Hi Thanks for you reply. I finally solved the problem. Thanks again!

----- 原始邮件 ----- 发件人: "Stephan Schiffels" notifications@github.com 收件人: "stschiff/msmc" msmc@noreply.github.com 抄送: "kentsing" xingk@mail.sysu.edu.cn, "Author" author@noreply.github.com 发送时间: 星期四, 2018年 8 月 23日 下午 7:22:52 主题: Re: [stschiff/msmc] MSMC error (#40)

Hi,

what's not to understand about these error messages? The first one suggests that you are using an index number in the -I flag that exceeds the number of haplotypes that are actually in your file. Note that indexing here is 0-based. The second error suggests that you have put multiple chromosome into one file, which is not allowed. You need to separate chromosomes into separate files and give all those files to MSMC on the command line.

Best, Stephan

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[zillurbmb51]

Hello there, I am having almost same problem here. In my case I have separate file for each chromosome. Whenever, I tried to put r and I flag I am getting the following error `core.exception.RangeError@model/data.d(188): Range violation

??:? _d_arrayboundsp [0x5b5ad2]`
Any help? My sample represents a single population. Should I use I 0,1,4,5 ? Whatever value I put for r and I, I am getting the same error. Without r and I the program runs without any error. Best regards Zillur

[kentsing]

maybe you should remove the indels and just keep the SNPs.

----- 原始邮件 ----- 发件人: "zillurbmb51" notifications@github.com 收件人: "stschiff/msmc" msmc@noreply.github.com 抄送: "kentsing" xingk@mail.sysu.edu.cn, "Author" author@noreply.github.com 发送时间: 星期二, 2019年 4 月 02日 上午 8:16:15 主题: Re: [stschiff/msmc] MSMC error (#40)

Hello there, I am having almost same problem here. In my case I have separate file for each chromosome. Whenever, I tried to put r and I flag I am getting the following error `core.exception.RangeError@model/data.d(188): Range violation

??:? _d_arrayboundsp [0x5b5ad2]` Any help? My sample represents a single population. Should I use I 0,1,4,5 ? Whatever value I put for r and I, I am getting the same error. Without r and I the program runs without any error. Best regards Zillur

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[zillurbmb51]

Thank you very much. I have only snps in my data, no indels. However, if I put "I 0,1" it runs without any error. How can I identify which value I need for my dataset? Best regards Zillur

[stschiff]

Hi, please send me a small dataset and a command line that reproducibly gives this error.

Thanks, Stephan

On 2 Apr 2019, at 16:03, zillurbmb51 notifications@github.com wrote:

Thank you very much. I have only snps in my data, no indels. However, if I put "I 0,1" it runs without any error. How can I identify which value I need for my dataset? Best regards Zillur

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[zillurbmb51]

Thank you very much. My command line was :

samtools mpileup -q 20 -Q 20 -C 50 -u -r Pf3D7_01_v3 -f pfal.fa SRR3305693_NoDup_addrplced.bam | bcftools call -c -V indels | /gondor/zillur/thesis/psmc/msmc-tools/bamCaller.py 331.781 chr1.mask.bed.gz | gzip -c > chr1.vcf.gz
/gondor/zillur/thesis/psmc/msmc-tools/generate_multihetsep.py --mask=chr1.mask.bed.gz chr1.vcf.gz > chr1.msmc.input.txt
/gondor/zillur/msmc2/build/release/msmc2 -t 16 -r 0.0115 -I 0,1,4,5 -o test1 chr1.msmc.input.txt

If I run without the "I" flag or "I 0,1" it works.

Just to clarify, the value of r should be mutation rate/recombination rate, right? Best regards Zillur chr1.mask.bed.gz chr1.msmc.input.txt chr1.vcf.gz

[rillaxy]

Thank you very much. My command line was :

samtools mpileup -q 20 -Q 20 -C 50 -u -r Pf3D7_01_v3 -f pfal.fa SRR3305693_NoDup_addrplced.bam | bcftools call -c -V indels | /gondor/zillur/thesis/psmc/msmc-tools/bamCaller.py 331.781 chr1.mask.bed.gz | gzip -c > chr1.vcf.gz
/gondor/zillur/thesis/psmc/msmc-tools/generate_multihetsep.py --mask=chr1.mask.bed.gz chr1.vcf.gz > chr1.msmc.input.txt
/gondor/zillur/msmc2/build/release/msmc2 -t 16 -r 0.0115 -I 0,1,4,5 -o test1 chr1.msmc.input.txt

If I run without the "I" flag or "I 0,1" it works.

Just to clarify, the value of r should be mutation rate/recombination rate, right? Best regards Zillur chr1.mask.bed.gz chr1.msmc.input.txt chr1.vcf.gz

Thank you very much. I have only snps in my data, no indels. However, if I put "I 0,1" it runs without any error. How can I identify which value I need for my dataset? Best regards Zillur

Hi ,Zillur ,

Thank you very much. I have only snps in my data, no indels. However, if I put "I 0,1" it runs without any error. How can I identify which value I need for my dataset? Best regards Zillur Hi, Zillur ,I am getting the same error with you.How do you solve this problem?

Thank you very much. I have only snps in my data, no indels. However, if I put "I 0,1" it runs without any error. How can I identify which value I need for my dataset? Best regards Zillur

Hi, Zillur ,I am getting the same error with you.How do you solve this problem? Looking forward to hearing from you .Thank you. Rilla

[zillurbmb51]

Hello Rilla, could share some part of your chr*.msmc.input.txt. Did you try with/without 'I' flag? Running without '-I' was OK for me. Best, Zillur

[rillaxy]

Hello Rilla, could share some part of your chr*.msmc.input.txt. Did you try with/without 'I' flag? Running without '-I' was OK for me. Best, Zillur

Hello Zillur, I send some part of my chr*.msmc.input.txt to you . This is no phased diploid genomes. The probelm is itcan run with 'I' flag if I put "I 0,1" or without the 'I' flag.But it can't run if I use I 0,1,4,5. Why ? Thanks for your reply. Below is my command and wrong information. Looking forward hearing from you. Rilla

msmc2 -r 0.00157 -I 0,1 -o msmc.test msmc-input-chr*（success） msmc2 -r 0.00157 -o msmc.test msmc-input-chr*（success） msmc2 -r 0.00157 -I 0,1,4,5 -o msmc.test msmc-input-chr*(wrong）

core.exception.RangeError@model/data.d(188): Range violation

??:? _d_arrayboundsp [0x5cfe25] ??:? bool model.data.has_missing_data(const(char[][]), ulong[2]) [0x560f44] ??:? model.data.SegSite_t[][] model.data.readSegSites(immutable(char)[], ulong[2][], bool) [0x560804] ??:? model.data.SegSite_t[][] msmc2.readDataFromFiles(immutable(char)[][], ulong[2][], bool) [0x585295] ??:? void msmc2.parseCommandLine(immutable(char)[][]) [0x5837e2] ??:? _Dmain [0x5830f7]

msmc-input-chr01.txt msmc-input-chr02.txt msmc-input-chr03.txt

[zillurbmb51]

Hello Rilla, I guess you have only two character in the snp column. AT/CG etc. Maybe that's why it wotk on 0,1 but not more that 1. Best, Zillur

[rillaxy]

Hello Rilla, I guess you have only two character in the snp column. AT/CG etc. Maybe that's why it wotk on 0,1 but not more that 1. Best, Zillur

Hello Zillur, I get it. Thank you very much. Best, Rilla