pinellolab / dictys

Context specific and dynamic gene regulatory network reconstruction and analysis
GNU Affero General Public License v3.0
110 stars 14 forks source link

Error with CPU Part 1, execution of Full Multiome Tutorial #69

Open emix-c opened 1 month ago

emix-c commented 1 month ago

Checks before submitting the issue

Describe the error

%%bash set -eo pipefail cd ..

Run CPU part of inference

make -f makefiles/static.mk -j 8 -k cpu || true

I ran into this error: Traceback (most recent call last): File "/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/runpy.py", line 197, in _run_module_as_main return _run_code(code, main_globals, None, File "/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/runpy.py", line 87, in _run_code exec(code, run_globals) File "/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/main.py", line 13, in docstringrunner(package) File "/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 340, in docstringrunner run_args(pkgname,funcs,args) File "/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/docstring2argparse/init.py", line 330, in run_args return func(*a,**ka) File "/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/chromatin.py", line 67, in macs2 d2 = shell.cmdfile(cmd,[],infiles={'cellnames.txt': namestxt},quiet=False,cd=True) File "/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/utils/shell.py", line 181, in cmdfile raise RuntimeError('Command failed, possibly due to program error: ' + cmda) RuntimeError: Command failed, possibly due to program error: /home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/scripts/chromatin_macs2.sh cellnames.txt /home/groups/CEDAR/chaoe/projects/Dictys/data/bams /home/groups/CEDAR/chaoe/projects/Dictys/tmp_static/Subset5/reads.bam /home/groups/CEDAR/chaoe/projects/Dictys/tmp_static/Subset5/reads.bai /home/groups/CEDAR/chaoe/projects/Dictys/tmp_static/Subset5/peaks.bed hs 0.05 8 [bam_sort_core] merging from 2 files and 8 in-memory blocks... /home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/scripts/chromatin_macs2.sh: line 38: 1597134 Killed samtools sort -o "$output_bam" $nodes2 -l 1 02-filtered.bam

make: *** [makefiles/common.mk:138: tmp_static/Subset5/reads.bam] Error 1 makefiles/common.mk:138: warning: pattern recipe did not update peer target 'tmp_static/Subset5/peaks.bed'. makefiles/common.mk:138: warning: pattern recipe did not update peer target 'tmp_static/Subset5/reads.bai'.

Optional steps (may accelerate troubleshooting) I did not do any optional steps.

lingfeiwang commented 1 month ago

Hi emix-c,

Probably your computer ran out of memory. Could you try again with -j 4 instead?

Lingfei

emix-c commented 1 month ago

Hi Lingfei, Yes I got it working by reducing the number of jobs! I do have a quick question, since I'm running pytorch with CPU only, I only run 1.1 CPU part execution and then 4.1 Aggregating Network part execution, so I skip 2.1 GPU execution and 3.1 CPU part 2, execution, is that correct?

I ran 1.1 CPU part execution and tried to run 4.1 but got these errors.

WARNING:2724116:2024-10-22 09:36:31,129:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset1 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,156:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset1 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,158:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset10 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,159:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset10 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,602:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset11 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,603:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset12 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,604:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset12 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,682:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset14 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,683:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset2 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,683:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset2 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,683:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset3 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,684:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset3 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,684:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset4 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,684:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset4 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,684:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset5 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,685:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset5 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,685:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset6 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,685:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset6 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,686:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset7 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,686:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset7 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,686:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset8 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,687:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset8 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,687:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset9 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:36:31,687:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:403:Skipping cell subset Subset9 due to error: FileNotFoundError(2, 'No such file or directory') WARNING:2724116:2024-10-22 09:37:00,168:/home/exacloud/gscratch/CEDAR/chaoe/miniconda3/envs/dictys/lib/python3.9/site-packages/dictys/net/init.py:510:Removing 11/14 failed subsets.

lingfeiwang commented 1 month ago

These errors are not anticipated in the tutorial notebook. Did you specify DEVICE to cpu in 2-makefile.ipynb first? Are these the first error you encountered? I suggest to rerun the whole tutorial in a new folder to find and report the first error you encounter.

github-actions[bot] commented 1 day ago

Stale issue message