caleblareau
commented
9 months ago hi,
-n should be something like “MySample” — a string outlining the name of the objects to be created rather than a directory… if you change that variable, I think it should work
On Jan 1, 2024, at 8:56 PM, LY @.***> wrote:
Describe the bug I'm encountering an error with mgatk when processing my own data, despite being able to run the example successfully. cp: cannot create regular file ‘mgatk_out/logs//public/home/samples/Cellranger/control.parameters.txt’: No such file or directory sh: mgatk_out/logs//public/home/samples/Cellranger/control.snakemake_tenx.log: No such file or directory Error in checkGrep(grep(".A.txt", files)) : Improper folder specification; file missing / extra file present. See documentation Calls: importMito -> checkGrep Execution halted
A summary of .log files my .log files looks like this cat base.mgatk.log Tue Jan 02 09:38:40 CST 2024: Starting analysis with mgatk Tue Jan 02 09:38:40 CST 2024: Processing samples with 8 threads Tue Jan 02 09:38:40 CST 2024: mgatk successfully processed the supplied .bam files Tue Jan 02 09:38:45 CST 2024: Successfully created final output files Tue Jan 02 09:38:45 CST 2024: Temporary files not deleted since --keep-temp-files was specified.
Post an ls -lRh of mgatk_output_folder ls -lRh mgatk_out/ mgatk_out/: total 2.5K drwxr-xr-x 1 samples 4.0K Jan 2 09:29 fasta drwxr-xr-x 1 samples 4.0K Jan 2 09:29 final drwxr-xr-x 1 samples 4.0K Jan 2 09:31 logs drwxr-xr-x 1 samples 4.0K Jan 2 09:31 qc drwxr-xr-x 1 samples 4.0K Jan 2 09:31 temp
mgatk_out/fasta: total 18K -rw-r--r-- 1 samples 17K Jan 2 09:29 chrM.fasta -rw-r--r-- 1 samples 19 Jan 2 09:29 chrM.fasta.fai
mgatk_out/final: total 119K -rw-r--r-- 1 samples 119K Jan 2 09:29 chrM_refAllele.txt
mgatk_out/logs: total 1.5K -rw-r--r-- 1 samples 373 Jan 2 09:31 base.mgatk.log drwxr-xr-x 1 samples 4.0K Jan 2 09:31 filterlogs drwxr-xr-x 1 samples 4.0K Jan 2 09:31 rmdupslogs
mgatk_out/logs/filterlogs: total 0
mgatk_out/logs/rmdupslogs: total 0
mgatk_out/qc: total 1.0K drwxr-xr-x 1 samples 4.0K Jan 2 09:31 depth drwxr-xr-x 1 samples 4.0K Jan 2 09:31 quality
mgatk_out/qc/depth: total 0
mgatk_out/qc/quality: total 0
mgatk_out/temp: total 3.0K drwxr-xr-x 1 samples 4.0K Jan 2 09:31 barcoded_bams drwxr-xr-x 1 samples 4.0K Jan 2 09:29 barcode_files drwxr-xr-x 1 samples 4.0K Jan 2 09:31 quality drwxr-xr-x 1 samples 4.0K Jan 2 09:31 ready_bam drwxr-xr-x 1 samples 4.0K Jan 2 09:31 sparse_matrices drwxr-xr-x 1 samples 4.0K Jan 2 09:31 temp_bam
mgatk_out/temp/barcoded_bams: total 768M -rw-r--r-- 1 samples 87M Jan 2 09:30 barcodes.1.bam -rw-r--r-- 1 samples 1.9K Jan 2 09:31 barcodes.1.bam.bai -rw-r--r-- 1 samples 99M Jan 2 09:30 barcodes.2.bam -rw-r--r-- 1 samples 1.9K Jan 2 09:30 barcodes.2.bam.bai -rw-r--r-- 1 samples 99M Jan 2 09:30 barcodes.3.bam -rw-r--r-- 1 samples 1.9K Jan 2 09:30 barcodes.3.bam.bai -rw-r--r-- 1 samples 95M Jan 2 09:30 barcodes.4.bam -rw-r--r-- 1 samples 1.8K Jan 2 09:30 barcodes.4.bam.bai -rw-r--r-- 1 samples 100M Jan 2 09:30 barcodes.5.bam -rw-r--r-- 1 samples 1.9K Jan 2 09:31 barcodes.5.bam.bai -rw-r--r-- 1 samples 95M Jan 2 09:30 barcodes.6.bam -rw-r--r-- 1 samples 1.9K Jan 2 09:30 barcodes.6.bam.bai -rw-r--r-- 1 samples 99M Jan 2 09:30 barcodes.7.bam -rw-r--r-- 1 samples 1.9K Jan 2 09:30 barcodes.7.bam.bai -rw-r--r-- 1 samples 97M Jan 2 09:30 barcodes.8.bam -rw-r--r-- 1 samples 1.9K Jan 2 09:30 barcodes.8.bam.bai
