Numpy Error with dumpSTR

[alig99]

Hi,
Trying to run dumpSTR on a gangSTR output with this command
dumpSTR --vcf MY.vcf --gangstr-max-call-DP 1000 --gangstr-filter-spanbound-only --gangstr-filter-badCI --gangstr-expansion-prob-het 0.8 --drop-filtered --out dumpSTR.out
And get the following error
Traceback (most recent call last):
File "/opt/miniconda3/bin/dumpSTR", line 10, in
sys.exit(run())
File "/opt/miniconda3/lib/python3.7/site-packages/trtools/dumpSTR/dumpSTR.py", line 1245, in run
retcode = main(args)
File "/opt/miniconda3/lib/python3.7/site-packages/trtools/dumpSTR/dumpSTR.py", line 1183, in main
record = ApplyCallFilters(record, call_filters, sample_info, invcf.samples)
File "/opt/miniconda3/lib/python3.7/site-packages/trtools/dumpSTR/dumpSTR.py", line 599, in ApplyCallFilters
record.vcfrecord.set_format('FILTER', np.char.encode(all_filter_text))
File "cyvcf2/cyvcf2.pyx", line 1390, in cyvcf2.cyvcf2.Variant.set_format
Exception: ('format: currently only float and int numpy arrays are supported. got %s', dtype('S33'))
Any help would be great thanks ali

[nmmsv]

Hello,
Thanks for reporting this issue. I'm CCing Jonathan who has more experience with cyvcf2 and has a better insight on what may be going on.
Best,
Nima

[LiterallyUniqueLogin]

Hi there,

What version of cyvcf2 are you using? Please run python -c 'import cyvcf2; print(cyvcf2.__version__)'

TRTools requires cyvcf2 >= 0.30.1, perhaps that's the problem?

Also, if it doesn't contain sensitive information, can you share your VCF file with us? I can't reproduce the issue when running your command on my machine with the VCF example-files/trio_chr21_gangstr.sorted.vcf.gz from our github

[alig99]

Hi there, Thank you for your quick response. The version of cyvcf2 I was using was 0.11.5 I got the same issue when running my command with the VCF example - trio_chr21_gangstr.sorted.vcf.gz I have updated the version of cyvcf2 to 0.30.4 and the error has gone. Thanks again, Ali Alison Gardner, BA Work days: Monday/Tuesday/Thursday Postal Address: ATTN: Alison Gardner: Neurogenetics Research Program Adelaide Medical School Faculty of Health and Medical Sciences Level 8, Adelaide Health & Medical Sciences Building The University of Adelaide SA 5005 Australia T: +61 8 8313 7961 E: alison.gardner@adelaide.edu.au

…

________________________________ From: LiterallyUniqueLogin <notifications@github.com> Sent: Thursday, 4 March 2021 8:39 AM To: gymreklab/TRTools <TRTools@noreply.github.com> Cc: Alison Gardner <alison.gardner@adelaide.edu.au>; Author <author@noreply.github.com> Subject: Re: [gymreklab/TRTools] Numpy Error with dumpSTR (#136) Hi there, What version of cyvcf2 are you using? Also, if it doesn't contain sensitive information, can you share your VCF file with us? I can't reproduce the issue when running your command on my machine with the VCF example-files/trio_chr21_gangstr.sorted.vcf.gz from our github — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub<#136 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AA25PKKM4D3NAW3LDFYM5XDTB2XS5ANCNFSM4YNRIYXQ>.