Open davhg96 opened 4 months ago
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):
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"
pip freeze
Now I'm running into different issues though
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, inAdditional context Version 0.7 running inside a singularity VM. When Running the test files the error is different it seems.