Mar 22, 2018 11:18:37 AM ngsep.vcf.VCFFileReader loadGenomicVariant
SEVERE: Can not load genomic variant at chr_Ft1:60331664. Unrecognized sequence name. Changes have been disabled for this collection
I haven't had any other problems with the sequence names file, or with any other step in the pipeline. Everything is in the correct directory. Any insight into what might be going on?
Thanks!
Joanna Rifkin
--
Joanna Rifkin PhD
Department of Ecology and Evolutionary Biology
The University of Toronto
25 Willcocks St.
Toronto, ON M5S 3B2
Thanks for reporting this issue. In the last version we modified the CompareVCF command to improve the comparison of indels that may not have the exact same coordinates in different VCFs. However, the downside of this improvement is that the command now requires the complete reference genome instead of the sequence names file. We updated the inline help with this change but i just noticed that we did not update accordingly the README, so I just uploaded a new version of the README with the documentation of this change. Please use then the fasta file of your reference genome instead of the file "dovetailsequencenames.txt" and let us know if it works.
Best regards
Jorge
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Anonymous
Anonymous
-
2018-03-26
Hi Jorge,
Thanks, that fixed it perfectly!
Cheers,
Joanna
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Hi there,
I'm trying to run CompareVCF on my VCFs, but I'm getting a strange error.
The command I'm using is:
java -jar /ohta/joanna.rifkin/NGSEPcore_3.1.1/NGSEPcore.jar CompareVCF -g 0 -d 100 dovetailsequencenames.txt mappingpopulation.vcf mappingpopulation.vcf 1>population_sampleComparation.txt
The error is (repetitions of):
Mar 22, 2018 11:18:37 AM ngsep.vcf.VCFFileReader loadGenomicVariant
SEVERE: Can not load genomic variant at chr_Ft1:60331664. Unrecognized sequence name. Changes have been disabled for this collection
I haven't had any other problems with the sequence names file, or with any other step in the pipeline. Everything is in the correct directory. Any insight into what might be going on?
Thanks!
Joanna Rifkin
--
Joanna Rifkin PhD
Department of Ecology and Evolutionary Biology
The University of Toronto
25 Willcocks St.
Toronto, ON M5S 3B2
Hi Johanna
Thanks for reporting this issue. In the last version we modified the CompareVCF command to improve the comparison of indels that may not have the exact same coordinates in different VCFs. However, the downside of this improvement is that the command now requires the complete reference genome instead of the sequence names file. We updated the inline help with this change but i just noticed that we did not update accordingly the README, so I just uploaded a new version of the README with the documentation of this change. Please use then the fasta file of your reference genome instead of the file "dovetailsequencenames.txt" and let us know if it works.
Best regards
Jorge
Hi Jorge,
Thanks, that fixed it perfectly!
Cheers,
Joanna
No problem. Let us know if you need any further help.
Jorge