armando-caballero
commented
1 month ago You probably have too few SNPs, or they are too far apart from one another, to make a sufficient number of recombination bins for analysis. Best wishes, Armando.
Open ModiShrushti opened 1 month ago
armando-caballero
commented
1 month ago You probably have too few SNPs, or they are too far apart from one another, to make a sufficient number of recombination bins for analysis. Best wishes, Armando.
ModiShrushti
commented
1 month ago Hi Armando, Thanks for your reply. I have another question regarding using scaffold-level genome assembly as a reference. I have tried using the top 200 scaffolds as chromosomes and using it as input for GONE but I am getting errors in LDfile generation. Do you have any specific pipeline for filtering the tip scaffolds and using it as input for GONe. I am using bcftools query and view, which is working fine until filtering, but when I am converting it into .map file, it is giving me only 10, 100, and 1000 as scaffold numbers and I think that is why it is not working. Thanks in advance for your help.
Best Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Fri, Aug 9, 2024 at 2:42 AM armando-caballero @.***> wrote:
You probably have too few SNPs, or they are too far apart from one another, to make a sufficient number of recombination bins for analysis. Best wishes, Armando.
— Reply to this email directly, view it on GitHub https://github.com/esrud/GONE/issues/45#issuecomment-2277352833, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUFH5JT34QKJ6OIP2PYDUNLZQRXHBAVCNFSM6AAAAABMHBKEIKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDENZXGM2TEOBTGM . You are receiving this because you authored the thread.Message ID: @.***>
armando-caballero
commented
1 month ago You can use scaffolds instead of chromosomes, but they should have a large enough number of SNPs and have to be numbered in the map file as the chromosomes: 1, 2, 3, ... Otherwise it will not work. Best wishes, Armando.
ModiShrushti
commented
1 month ago Thanks for the quick response. I renamed the scaffolds as the numbers as per your suggestion, but now I am getting another
DIVIDE .ped AND .map FILES IN CHROMOSOMES
RUNNING ANALYSIS OF CHROMOSOMES ...
CHROMOSOME ANALYSES took 0 seconds
Running GONE
Specify a sample size larger than 1.
Specify a sample size larger than 1. Specify a sample size larger than 1. Thanks in advance
Best Regards Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Mon, Aug 12, 2024 at 6:35 AM armando-caballero @.***> wrote:
You can use scaffolds instead of chromosomes, but they should have a large enough number of SNPs and have to be numbered in the map file as the chromosomes: 1, 2, 3, ... Otherwise it will not work. Best wishes, Armando.
— Reply to this email directly, view it on GitHub https://github.com/esrud/GONE/issues/45#issuecomment-2283731355, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUFH5JVF3YF6TAJNUHVXA6DZRCMX7AVCNFSM6AAAAABMHBKEIKVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOBTG4ZTCMZVGU . You are receiving this because you authored the thread.Message ID: @.***>
armando-caballero
commented
1 month ago Send me the start of the map and ped files and I will have a look. Armando.
De: ModiShrushti @.> Enviado: lunes, 12 de agosto de 2024 20:13 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Too few bin (Issue #45)
Thanks for the quick response. I renamed the scaffolds as the numbers as per your suggestion, but now I am getting another
DIVIDE .ped AND .map FILES IN CHROMOSOMES
RUNNING ANALYSIS OF CHROMOSOMES ...
CHROMOSOME ANALYSES took 0 seconds
Running GONE
Specify a sample size larger than 1.
Specify a sample size larger than 1. Specify a sample size larger than 1. Thanks in advance
Best Regards Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Mon, Aug 12, 2024 at 6:35 AM armando-caballero @.***> wrote:
You can use scaffolds instead of chromosomes, but they should have a large enough number of SNPs and have to be numbered in the map file as the chromosomes: 1, 2, 3, ... Otherwise it will not work. Best wishes, Armando.
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ModiShrushti
commented
1 month ago Here it is .map
1 1_4233777 0 4233777
2 2_3534407 0 3534407
3 3_3344604 0 3344604
3 3_3344607 0 3344607
4 4_3205596 0 3205596
5 5_3190107 0 3190107
6 6_2989345 0 2989345
7 7_2739420 0 2739420
8 8_2511301 0 2511301
9 9_2446179 0 2446179 .ped
sample_13T19merged_sorted.bam sample_13T19merged_sorted.bam 0 0 0 -9 A G C C GAA GAA ACC AC T T A A GTTTTTTTTTTTTTTTTTT GTTTTTTTTTTTTTTTTT C C A A G C T C T T C C G A G T C C T T G G C C A G G G ATTTGTTTGTTT>
sample_24T9_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_24T9_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G T C GAAA GAAA AC AC C C A A GTTTTTTTTTTTTTTTTTT GTTTTTTTTTTTTTTTTT C C AG A C C T C C T >
sample_38T3_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_38T3_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G T C GAA GAA AC AC 0 0 A A 0 0 C C A A C C T T C T C C A A T T C C C T 0 0 T T A G G G 0 >
Thanks Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Tue, Aug 13, 2024 at 4:36 AM armando-caballero @.***> wrote:
Send me the start of the map and ped files and I will have a look. Armando.
