FileNotFoundError: [Errno 2] No such file or directory: 'QTLseq/snp_index.tsv.temp'

[WangWaud]

Hi, I got an error when using QTL-seq.It said "FileNotFoundError: [Errno 2] No such file or directory: 'QTLseq/snp_index.tsv.temp'",but the temp shouldn't be created by the software?I don't know why.

Below is Traceback and error Traceback (most recent call last): File "/home/zwang/anaconda3/envs/SNP/bin/qtlplot", line 10, in <module> sys.exit(main()) File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/qtlseq/qtlplot.py", line 208, in main qp.run() File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/qtlseq/qtlplot.py", line 193, in run v2i.run() File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/qtlseq/vcf2index.py", line 343, in run self.calculate_SNPindex() File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/qtlseq/vcf2index.py", line 338, in calculate_SNPindex self.table_sort() File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/qtlseq/vcf2index.py", line 297, in table_sort 'delta_SNPindex']) File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/pandas/io/parsers.py", line 610, in read_csv return _read(filepath_or_buffer, kwds) File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/pandas/io/parsers.py", line 462, in _read parser = TextFileReader(filepath_or_buffer, **kwds) File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/pandas/io/parsers.py", line 819, in __init__ self._engine = self._make_engine(self.engine) File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/pandas/io/parsers.py", line 1050, in _make_engine return mapping[engine](self.f, **self.options) # type: ignore[call-arg] File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/pandas/io/parsers.py", line 1867, in __init__ self._open_handles(src, kwds) File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/pandas/io/parsers.py", line 1368, in _open_handles storage_options=kwds.get("storage_options", None), File "/home/zwang/anaconda3/envs/SNP/lib/python3.7/site-packages/pandas/io/common.py", line 647, in get_handle newline="", FileNotFoundError: [Errno 2] No such file or directory: 'QTLseq/snp_index.tsv.temp'

My command is qtlplot -v ./ZM895_Rbuk_Sbuk_merged.vcf.gz \ -o QTLseq \ -n1 30 \ -n2 30 \ -F 2 \ --species Wheat \ -w 2000 \ -s 200

The vcf file "ZM895_Rbuk_Sbuk_merged.vcf.gz" contains AD format and three columns of parent, bulk1 and bulk2 in this order.And I have created the output file folder QTLseq.

The vcf file is like `

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT ZM895_FRAS220033950-2r ZM-Rbuk_FRAS220033948-2r ZM-Sbuk_FRAS220033949-2r

1A 7638 . A C 213.78 . BaseQRankSum=2.638;ClippingRankSum=-0;ExcessHet=3.0103;FS=0;MQ=60;MQRankSum=-0;QD=21.38;ReadPosRankSum=0.61;SOR=0.569;DP=10;AF=0.5;MLEAC=1;MLEAF=0.5;AN=2;AC=1 GT:AD:DP:GQ:PL ./.:.:.:.:. 0/1:3,7:10:25:242,0,25 ./.:.:.:.:.`

Thanks!

[YuSugihara]

I am sorry for my late reply. Did you check the markers in VCF?

At least, the line that you pasted has missing genotype.

[WangWaud]

It's a data merged by 3 vcf(parent,bulk1 and bulk2).I think just some SNPs has missing genotype.

[YuSugihara]

At least, the SNPs in the screenshot cannot be used in QTL-seq. For example, QTL-seq retains the SNPs that are homozygous in the parent. This is because the heterozygous genotypes in the parent are not reliable to calculate SNP-index.

The regions in the screenshot looks heterozygous in the parent.

A possible error is that there were no useful SNPs in the VCF, and QTL-seq could not output any information in temporary file, and QTL-seq could not find the temporary file.