ATACorrect hangs at 99% during normalization step

[MauricioALM]

When running the ATACorrect tool, the process consistently hangs at 99% during the normalization step (Estimating normalization factors) without throwing any errors. The process does not complete even after several hours.

TOBIAS ATACorrect
--bam trHF4_partial_footprint.bam
--genome "/home/aguilar-admin/Mau/genomes/mm39/mm39_filtered.fa"
--peaks trHF4_idr.narrowPeak
--outdir trHF4
--cores 30

The tool outputs the following log message and then stops progressing:

lua
Copiar código
2025-01-07 18:57:35 (3593677) [INFO] ----- Estimating normalization factors -----

The progress reaches 99% but does not move further.

[mohobein]

Hey @MauricioALM,

when you say consistently, do you mean every time you run TOBIAS in general, or every time you run it with these input files? If it is the latter, can you try to reproduce the error with another bam/peak file of yours and, if that causes the same problem, the test data?

If the issues is specific to your data instead of TOBIAS in general, there might a formatting issues. When you cancel the analysis with CTRL+C, what is the error message? This might tell me at which step in the algorithm it is stuck.

Best regards,
Moritz

[MauricioALM]

Hi, sorry for the delay, I ran the command again with other input data and the problem still occurs. When stopping Tobias with control + C, I receive the following message continuously:

Traceback (most recent call last):
File "/home/aguilar-admin/.local/bin/TOBIAS", line 8, in
sys.exit(main())
File "/home/aguilar-admin/.local/lib/python3.8/site-packages/tobias/TOBIAS.py", line 162, in main
args.func(args)
File "/home/aguilar-admin/.local/lib/python3.8/site-packages/tobias/tools/atacorrect.py", line 285, in run_atacorrect
reads_peaks = sum(run_parallel(count_reads, peak_region_chunks, [args], args.cores, logger))
File "/home/aguilar-admin/.local/lib/python3.8/site-packages/tobias/utils/utilities.py", line 72, in run_parallel
time.sleep(0.5)
KeyboardInterrupt
Traceback (most recent call last):
File "/usr/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/usr/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/usr/lib/python3.8/multiprocessing/pool.py", line 114, in worker
task = get()
File "/usr/lib/python3.8/multiprocessing/queues.py", line 355, in get
with self._rlock:
File "/usr/lib/python3.8/multiprocessing/synchronize.py", line 95, in enter
return self._semlock.enter()
KeyboardInterrupt
Process Process-2:
Traceback (most recent call last):
File "/usr/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/usr/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/aguilar-admin/.local/lib/python3.8/site-packages/tobias/utils/logger.py", line 151, in main_logger_process
record = self.queue.get()
File "", line 2, in get
File "/usr/lib/python3.8/multiprocessing/managers.py", line 835, in _callmethod
kind, result = conn.recv()
File "/usr/lib/python3.8/multiprocessing/connection.py", line 250, in recv
buf = self._recv_bytes()
File "/usr/lib/python3.8/multiprocessing/connection.py", line 414, in _recv_bytes
buf = self._recv(4)
File "/usr/lib/python3.8/multiprocessing/connection.py", line 379, in _recv
chunk = read(handle, remaining)
KeyboardInterrupt

[mohobein]

Thanks for the additional information.

Just to clarify, did you also try it out with the test data provided by TOBIAS? From the error I can gather that it is stuck at 99% percent because it starts multiple parallel processes to read the input files, which advances the progress bar, but it is stuck at actually reading the files. That strongly suggests to me that there is something wrong with the file format.

Could you provide me with a small reproducible example if possible, so that I can investigate the problem on my own machine? Just a small part of your bam and bed files that still run into the problem would be great :) Also, which TOBIAS version are you using?