dDocent stopped (line 1193: 1803 Killed)

a.w...@uni-bayreuth.de

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May 19, 2021, 2:51:06 AM5/19/21

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Hello,

I have started a dDocent run using a cnv-map file for the freebayes steps. (the plant species tends to hybridize with mixed ploid levels from 2 to 5).

I have attached the last output, the LOG file, the ls -l output, the popfile and the cnv-map file to this post.

I have tested the use of popmap and cnv-map file before with a small dataset and it worked just fine (the samples showed the ploidy details in the TotalRawSNPs.vcf as expected).

Any idea what might has gone wrong?

Thanks for any suggestion!

out_last-messages.txt

out_ls-l.txt

cnv-map

dDocent_main.LOG

popmap

a.w...@uni-bayreuth.de

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May 19, 2021, 7:33:28 AM5/19/21

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Short additional question: are symbolic links a problem for the dDocent pipeline?

Jon Puritz

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May 19, 2021, 3:51:02 PM5/19/21

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It looks like your OS killed the "bedtools merge" command, likely because of memory issues. Symbolic links are not a problem for dDocent.

Hope that helps,

Jon

Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881

Webpage: MarineEvoEco.com

Cell: 401-338-8739

Work: 401-874-9020

"The most valuable of all talents is that of never using two words when one will do.” -Thomas Jefferson

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a.w...@uni-bayreuth.de

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May 21, 2021, 3:59:02 AM5/21/21

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Hi Jon,

after a few more tests, I realized that the cnv-map file for mixed-ploidy samples had one additional tab behind col 2 in one sample. Corrected it and dDocent completed sucessfully!

The TotalRawSNPs.vcf does indeed contain samples with the respecitiv ploidy (in this case 2n and 4n). However, when I look at the corresponding log file (VCFtools.log) I see an error message at the bottom telling me that polyploidy is not supported in vcfools. I assume that TotalRawSNPs.vcf has been prepared by a step before and should be ok, but Final.recode.vcf should be treated with care, right?

When inspecting other log file, I found a line in assemble.trim.log: Duplication rate (may be overestimated since this is SE data): 23.494%

Is this message correct? I specified PE for assembly, and the sample-specific *.trim.log indicate that paired end data were used.

I also looked in the dDocent_main.LOG to see tha parameters entered during start of the analysis. But the entered parameters are not avialable. Where can I find e.g. the two data cutoff values used in the analysis?

Best regards!

jpu...@gmail.com schrieb am Mittwoch, 19. Mai 2021 um 21:51:02 UTC+2:

It looks like your OS killed the "bedtools merge" command, likely because of memory issues. Symbolic links are not a problem for dDocent.

Hope that helps,
Jon

Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881

Webpage: MarineEvoEco.com

Cell: 401-338-8739
Work: 401-874-9020

"The most valuable of all talents is that of never using two words when one will do.” -Thomas Jefferson

On Wed, May 19, 2021 at 2:51 AM, a.w...@uni-bayreuth.de <a.w...@uni-bayreuth.de> wrote:
Hello,
I have started a dDocent run using a cnv-map file for the freebayes steps. (the plant species tends to hybridize with mixed ploid levels from 2 to 5).

I have attached the last output, the LOG file, the ls -l output, the popfile and the cnv-map file to this post.
I have tested the use of popmap and cnv-map file before with a small dataset and it worked just fine (the samples showed the ploidy details in the TotalRawSNPs.vcf as expected).

Any idea what might has gone wrong?
Thanks for any suggestion!

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assemble.trim.log

VCFtools.log

dDocent_main.LOG

Jon Puritz

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May 28, 2021, 11:15:36 AM5/28/21

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They are in the dDocent.runs file

Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881

Webpage: MarineEvoEco.com

Cell: 401-338-8739

Work: 401-874-9020

"The most valuable of all talents is that of never using two words when one will do.” -Thomas Jefferson

On Fri, May 21, 2021 at 3:59 AM, a.w...@uni-bayreuth.de <a.w...@uni-bayreuth.de> wrote:

Hi Jon,
after a few more tests, I realized that the cnv-map file for mixed-ploidy samples had one additional tab behind col 2 in one sample. Corrected it and dDocent completed sucessfully!

The TotalRawSNPs.vcf does indeed contain samples with the respecitiv ploidy (in this case 2n and 4n). However, when I look at the corresponding log file (VCFtools.log) I see an error message at the bottom telling me that polyploidy is not supported in vcfools. I assume that TotalRawSNPs.vcf has been prepared by a step before and should be ok, but Final.recode.vcf should be treated with care, right?

When inspecting other log file, I found a line in assemble.trim.log: Duplication rate (may be overestimated since this is SE data): 23.494%
Is this message correct? I specified PE for assembly, and the sample-specific *.trim.log indicate that paired end data were used.

I also looked in the dDocent_main.LOG to see tha parameters entered during start of the analysis. But the entered parameters are not avialable. Where can I find e.g. the two data cutoff values used in the analysis?

Best regards!

jpu...@gmail.com schrieb am Mittwoch, 19. Mai 2021 um 21:51:02 UTC+2:

It looks like your OS killed the "bedtools merge" command, likely because of memory issues. Symbolic links are not a problem for dDocent.

Hope that helps,
Jon

Jon Puritz, PhD

Assistant Professor
Department of Biological Sciences
University of Rhode Island
120 Flagg Road, Kingston, RI 02881

Webpage: MarineEvoEco.com

Cell: 401-338-8739
Work: 401-874-9020

"The most valuable of all talents is that of never using two words when one will do.” -Thomas Jefferson

On Wed, May 19, 2021 at 2:51 AM, a.w...@uni-bayreuth.de <a.w...@uni-bayreuth.de> wrote:
Hello,
I have started a dDocent run using a cnv-map file for the freebayes steps. (the plant species tends to hybridize with mixed ploid levels from 2 to 5).

I have attached the last output, the LOG file, the ls -l output, the popfile and the cnv-map file to this post.
I have tested the use of popmap and cnv-map file before with a small dataset and it worked just fine (the samples showed the ploidy details in the TotalRawSNPs.vcf as expected).

Any idea what might has gone wrong?
Thanks for any suggestion!

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