De: ModiShrushti @.> Enviado: lunes, 12 de agosto de 2024 20:13 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Too few bin (Issue #45)
Thanks for the quick response. I renamed the scaffolds as the numbers as per your suggestion, but now I am getting another
DIVIDE .ped AND .map FILES IN CHROMOSOMES
RUNNING ANALYSIS OF CHROMOSOMES ...
CHROMOSOME ANALYSES took 0 seconds
Running GONE
Specify a sample size larger than 1.
Specify a sample size larger than 1. Specify a sample size larger than 1. Thanks in advance
Best Regards Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Mon, Aug 12, 2024 at 6:35 AM armando-caballero @.***> wrote:
You can use scaffolds instead of chromosomes, but they should have a large enough number of SNPs and have to be numbered in the map file as the chromosomes: 1, 2, 3, ... Otherwise it will not work. Best wishes, Armando.
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armando-caballero
commented
1 month ago This map is useless. According to this, scaffold 1 has only one SNP, scaffold 2 has only one SNP, scaffold 3 has only two SNPs, etc. Impossible to estimate anything with this. Each scaffold must have many SNPs (hundreds or thousands). Best wishes, Armando
De: ModiShrushti @.> Enviado: martes, 13 de agosto de 2024 17:36 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Too few bin (Issue #45)
Here it is .map
1 1_4233777 0 4233777
2 2_3534407 0 3534407
3 3_3344604 0 3344604
3 3_3344607 0 3344607
4 4_3205596 0 3205596
5 5_3190107 0 3190107
6 6_2989345 0 2989345
7 7_2739420 0 2739420
8 8_2511301 0 2511301
9 9_2446179 0 2446179 .ped
sample_13T19merged_sorted.bam sample_13T19merged_sorted.bam 0 0 0 -9 A G C C GAA GAA ACC AC T T A A GTTTTTTTTTTTTTTTTTT GTTTTTTTTTTTTTTTTT C C A A G C T C T T C C G A G T C C T T G G C C A G G G ATTTGTTTGTTT>
sample_24T9_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_24T9_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G T C GAAA GAAA AC AC C C A A GTTTTTTTTTTTTTTTTTT GTTTTTTTTTTTTTTTTT C C AG A C C T C C T >
sample_38T3_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_38T3_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G T C GAA GAA AC AC 0 0 A A 0 0 C C A A C C T T C T C C A A T T C C C T 0 0 T T A G G G 0 >
Thanks Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Tue, Aug 13, 2024 at 4:36 AM armando-caballero @.***> wrote:
Send me the start of the map and ped files and I will have a look. Armando.
De: ModiShrushti @.> Enviado: lunes, 12 de agosto de 2024 20:13 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Too few bin (Issue #45)
Thanks for the quick response. I renamed the scaffolds as the numbers as per your suggestion, but now I am getting another
DIVIDE .ped AND .map FILES IN CHROMOSOMES
RUNNING ANALYSIS OF CHROMOSOMES ...
CHROMOSOME ANALYSES took 0 seconds
Running GONE
Specify a sample size larger than 1.
Specify a sample size larger than 1. Specify a sample size larger than 1. Thanks in advance
Best Regards Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Mon, Aug 12, 2024 at 6:35 AM armando-caballero @.***> wrote:
You can use scaffolds instead of chromosomes, but they should have a large enough number of SNPs and have to be numbered in the map file as the chromosomes: 1, 2, 3, ... Otherwise it will not work. Best wishes, Armando.
