Batch file contains wrong filename for read 1

[jma1991]

Describe the issue
The batch file produced by kb count (kb_python 0.25.1) uses the read 2 filename for both the read 1 and read 2 columns.

What is the exact command that was run?

kb count -i index.idx -g t2g.txt -x SMARTSEQ -o output -t 2 fastq/ERR1830349_1.fastq.gz fastq/ERR1830349_2.fastq.gz

Command output (with --verbose flag)

[2021-04-06 15:37:22,088]   DEBUG Printing verbose output
[2021-04-06 15:37:22,088]   DEBUG kallisto binary located at /opt/miniconda3/envs/kb-python/lib/python3.8/site-packages/kb_python/bins/darwin/kallisto/kallisto
[2021-04-06 15:37:22,088]   DEBUG bustools binary located at /opt/miniconda3/envs/kb-python/lib/python3.8/site-packages/kb_python/bins/darwin/bustools/bustools
[2021-04-06 15:37:22,089]   DEBUG Creating output/tmp directory
[2021-04-06 15:37:22,089]   DEBUG Namespace(c1=None, c2=None, cellranger=False, command='count', dry_run=False, fastqs=['fastq/ERR1830349_1.fastq.gz', 'fastq/ERR1830349_2.fastq.gz'], filter=None, g='t2g.txt', h5ad=False, i='index.idx', keep_tmp=False, lamanno=False, list=False, loom=False, m='4G', mm=False, no_inspect=False, no_validate=False, nucleus=False, o='output', overwrite=False, report=False, t=2, tcc=False, tmp=None, verbose=True, w=None, workflow='standard', x='SMARTSEQ')
[2021-04-06 15:37:22,089]    INFO Found the following FASTQs:
[2021-04-06 15:37:22,089]    INFO         0    fastq/ERR1830349_2.fastq.gz  fastq/ERR1830349_2.fastq.gz
[2021-04-06 15:37:22,089]    INFO Writing batch definition TSV to output/batch.txt
[2021-04-06 15:37:22,090]    INFO Using index index.idx to generate matrices to output
[2021-04-06 15:37:22,090]   DEBUG kallisto pseudo --quant -i index.idx -o output -b output/batch.txt -t 2
[2021-04-06 15:38:07,160]   DEBUG
[2021-04-06 15:38:07,160]   DEBUG [quant] fragment length distribution will be estimated from the data
[2021-04-06 15:38:07,160]   DEBUG [index] k-mer length: 31
[2021-04-06 15:38:07,160]   DEBUG [index] number of targets: 140,725
[2021-04-06 15:38:07,160]   DEBUG [index] number of k-mers: 120,554,425
[2021-04-06 15:38:07,161]   DEBUG [index] number of equivalence classes: 509,144
[2021-04-06 15:38:07,161]   DEBUG [quant] running in paired-end mode
[2021-04-06 15:38:07,161]   DEBUG [quant] will process pair 1: fastq/ERR1830349_2.fastq.gz
[2021-04-06 15:38:07,161]   DEBUG fastq/ERR1830349_2.fastq.gz
[2021-04-06 15:38:07,161]   DEBUG [quant] finding pseudoalignments for all files ... done
[2021-04-06 15:38:07,161]   DEBUG [quant] processed 1,905,288 reads, 1,479,192 reads pseudoaligned
[2021-04-06 15:38:07,161]   DEBUG [quant] Running EM algorithm for each cell .. done
[2021-04-06 15:38:07,161]   DEBUG
[2021-04-06 15:38:07,211]   DEBUG output/matrix.abundance.mtx passed validation
[2021-04-06 15:38:07,756]   DEBUG Removing output/tmp directory

Possible cause
I think this problem might be caused by the following line of code:

kb_python/kb_python/main.py

Line 276 in 0b48389

cells[cell_id] = (fastq_2, fastq_2)

[Lioscro]

Hi, @jma1991,
Thanks for reporting the issue!
I've pushed a fix to the devel branch. Could you please try that out and verify that the change fixes the issue?
You can install the development version with the following command.

pip install git+https://github.com/pachterlab/kb_python@devel

[jma1991]

Yes, that is working. Thank you.

Do you know when you are likely to incorporate the change into main? I would like to update the bioconda recipe for kb-python as well.