Error in checkGrep(grep(".A.txt", files)) and Attribute error in 'pulp'

[davhg96]

Describe the bug

Hi, Im trying to run mgatk on a tenx run I did using the dogmaseq protocol.
When running:
mgatk tenx -i ./PATHTO/atac_possorted_bam.bam -n mtMSC -o /PATHTOOUT/mtMSC -bt CB -b /PATHTOBarcodes/barcodes.tsv

And I get

`
Thu May 23 15:38:01 CEST 2024: mgatk v0.7.0

Thu May 23 15:38:01 CEST 2024: Found bam file: /3_Data/InVitroDogma/atac_possorted_bam.bam for genotyping.
Thu May 23 15:38:01 CEST 2024: Found file of barcodes to be parsed: ./3_Data/InVitroDogma/barcodes.tsv
Thu May 23 15:38:01 CEST 2024: User specified mitochondrial genome matches .bam file
Thu May 23 15:38:11 CEST 2024: Finished determining/splitting barcodes for genotyping.
Thu May 23 15:38:12 CEST 2024: Genotyping samples with 20 threads
Traceback (most recent call last):
File "/opt/mamba24/bin/snakemake", line 8, in sys.exit(main())
File "/opt/mamba24/lib/python3.10/site-packages/snakemake/init.py", line 2736, in main parser get_argument_parser()
File "/opt/mamba24/lib/python3.10/site-packages/snakemake/init_.py", line 1607, in get_argument_parser lp_solvers pulp.list_solvers(onlyAvailable True)
AttributeError: module 'pulp' has no attribute 'list solvers'. Did you mean: 'ListSolvers'? Improper folder specification; file missing / extra file present. See documentation
Error in checkGrep(grep(".A.txt", files)):

Calls: importMito -> checkGrep
Execution halted`

A summary of .log files
Output of the Log files

cat logs/*log |  

Thu May 23 15:29:28 CEST 2024: Starting analysis with mgatk
Thu May 23 15:29:28 CEST 2024: Processing samples with 20 threads
Thu May 23 15:29:28 CEST 2024: mgatk successfully processed the supplied bam files
Thu May 23 15:29:37 CEST 2024: Successfully created final output files
Thu May 23 15:29:37 CEST 2024: Intermediate files successfully removed.
Thu May 23 15:38:12 CEST 2024: Starting analysis with mgatk
Thu May 23 15:38:12 CEST 2024: Processing samples with 20 threads
Thu May 23 15:38:12 CEST 2024: mgatk successfully processed the supplied .bam files
Thu May 23 15:38:17 CEST 2024: Successfully created final output files
Thu May 23 15:38:17 CEST 2024: Intermediate files successfully removed.

Post an ls -lRh of mgatk_output_folder
ls -IRh final logs qc

Describe the sequencing assay being analyzed
The data was produced using the 10x multiome ATAC + RNA, and the Dogma seq protocol. Looking at the QC there were ~15% Mt reads

Clarify if the execution successful on the test data provided in the repository
Ran the test files in the VM this is the output

mgatk tenx -i barcode/test_barcode.bam -n bc1 -o bc1dmem -bt CB -b barcode/test_barcodes.txt -c 2
Fri May 24 09:57:17 CEST 2024: mgatk v0.7.0
Fri May 24 09:57:18 CEST 2024: Found bam file: barcode/test_barcode.bam for genotyping.
Fri May 24 09:57:18 CEST 2024: Found file of barcodes to be parsed: barcode/test_barcodes.txt
Fri May 24 09:57:18 CEST 2024: User specified mitochondrial genome matches .bam file
Traceback (most recent call last):
File "/opt/mamba24/bin/mgatk", line 8, in
sys.exit(main())
File "/opt/mamba24/lib/python3.10/site-packages/click/core.py", line 1157, in call
return self.main(*args, **kwargs)
File "/opt/mamba24/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/opt/mamba24/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/opt/mamba24/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/opt/mamba24/lib/python3.10/site-packages/mgatk/cli.py", line 219, in main
pool = Pool(processes=int(ncores))
File "/opt/mamba24/lib/python3.10/multiprocessing/context.py", line 119, in Pool
return Pool(processes, initializer, initargs, maxtasksperchild,
File "/opt/mamba24/lib/python3.10/multiprocessing/pool.py", line 191, in init
self._setup_queues()
File "/opt/mamba24/lib/python3.10/multiprocessing/pool.py", line 346, in _setup_queues
self._inqueue = self._ctx.SimpleQueue()
File "/opt/mamba24/lib/python3.10/multiprocessing/context.py", line 113, in SimpleQueue
return SimpleQueue(ctx=self.get_context())
File "/opt/mamba24/lib/python3.10/multiprocessing/queues.py", line 341, in init
self._rlock = ctx.Lock()
File "/opt/mamba24/lib/python3.10/multiprocessing/context.py", line 68, in Lock
return Lock(ctx=self.get_context())
File "/opt/mamba24/lib/python3.10/multiprocessing/synchronize.py", line 162, in init
SemLock.init(self, SEMAPHORE, 1, 1, ctx=ctx)
File "/opt/mamba24/lib/python3.10/multiprocessing/synchronize.py", line 57, in init
sl = self._semlock = _multiprocessing.SemLock(
FileNotFoundError: [Errno 2] No such file or directory

Additional context
Version 0.7 running inside a singularity VM. When Running the test files the error is different it seems.

[tybottorff]

I got a very similar error using mgatk call for bulk ATACseq data if @davhg96 you resolved this perhaps

Update: I actually think I got around this (ran into a different issue) by editing the init.py file's (for me in venv3/lib/python3.9/site-packages/pulp/apis) function definition to rename the function to def list_solvers(onlyAvailable=False): from def listSolvers(onlyAvailable=False):

[danieljrichard]

This I believe is a bug with 'pulp' - where the newer version has changed the name of a function.
The solution I found working was to down-grade pulp
pip3 install --force-reinstall -v "pulp==2.7"
##confim we down-graded successfully
pip freeze

Now I'm running into different issues though