MSMC error about msmc

[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" <[email protected]> 收件人: "stschiff/msmc" <[email protected]> 抄送: "kentsing" <[email protected]>, "Author" <[email protected]> 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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or mute the thread .

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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" <[email protected]> 收件人: "stschiff/msmc" <[email protected]> 抄送: "kentsing" <[email protected]>, "Author" <[email protected]> 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 — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub , or mute the thread .

-------------------------------------------------------------------------------- 本邮件及其附件含有发送给特定个人和用于特定目的的保密信息。如果您不是预期的收件人，请立即删除本邮件并通知发件人。严禁任何非预期的收件人使用、传播、分发或复制本邮件或其附件。 This email and its attachments may contain confidential information intended for a specific individual and purpose. If you are not the intended recipient, you should delete this email and notify the sender immediately. Any use, dissemination, distribution, or copying of this email or its attachments by persons other than the intended recipient(s), is strictly prohibited.

[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 ***@***.***> 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 — You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub <#40 (comment)>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AAbQmluw11K7c7JTGOd3FhEotC1Chv7Aks5vc2M1gaJpZM4WJGsC>.

[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