Error when bedgraph files are not in the output directory

[fgypas]

Hi

I encountered an error when I run ALFA with bedgraph in combination with the -o option.

Following these steps you can reproduce the error (I have alfa and bedtools installed in my path).

clone the ALFA repository
git clone https://github.com/biocompibens/ALFA

Create a genome coverage with bedtools

bedtools genomecov -bg -strand + -ibam ALFA/Quick_start/quick_start.bam > test.plus.bg
bedtools genomecov -bg -strand - -ibam ALFA/Quick_start/quick_start.bam > test.minus.bg

Generate the alfa index:

alfa -a ALFA/Quick_start/quick_start.gtf -g ALFA/Quick_start/quick_start --chr_len ALFA/Quick_start/quick_start.chr_len.txt

The first error occurs when I run:

alfa -g ALFA/Quick_start/quick_start --bedgraph test.plus.bg test.minus.bg test_label --strandness forward -o results

, because the test.minus.bg is empty

To avoid this I just copy the plus to minus:

cp test.plus.bg test.minus.bg

Then the main error arises when I run the following (I also deleted the empty results directory):

alfa -g ALFA/Quick_start/quick_start --bedgraph test.plus.bg test.minus.bg test_label --strandness forward -o results

This is what I get in the log:

ALFA

The output directory doesn't exist yet, it is created.

Checking parameters

Intersecting index and BedGraph files

Intersecting BAM and genome N/A% | |0 of 2|Elapsed Time: 0:00:00multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/local/lib/python3.7/multiprocessing/pool.py", line 121, in worker
result = (True, func(*args, **kwds))
File "/usr/local/lib/python3.7/site-packages/alfa.py", line 544, in intersect_bedgraphs_and_index_to_count_categories_1_file
if os.stat(bedgraph_files + strand + bedgraph_extension).st_size == 0:
FileNotFoundError: [Errno 2] No such file or directory: 'results/test.plus.bg'
"""

The above exception was the direct cause of the following exception:

Traceback (most recent call last):
File "/usr/local/bin/alfa", line 6, in
alfa.main()
File "/usr/local/lib/python3.7/site-packages/alfa.py", line 1655, in main
cpt = intersect_bedgraphs_and_index_to_count_categories(labels, bedgraphs, options, bedgraph_extension, genome_index, prios, index_chrom_list, unknown_cat) # TODO: Write the counts to an output file
File "/usr/local/lib/python3.7/site-packages/alfa.py", line 645, in intersect_bedgraphs_and_index_to_count_categories
results = list(pbar(pool.imap_unordered(intersect_bedgraphs_and_index_to_count_categories_1_file, inputs)))
File "/usr/local/lib/python3.7/site-packages/progressbar/bar.py", line 453, in next
value = next(self._iterable)
File "/usr/local/lib/python3.7/multiprocessing/pool.py", line 748, in next
raise value
FileNotFoundError: [Errno 2] No such file or directory: 'results/test.plus.bg'
Intersecting BAM and genome 100% |##################################################################|2 of 2|Elapsed Time: 0:00:00

It seems that it looks for the bedgraph files in the output directory. I think the problme lies in these lines:
https://github.com/biocompibens/ALFA/blob/master/alfa.py#L1459-L1481

Can you please have a look.

Thank you in advance for your help

Best
Foivos

[mbahin]

Hi Foivos,

Thanks for message (and it's very convenient/appreciable to have such a good detail level!).

I don't have so much time to deal with it right now (and I'm not so comfortable because I have to work from home).

About the empty minus bedgraph file, you're right, I guess this would never happen with a real dataset so we didn't take care of it and we wanted the toy example as simple as possible.

Regarding the other one, I can't easily commit the fix properly from here but I think that you can change the line 1.482 to:
bedgraphs.append(re.sub("(.(plus|minus))?" + bedgraph_extension, "", options.bedgraph[sample_package_nb + sample_file]))
Just remove the "options.output_dir + ", it should do the trick.
I'll fix it when we are back to the office.

Let me know if this works for you.

Cheers,
Mathieu

[fgypas]

Hi Mathieu

Thank you for your reply. I will wait for a permanent fix from you when you have more time. For the time being, I access the output directory and run the command (not optimal but works). Just ping me when this is fixed.

Thanks again for your help

Best
Foivos