Error with CPU Part 1, execution of Full Multiome Tutorial #69
Comments
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Hi emix-c, Probably your computer ran out of memory. Could you try again with Lingfei |
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Hi Lingfei, 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') |
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These errors are not anticipated in the tutorial notebook. Did you specify |
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Stale issue message |
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Describe the error
I installed using conda.
The full multiome tutorial.
I am encountering an error when trying to run the CPU Part1, execution block.
I am specifically running into an error with Subset5, I am not seeing this error with any else.
I adjusted the number of threads so that my system could handle it. Before, when I had it set to -j 36, some of the make commands to make expression0.tsv.gz were getting killed.
Whenever I made adjustments, I deleted the entire tmp_static folder and reran the below block.
%%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'.
No I didn't.
Optional steps (may accelerate troubleshooting)
I did not do any optional steps.
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