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llecompte / SVJedi

SV genotyping with long reads
GNU Affero General Public License v3.0
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UnboundLocalError #6

Closed Fishball-zyw closed 3 years ago

Fishball-zyw commented 3 years ago

After running: python svjedi.py -v merge.new.vcf -r GCA_000001405.15_GRCh38_no_alt_analysis_set.fna -i group7.fq.gz -o group7.svjedi.vcf -d ont -t 4

I got this error: Traceback (most recent call last): File "/hwfssz4/BC_PUB/Software/07.User-defined/04.Medical/zhangyuanwei/SVJedi/svjedi.py", line 193, in main(sys.argv[1:]) File "/hwfssz4/BC_PUB/Software/07.User-defined/04.Medical/zhangyuanwei/SVJedi/svjedi.py", line 186, in main genotype.genotype(paf_file, vcf_file, output_file, min_support, d_over, d_end, l_adj) File "/hwfssz4/BC_PUB/Software/07.User-defined/04.Medical/zhangyuanwei/SVJedi/modules/genotype.py", line 135, in genotype decision_vcf(dict_of_informative_aln, vcf_without_gt, outputfile, min_aln, l_adj) File "/hwfssz4/BC_PUB/Software/07.User-defined/04.Medical/zhangyuanwei/SVJedi/modules/genotype.py", line 366, in decision_vcf

And it is strange that I only got this error on 3 of 7 samples from the same ONT sequencing batch.

Please help me.

robinycfang commented 3 years ago

same here...my output vcf has only header lines

clemaitre commented 3 years ago

Hi @Fishball-zyw and @robinycfang,

thank you for letting us know of this bug. commit 967a3f4 should fix this bug. If this is not the case, please let us know ! It happened to some datasets only, those where the first variant of the vcf has not enough support to be genotyped (missing genotype).

Regards, Claire

hdore commented 3 years ago

Hello, Thank you for developing this tool! Just a comment here: this is not yet fixed in the version available through conda (1.1.4). It's easy to fix by changing "prob" to "proba" in line 332 of genotype.py (I think).

Hugo

clemaitre commented 3 years ago

Hi Hugo,

Thank you for using SVJedi and for your comment. The conda version is now up to date (version 1.1.5, thank you @llecompte !) and contains this bug fix.

Best regards, Claire