FileNotFoundError: [Errno 2] No such file or directory: '/xxx/pyramids'

[mcariou]

Hello,

I am trying to run instaGRAAL on a linux machine using docker with this command:

sudo docker run --gpus all koszullab/instagraal instagraal $OUT_HICSTUFF $ASSEMBLY $OUT_INSTA

It gave this error:

Traceback (most recent call last): File "/usr/local/bin/instagraal", line 11, in load_entry_point('instagraal', 'console_scripts', 'instagraal')() File "/src/instagraal/instagraal/instagraal.py", line 1178, in main output_folder=output_folder, File "/src/instagraal/instagraal/instagraal.py", line 160, in init output_folder=output_folder, File "/src/instagraal/instagraal/simu_single.py", line 74, in init self.select_data_set(name) File "/src/instagraal/instagraal/simu_single.py", line 743, in select_data_set thresh_factor=self.thresh_factor, File "/src/instagraal/instagraal/pyramid_sparse.py", line 58, in build_and_filter os.mkdir(all_pyramid_folder) FileNotFoundError: [Errno 2] No such file or directory: '/xxx/pyramids'

I found this other issue https://github.com/koszullab/instaGRAAL/issues/24 which seems similar, but with singularity, and attempted to reproduce the proposed solution in docker using "-v $PWD:/data" (instead of -B $PWD:/data), but obtained the same error.

The HiC matrix is produced from Hicstuff and the assembly is a fasta file (from wtdbg2).

Thanks in advance for any help and sorry if I didn't include sufficient information. Best regards