mgatk_out/temp/barcode_files: total 152K -rw-r--r-- 1 samples 19K Jan 2 09:29 barcodes.1.txt -rw-r--r-- 1 samples 19K Jan 2 09:29 barcodes.2.txt -rw-r--r-- 1 samples 19K Jan 2 09:29 barcodes.3.txt -rw-r--r-- 1 samples 19K Jan 2 09:29 barcodes.4.txt -rw-r--r-- 1 samples 19K Jan 2 09:29 barcodes.5.txt -rw-r--r-- 1 samples 19K Jan 2 09:29 barcodes.6.txt -rw-r--r-- 1 samples 19K Jan 2 09:29 barcodes.7.txt -rw-r--r-- 1 samples 19K Jan 2 09:29 barcodes.8.txt
mgatk_out/temp/quality: total 0
mgatk_out/temp/ready_bam: total 0
mgatk_out/temp/sparse_matrices: total 0
mgatk_out/temp/temp_bam: total 0
Describe the sequencing assay being analyzed My data is 10x 3' scRNA-seq and here's my code to run mgatk mgatk tenx -i $wkdir/outs/possorted_genome_bam.bam \ -n $wkdir -ub UB \ -g hg38 -bt CB -b $wkdir/outs/filtered_feature_bc_matrix/barcodes.tsv -z -c 8 gzip $wkdir/outs/filtered_feature_bc_matrix/barcodes.tsv
Clarify if the execution successful on the test data provided in the repository I've run example of mgatk successfully mgatk tenx -i barcode/test_barcode.bam -n bc1 -o bc1dmem -ub UB \ -bt CB -b barcode/test_barcodes.txt -c 2
Here's my output ls -lRh bc1dmem bc1dmem: total 1.5K drwxr-xr-x 1 samples 4.0K Dec 30 10:03 final drwxr-xr-x 1 samples 4.0K Dec 30 10:01 logs drwxr-xr-x 1 samples 4.0K Dec 30 10:01 qc
bc1dmem/final: total 1.7M -rw-r--r-- 1 samples 96K Dec 30 10:02 bc1.A.txt.gz -rw-r--r-- 1 samples 194K Dec 30 10:02 bc1.coverage.txt.gz -rw-r--r-- 1 samples 96K Dec 30 10:02 bc1.C.txt.gz -rw-r--r-- 1 samples 76 Dec 30 10:02 bc1.depthTable.txt -rw-r--r-- 1 samples 50K Dec 30 10:02 bc1.G.txt.gz -rw-r--r-- 1 samples 537K Dec 30 10:03 bc1.rds -rw-r--r-- 1 samples 477K Dec 30 10:03 bc1.signac.rds -rw-r--r-- 1 samples 77K Dec 30 10:02 bc1.T.txt.gz -rw-r--r-- 1 samples 119K Dec 30 10:01 chrM_refAllele.txt
bc1dmem/logs: total 10K -rw-r--r-- 1 samples 347 Dec 30 10:03 base.mgatk.log -rw-r--r-- 1 samples 515 Dec 30 10:01 bc1.parameters.txt -rw-r--r-- 1 samples 7.4K Dec 30 10:03 bc1.snakemake_tenx.log drwxr-xr-x 1 samples 4.0K Dec 30 10:02 filterlogs drwxr-xr-x 1 samples 4.0K Dec 30 10:02 rmdupslogs
bc1dmem/logs/filterlogs: total 1.0K -rw-r--r-- 1 samples 22 Dec 30 10:02 barcodes.1.filter.log -rw-r--r-- 1 samples 21 Dec 30 10:01 barcodes.2.filter.log
bc1dmem/logs/rmdupslogs: total 3.0K -rw-r--r-- 1 samples 1.5K Dec 30 10:02 barcodes.1.rmdups.log -rw-r--r-- 1 samples 1.5K Dec 30 10:02 barcodes.2.rmdups.log
bc1dmem/qc: total 1.0K drwxr-xr-x 1 samples 4.0K Dec 30 10:02 depth drwxr-xr-x 1 samples 4.0K Dec 30 10:01 quality
bc1dmem/qc/depth: total 1.0K -rw-r--r-- 1 samples 50 Dec 30 10:02 barcodes.1.depth.txt -rw-r--r-- 1 samples 26 Dec 30 10:02 barcodes.2.depth.txt
bc1dmem/qc/quality: total 0
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FionaMoon
Describe the bug I'm encountering an error with
mgatkwhen processing my own data, despite being able to run the example successfully.A summary of .log files
my .log files looks like this
Post an ls -lRh of mgatk_output_folder
Describe the sequencing assay being analyzed
My data is 10x 3' scRNA-seq and here's my code to run
mgatkClarify if the execution successful on the test data provided in the repository
I've run example of mgatk successfully
Here's my output