snp_index.tsv.temp not found error

[ramendra-sarma]

. I have removed the previous installation of qtlseq and freshly installed qtlseq using bioconda3. Again the same issue of "FileNotFoundError: [Errno 2] No such file or directory: '/home/rnsarma/Desktop/niharika/qtlseq_test/qtlseq_out_run1/40_qtlseq/snp_index.tsv.temp" at the end with the test dataset. I am clueless. Please suggest.
base) rnsarma@aryabhatta:~/Desktop/niharika/qtlseq_test$ conda activate qtlseq

(qtlseq) rnsarma@aryabhatta:~/Desktop/niharika/qtlseq_test$ qtlseq --version
qtlseq 2.2.9

(qtlseq) rnsarma@aryabhatta:~/Desktop/niharika/qtlseq_test$ qtlseq -r ~/Desktop/niharika/qtlseq_test/10_ref/qtlseq_ref.fasta -p /Desktop/niharika/qtlseq_test/00_fastq/qtlseq_parent.1.fastq.gz,/Desktop/niharika/qtlseq_test/00_fastq/qtlseq_parent.2.fastq.gz -b1 /Desktop/niharika/qtlseq_test/00_fastq/qtlseq_bulk1.1.fastq.gz,/Desktop/niharika/qtlseq_test/00_fastq/qtlseq_bulk1.2.fastq.gz -b2 /Desktop/niharika/qtlseq_test/00_fastq/qtlseq_bulk2.1.fastq.gz,/Desktop/niharika/qtlseq_test/00_fastq/qtlseq_bulk2.2.fastq.gz -n1 20 -n2 20 -o ~/Desktop/niharika/qtlseq_test/qtlseq_out_run1
[QTL-seq:2025-05-22 12:02:18] Starting QTL-seq analysis.
[QTL-seq:2025-05-22 12:02:18] Indexing the reference FASTA.
[QTL-seq:2025-05-22 12:02:20] Reference FASTA indexing completed successfully.
[QTL-seq:2025-05-22 12:02:20] Aligning reads for parent.0000 using BWA.
[QTL-seq:2025-05-22 12:02:20] Alignment of parent.0000 completed successfully.
[QTL-seq:2025-05-22 12:02:20] Aligning reads for bulk1.0000 using BWA.
[QTL-seq:2025-05-22 12:02:28] Alignment of bulk1.0000 completed successfully.
[QTL-seq:2025-05-22 12:02:28] Aligning reads for bulk2.0000 using BWA.
[QTL-seq:2025-05-22 12:02:35] Alignment of bulk2.0000 completed successfully.
[QTL-seq:2025-05-22 12:02:35] Sorting BAM files.
[QTL-seq:2025-05-22 12:02:52] BAM file sorting completed successfully.
[QTL-seq:2025-05-22 12:02:52] Calling variants.
[QTL-seq:2025-05-22 12:03:04] Variant calling completed successfully.
[QTL-seq:2025-05-22 12:03:04] Indexing the VCF file.
[QTL-seq:2025-05-22 12:03:04] VCF indexing completed successfully.
[QTL-seq:2025-05-22 12:03:09] Starting QTL-plot.
[QTL-seq:2025-05-22 12:03:09] Calculating SNP-index.
Traceback (most recent call last):
File "/usr/local/bioconda3/envs/qtlseq/bin/qtlplot", line 10, in
sys.exit(main())
~~~~^^
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/qtlseq/qtlplot.py", line 218, in main
qp.run()
~~~~~~^^
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/qtlseq/qtlplot.py", line 203, in run
v2i.run()
~~~~~~~^^
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/qtlseq/vcf2index.py", line 287, in run
self.calculate_SNPindex()
~~~~~~~~~~~~~~~~~~~~~~~^^
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/qtlseq/vcf2index.py", line 282, in calculate_SNPindex
self.table_sort()
~~~~~~~~~~~~~~~^^
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/qtlseq/vcf2index.py", line 230, in table_sort
snp_index = pd.read_csv('{}/snp_index.tsv.temp'.format(self.out),
sep='\t',
...<8 lines>...
'bulk2_SNPindex',
'delta_SNPindex'])
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/pandas/io/parsers/readers.py", line 1026, in read_csv
return _read(filepath_or_buffer, kwds)
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/pandas/io/parsers/readers.py", line 620, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/pandas/io/parsers/readers.py", line 1620, in init
self._engine = self._make_engine(f, self.engine)
~~~~~~~~~~~~~~~~~^^^^^^^^^^^^^^^^
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/pandas/io/parsers/readers.py", line 1880, in _make_engine
self.handles = get_handle(
~~~~~~~~~~^
f,
^^
...<6 lines>...
storage_options=self.options.get("storage_options", None),
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
)
^
File "/usr/local/bioconda3/envs/qtlseq/lib/python3.13/site-packages/pandas/io/common.py", line 873, in get_handle
handle = open(
handle,
...<3 lines>...
newline="",
)
FileNotFoundError: [Errno 2] No such file or directory: '/home/rnsarma/Desktop/niharika/qtlseq_test/qtlseq_out_run1/40_qtlseq/snp_index.tsv.temp'

[hidvegin]

I encountered the same error. QTL-seq was installed correctly. I checked the test datasets and found that everything was good. The VCF files contain SNPs that PASS records. Anybody could help me with this error?

[YuSugihara]

Hi,

If you can send the VCF file to sugihara.yu.85s[at]kyoto-u.jp with the command you used, I might be able to check it.

The SNPs with "PASS" in the VCF file do not mean that they passed the quality check.

The filtering step will occur in QTL-plot, and the SNPs can be filtered out for various reasons (the depth, strand bias, the parent genotype, etc.).

If the test dataset is working, it is a unique problem in your dataset.

I recommend carefully checking the inside of the VCF file.

Best,
Yu

[rnsarma]

Hi,

If you can send the VCF file to sugihara.yu.85s[at]kyoto-u.jp with the command you used, I might be able to check it.

The SNPs with "PASS" in the VCF file do not mean that they passed the quality check.

The filtering step will occur in QTL-plot, and the SNPs can be filtered out for various reasons (the depth, strand bias, the parent genotype, etc.).

If the test dataset is working, it is a unique problem in your dataset.

I recommend carefully checking the inside of the VCF file.

Best, Yu

The address not found: "Address not found
Your message wasn't delivered to yu.85s@kyoto-u.jp because the address couldn't be found, or is unable to receive mail."

[YuSugihara]

My email address is sugihara.yu.85s[at]kyoto-u.jp.