No results obtained after step two

[tjcu408]

the files (metadata.txt and extracted.fa) were obtained successfully after the commond line (args_oap stage_one -i input -o output -f fa -t 8), while we got no results after the commond line (args_oap stage_two -i output -t 8) on our own data, the results were show below,

[xinehc]

Hi,

The default value for --length in stage-two is 25aa so if your reads are too short (say 75bp), then no one will pass this filter. You may consider changing the cutoffs in stage-two.

[tjcu408]

The reads in the extracted.fa of my data were 150bp (shown below). And I changed the value of --length to be 15 in stage-two (args_oap stage_two -i args -t 92 --length 15), and no results obtained still. Two weeks ago, all the default command line go well on my one data, while it did not work after I changede the hard disk and rebuild the conda envs. What is the issues?

(less extracted.fa:

11_1@0@A00920:381:HCCGFDSXY:2:1101:20012:1391 GCCTGCGGTAACTTTCGCATGGCTGATTGCAGCTGGTTTTGTACTTGCTGCACGGCTTCGTCCGGATCGGTGCCTGCTTTAAAACTTAAAGTGACAGATGCCTGACCGGTGCCACTGCTCTGAGATGACATATACATGAGATTATCGAGG)

[xinehc]

I can confirm this is a bug. This happens because all your samples are named using integers (e.g. 11.fa/fq).

This commit 4afa4b1f01b2686cfc08457f1748518f4ec89225 should fix the issue.

[tjcu408]

yet, the data named like: ddk1_R1.fq, ddk1_R2.fq; the default command line does not work still.

[xinehc]

Fixed in 0d0cede0506579bb263f26bda7dbd663c4b90fa5.

[tjcu408]

Regretally, the default command produce no results still, with the above fixation alone or synergistically on my own data. And I copied the old conda env to the current conda environment, it worked.

[xinehc]

That's wired, did you install the latest commit in your current conda env using git clone and then python setup.py install? I haven't uploaded 0d0cede0506579bb263f26bda7dbd663c4b90fa5 to bioconda so conda install will still load the old version.

If this does not solve your issue, can you show your current env using conda env list and send me a minimal reproducible example of your input files?

[tjcu408]

After testing, the sample names might be the issues, the names of integers was not supported by the current args_oap stage_two, and the pair sample names including R1 and R2 seemly not accepted too.

[yikiii]

That's wired, did you install the latest commit in your current conda env using git clone and then python setup.py install? I haven't uploaded 0d0cede to bioconda so conda install will still load the old version.

If this does not solve your issue, can you show your current env using conda env list and send me a minimal reproducible example of your input files?

I got the same problem. I installed from conda yesterday. My pair sample names including R1,R2 and integers too.

[xinehc]

https://github.com/xinehc/args_oap/releases/tag/v3.2.2