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ModiShrushti
commented
1 month ago Hi Armando. Thanks for pointing that out. I have made the .map and .ped files gain and now they seem okay to me but still I am getting a syntax error. I am using the sam script for another species with chromosomal level assembly and that works fine. Here is the new map and ped files. sample_CC20T2_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_CC20T2_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 A G A G GCCCCC GCCCC GCGGGCACG GCG G A GAAAAAAAA GAAAAAAAA A A G A G> sample_CC20T6_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_CC20T6_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G G G GCCCC GCCCC GCG GCG A A GAAAAAAAA GAAAAAAAA A A A A T T C C >
1 1_560 0 560 1 1_576 0 576 1 1_640 0 640 1 1_753 0 753 1 1_1022 0 1022 1 1_1201 0 1201 1 1_1970 0 1970 1 1_2030 0 2030 1 1_2161 0 2161 1 1_2333 0 2333
and the error I am getting is script_GONE.sh: line 71: ((: i<=: syntax error: operand expected (error token is "<=") script_GONE.sh: line 81: ((: i<=: syntax error: operand expected (error token is "<=") DIVIDE .ped AND .map FILES IN CHROMOSOMES rm: cannot remove 'SNP_CHROM': No such file or directory RUNNING ANALYSIS OF CHROMOSOMES ... script_GONE.sh: line 132: ((: n<=: syntax error: operand expected (error token is "<=") CHROMOSOME ANALYSES took 0 seconds script_GONE.sh: line 144: ((: n<=: syntax error: operand expected (error token is "<=") mv: cannot stat 'outfileLD': No such file or directory rm: cannot remove 'parameters': No such file or directory cat: nsnp: No such file or directory cat: OUTPUT: No such file or directory cat: outfileLD: No such file or directory rm: cannot remove 'nsnp': No such file or directory rm: cannot remove 'OUTPUT': No such file or directory rm: cannot remove 'CHROM': No such file or directory Running GONE Error opening file outfileLD
Thanks Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Wed, Aug 14, 2024 at 4:36 AM armando-caballero @.***> wrote:
This map is useless. According to this, scaffold 1 has only one SNP, scaffold 2 has only one SNP, scaffold 3 has only two SNPs, etc. Impossible to estimate anything with this. Each scaffold must have many SNPs (hundreds or thousands). Best wishes, Armando
De: ModiShrushti @.> Enviado: martes, 13 de agosto de 2024 17:36 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Too few bin (Issue #45)
Here it is .map
1 1_4233777 0 4233777
2 2_3534407 0 3534407
3 3_3344604 0 3344604
3 3_3344607 0 3344607
4 4_3205596 0 3205596
5 5_3190107 0 3190107
6 6_2989345 0 2989345
7 7_2739420 0 2739420
8 8_2511301 0 2511301
9 9_2446179 0 2446179 .ped
sample_13T19merged_sorted.bam sample_13T19merged_sorted.bam 0 0 0 -9 A G C C GAA GAA ACC AC T T A A GTTTTTTTTTTTTTTTTTT GTTTTTTTTTTTTTTTTT C C A A G C T C T T C C G A G T C C T T G G C C A G G G ATTTGTTTGTTT>
sample_24T9_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_24T9_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G T C GAAA GAAA AC AC C C A A GTTTTTTTTTTTTTTTTTT GTTTTTTTTTTTTTTTTT C C AG A C C T C C T >
sample_38T3_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_38T3_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G T C GAA GAA AC AC 0 0 A A 0 0 C C A A C C T T C T C C A A T T C C C T 0 0 T T A G G G 0 >
Thanks Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Tue, Aug 13, 2024 at 4:36 AM armando-caballero @.***> wrote:
Send me the start of the map and ped files and I will have a look. Armando.
De: ModiShrushti @.> Enviado: lunes, 12 de agosto de 2024 20:13 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Too few bin (Issue #45)
Thanks for the quick response. I renamed the scaffolds as the numbers as per your suggestion, but now I am getting another
DIVIDE .ped AND .map FILES IN CHROMOSOMES
RUNNING ANALYSIS OF CHROMOSOMES ...
CHROMOSOME ANALYSES took 0 seconds
Running GONE
Specify a sample size larger than 1.
Specify a sample size larger than 1. Specify a sample size larger than 1. Thanks in advance
Best Regards Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Mon, Aug 12, 2024 at 6:35 AM armando-caballero @.***> wrote:
You can use scaffolds instead of chromosomes, but they should have a large enough number of SNPs and have to be numbered in the map file as the chromosomes: 1, 2, 3, ... Otherwise it will not work. Best wishes, Armando.
