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NVIDIA-Genomics-Research / AtacWorks

Deep learning based processing of Atac-seq data
https://clara-parabricks.github.io/AtacWorks/
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invalid_crossdevice_link #166

Closed ntadimeti closed 4 years ago

ntadimeti commented 4 years ago

This PR addresses one of the issues being tracked in #153 . User is getting the following error when running atacworks inference:

Inference -------------------- [ 0/29]

Inference time taken:  120.692s (Load    3.292s,Prediction  117.140s)

INFO:2020-05-15 02:53:50,337:AtacWorks-main] Waiting for writer to finish...

Process Process-2:

Traceback (most recent call last):

  File "/usr/lib/python3.6/shutil.py", line 550, in move

    os.rename(src, real_dst)

OSError: [Errno 18] Invalid cross-device link:
'/tmp/247693.tmpdir/tmptkst0za1/0/00001' ->
'./inference_output_2020.05.15_02.51/NK_inferred.track.bedGraph'

Although it's not reproducible on our end, the error seems to be because os.rename and shutile.move fail when source and destinations seem to be on different file systems.

An easy workaround for that is to use shutil.copy and os.remove`. Inspired from this thread : https://github.com/ewels/MultiQC/issues/806

-- Will wait for user to verify and report back that it works before merging.

ntadimeti commented 4 years ago

@tijyojwad @avantikalal -- should we merge this into master or dev-0.3.0 ?