Comments (4)
derrik-gratz
commented on August 18, 2024
podman run -v /yerkes-cifs:/yerkes-cifs -ti ghcr.io/bimberlab/nimble align \
--reference /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/mmul10_missing_features.json \
--output /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Processing/nimble/nimble_test.tsv \
--input /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/p23120_Amanda-230608A/p23120-s001_Capture-39-5-GEX-LIB_S1_L001_R1_001.fastq \
--input /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/p23120_Amanda-230608A/p23120-s001_Capture-39-5-GEX-LIB_S1_L001_R2_001.fastq
Aligning input .bam to the reference libraries
['--input', '/yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/p23120_Amanda-230608A/p23120-s001_Capture-39-5-GEX-LIB_S1_L001_R2_001.fastq', '-c', '1', '--strand_filter', 'unstranded', '-r', '/yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/mmul10_missing_features.json', '-o', '/yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Processing/nimble/nimble_test.tsv']
Loading and preprocessing reference data for /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/mmul10_missing_features.json
Total 156227 kmers to process in dbg
Making mphf of kmers
Assigning offsets to kmers
Total 156227 kmers to process in dbg
Making mphf of kmers
Assigning offsets to kmers
Loading read sequences and aligning
Spawning consumer thread 0
Spawning reader thread.
Spawning logging thread.
thread '<unnamed>' panicked at 'called `Result::unwrap()` on an `Err` value: BamOpen { target: "/yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/p23120_Amanda-230608A/p23120-s001_Capture-39-5-GEX-LIB_S1_L001_R2_001.fastq" }', src/parse/sorted_bam_reader.rs:14:50
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace
thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: Any { .. }', src/process/bam.rs:181:28
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derrik-gratz
commented on August 18, 2024
I'll throw this in here too, in case you are interested in allowing the wildcard expansion for the input field, you can specify nargs to an argparse argument to allow multiple entries
https://docs.python.org/3/library/argparse.html#nargs
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derrik-gratz
commented on August 18, 2024
Also, the non-parsing issue for fastq inputs happens with both .fastq and .fastq.gz extensions
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hextraza
commented on August 18, 2024
podman run -v /yerkes-cifs:/yerkes-cifs -ti ghcr.io/bimberlab/nimble align \ --reference /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/mmul10_missing_features.json \ --output /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Processing/nimble/nimble_test.tsv \ --input /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/p23120_Amanda-230608A/p23120-s001_Capture-39-5-GEX-LIB_S1_L001_R1_001.fastq \ --input /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/p23120_Amanda-230608A/p23120-s001_Capture-39-5-GEX-LIB_S1_L001_R2_001.fastqAligning input .bam to the reference libraries ['--input', '/yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/p23120_Amanda-230608A/p23120-s001_Capture-39-5-GEX-LIB_S1_L001_R2_001.fastq', '-c', '1', '--strand_filter', 'unstranded', '-r', '/yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/mmul10_missing_features.json', '-o', '/yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Processing/nimble/nimble_test.tsv'] Loading and preprocessing reference data for /yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/mmul10_missing_features.json Total 156227 kmers to process in dbg Making mphf of kmers Assigning offsets to kmers Total 156227 kmers to process in dbg Making mphf of kmers Assigning offsets to kmers Loading read sequences and aligning Spawning consumer thread 0 Spawning reader thread. Spawning logging thread. thread '<unnamed>' panicked at 'called `Result::unwrap()` on an `Err` value: BamOpen { target: "/yerkes-cifs/runs/Analysis/2023_Analyses/p23120_Amanda/Data/p23120_Amanda-230608A/p23120-s001_Capture-39-5-GEX-LIB_S1_L001_R2_001.fastq" }', src/parse/sorted_bam_reader.rs:14:50 note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: Any { .. }', src/process/bam.rs:181:28
Most recent release should fix this workflow, allowing multiple files to be passed to --input
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Related Issues (20)
- Handle odd UMIs HOT 1
- Do extra read checking
- --align-debug flag
- group_on, when the target field is null
- Enforce lack of comma in reference names, and also group_on fields
- Fix duplicated columns in library generation
- Check if discard_nonzero_mismatch is still in use
- Empty string as the feature name?
- Look into why gzip output seems broken
- Update nimble's I/O to always override outputs, rather than append
- Ensure align-debug output contains columns for all information relevant to filtering and decisions
- Implement a reference-library level option for 'max-hits-to-report'
- Sort mult-ref allele hits so the string is deterministic
- Add strandedness filters to alignment pipeline HOT 1
- Move baseline from 0->20 in score filter
- Ensure samtools sort call on the UR flag keeps paired-end reads together HOT 1
- Align should work with files instead of only paths
- Re-enable --debug
- Add validation to BAM/FASTQ input
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