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armando-caballero
commented
1 month ago Genotypes should have separated letters (alleles of genotyes). 0 0 0 -9 A G A G GCCCCC GCCCC GCGGGCACG This does not work. Please read the tutorial. Armando
De: ModiShrushti @.> Enviado: jueves, 15 de agosto de 2024 20:32 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Too few bin (Issue #45)
Hi Armando. Thanks for pointing that out. I have made the .map and .ped files gain and now they seem okay to me but still I am getting a syntax error. I am using the sam script for another species with chromosomal level assembly and that works fine. Here is the new map and ped files. sample_CC20T2_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_CC20T2_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 A G A G GCCCCC GCCCC GCGGGCACG GCG G A GAAAAAAAA GAAAAAAAA A A G A G> sample_CC20T6_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_CC20T6_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G G G GCCCC GCCCC GCG GCG A A GAAAAAAAA GAAAAAAAA A A A A T T C C >
1 1_560 0 560 1 1_576 0 576 1 1_640 0 640 1 1_753 0 753 1 1_1022 0 1022 1 1_1201 0 1201 1 1_1970 0 1970 1 1_2030 0 2030 1 1_2161 0 2161 1 1_2333 0 2333
and the error I am getting is script_GONE.sh: line 71: ((: i<=: syntax error: operand expected (error token is "<=") script_GONE.sh: line 81: ((: i<=: syntax error: operand expected (error token is "<=") DIVIDE .ped AND .map FILES IN CHROMOSOMES rm: cannot remove 'SNP_CHROM': No such file or directory RUNNING ANALYSIS OF CHROMOSOMES ... script_GONE.sh: line 132: ((: n<=: syntax error: operand expected (error token is "<=") CHROMOSOME ANALYSES took 0 seconds script_GONE.sh: line 144: ((: n<=: syntax error: operand expected (error token is "<=") mv: cannot stat 'outfileLD': No such file or directory rm: cannot remove 'parameters': No such file or directory cat: nsnp: No such file or directory cat: OUTPUT: No such file or directory cat: outfileLD: No such file or directory rm: cannot remove 'nsnp': No such file or directory rm: cannot remove 'OUTPUT': No such file or directory rm: cannot remove 'CHROM': No such file or directory Running GONE Error opening file outfileLD
Thanks Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Wed, Aug 14, 2024 at 4:36 AM armando-caballero @.***> wrote:
This map is useless. According to this, scaffold 1 has only one SNP, scaffold 2 has only one SNP, scaffold 3 has only two SNPs, etc. Impossible to estimate anything with this. Each scaffold must have many SNPs (hundreds or thousands). Best wishes, Armando
De: ModiShrushti @.> Enviado: martes, 13 de agosto de 2024 17:36 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Too few bin (Issue #45)
Here it is .map
1 1_4233777 0 4233777
2 2_3534407 0 3534407
3 3_3344604 0 3344604
3 3_3344607 0 3344607
4 4_3205596 0 3205596
5 5_3190107 0 3190107
6 6_2989345 0 2989345
7 7_2739420 0 2739420
8 8_2511301 0 2511301
9 9_2446179 0 2446179 .ped
sample_13T19merged_sorted.bam sample_13T19merged_sorted.bam 0 0 0 -9 A G C C GAA GAA ACC AC T T A A GTTTTTTTTTTTTTTTTTT GTTTTTTTTTTTTTTTTT C C A A G C T C T T C C G A G T C C T T G G C C A G G G ATTTGTTTGTTT>
sample_24T9_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_24T9_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G T C GAAA GAAA AC AC C C A A GTTTTTTTTTTTTTTTTTT GTTTTTTTTTTTTTTTTT C C AG A C C T C C T >
sample_38T3_trimmed_bwa_mapped_sorted_rmdup_uniq.bam sample_38T3_trimmed_bwa_mapped_sorted_rmdup_uniq.bam 0 0 0 -9 G G T C GAA GAA AC AC 0 0 A A 0 0 C C A A C C T T C T C C A A T T C C C T 0 0 T T A G G G 0 >
Thanks Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Tue, Aug 13, 2024 at 4:36 AM armando-caballero @.***> wrote:
Send me the start of the map and ped files and I will have a look. Armando.
De: ModiShrushti @.> Enviado: lunes, 12 de agosto de 2024 20:13 Para: esrud/GONE @.> Cc: Armando Caballero Rúa @.>; Comment @.> Asunto: Re: [esrud/GONE] Too few bin (Issue #45)
Thanks for the quick response. I renamed the scaffolds as the numbers as per your suggestion, but now I am getting another
DIVIDE .ped AND .map FILES IN CHROMOSOMES
RUNNING ANALYSIS OF CHROMOSOMES ...
CHROMOSOME ANALYSES took 0 seconds
Running GONE
Specify a sample size larger than 1.
Specify a sample size larger than 1. Specify a sample size larger than 1. Thanks in advance
Best Regards Shrushti
Shrushti Modi, Ph.D., Post-Doctoral Research Fellow Laboratories of Molecular Anthropology and Microbiome Research (LMAMR) University of Oklahoma Norman Email Address: @., @.
On Mon, Aug 12, 2024 at 6:35 AM armando-caballero @.***> wrote:
You can use scaffolds instead of chromosomes, but they should have a large enough number of SNPs and have to be numbered in the map file as the chromosomes: 1, 2, 3, ... Otherwise it will not work. Best wishes, Armando.
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Dear Armando, Thanks for GONE. I ran it successfully with my data first time but then I saw your comment about sex chromosomes and after removing the sex chromosome from my input file. It is showing me an error saying too few bins. Could you please help me with this ?
Thanks Shrushti