nrhorner
commented
7 months ago Hi @irzamsarfraz
Sorry that you are having problems with the workflow. This a known issue and a fix will be released very soon.
Closed irzamsarfraz closed 6 months ago
nrhorner
commented
7 months ago Hi @irzamsarfraz
Sorry that you are having problems with the workflow. This a known issue and a fix will be released very soon.
blindsey101112
commented
6 months ago Hi @nrhorner,
Thanks for looking into this. We have just had the same error. Do you know roughly when the fix might be released?
nrhorner
commented
6 months ago Hi @blindsey101112
The fix is on our pre-release branch. I'd be grateful if you could test it out for me.
nextflow run epi2me-labs/wf-single-cell -r prerelease ...
blindsey101112
commented
6 months ago Great, thank you very much. I've just set it running now and will let you know how it goes.
On Tue, 16 Jan 2024 at 09:58, Neil Horner @.***> wrote:
Hi @blindsey101112 https://github.com/blindsey101112
The fix is on our pre-release branch. I'd be grateful if you could test it out for me.
nextflow run epi2me-labs/wf-single-cell -r prerelease ...
— Reply to this email directly, view it on GitHub https://github.com/epi2me-labs/wf-single-cell/issues/66#issuecomment-1893414514, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZICVRREIW5YM42FIBCZOIDYOZFMPAVCNFSM6AAAAABAKJJ3TCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJTGQYTINJRGQ . You are receiving this because you were mentioned.Message ID: @.***>
blindsey101112
commented
6 months ago It worked fine with the pre-release. Thanks very much
On Tue, 16 Jan 2024 at 10:25, Benjamin Lindsey @.***> wrote:
Great, thank you very much. I've just set it running now and will let you know how it goes.
On Tue, 16 Jan 2024 at 09:58, Neil Horner @.***> wrote:
Hi @blindsey101112 https://github.com/blindsey101112
The fix is on our pre-release branch. I'd be grateful if you could test it out for me.
nextflow run epi2me-labs/wf-single-cell -r prerelease ...
— Reply to this email directly, view it on GitHub https://github.com/epi2me-labs/wf-single-cell/issues/66#issuecomment-1893414514, or unsubscribe https://github.com/notifications/unsubscribe-auth/AZICVRREIW5YM42FIBCZOIDYOZFMPAVCNFSM6AAAAABAKJJ3TCVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTQOJTGQYTINJRGQ . You are receiving this because you were mentioned.Message ID: @.***>
nrhorner
commented
6 months ago Great. Thanks for letting us know. I'll close this ticket now
irzamsarfraz
commented
6 months ago @nrhorner This seems to work with one of the smaller samples but with another larger sample, I seem to get error again for some reason.
Nextflow command:
nextflow run epi2me-labs/wf-single-cell -r prerelease -w results_1415/workspace -profile singularity --fastq /restricted/projectnb/camplab/projects/20231027_Cam_Oxford_Nanopore/data/raw/231027Cam/PseudoID-1415/20231101_1447_2C_PAQ97447_72c9ab2d/fastq_pass/all_merged/all_merged.fastq --kit_name 5prime --kit_version v1 --expected_cells 100000 --ref_genome_dir refdata-gex-GRCh38-2020-A/ --out_dir results_1415 --max_threads 22 --matrix_min_genes 10 --resources_mm2_max_threads 22 --matrix_min_genes 1 --matrix_min_cells 1 --barcode_max_ed 2 --barcode_min_ed_diff 1 --plot_umaps False --umap_n_repeats 0
Error: Error executing process > 'pipeline:process_bams:tag_bams (16)'
Caused by: Process
pipeline:process_bams:tag_bams (16)terminated with an error exit status (1)Command executed:
workflow-glue tag_bam --in_bam align.bam --tags tags.tsv --out_bam all_merged.chrY.tagged.bam --chrom chrY
samtools index all_merged.chrY.tagged.bam
Command exit status: 1
Command output: (empty)
Command error: /home/epi2melabs/conda/lib/python3.8/site-packages/umap/distances.py:1063: NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.[0m @numba.jit() /home/epi2melabs/conda/lib/python3.8/site-packages/umap/distances.py:1071: NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.[0m @numba.jit() /home/epi2melabs/conda/lib/python3.8/site-packages/umap/distances.py:1086: NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.[0m @numba.jit() /home/epi2melabs/conda/lib/python3.8/site-packages/umap/umap_.py:660: NumbaDeprecationWarning: [1mThe 'nopython' keyword argument was not supplied to the 'numba.jit' decorator. The implicit default value for this argument is currently False, but it will be changed to True in Numba 0.59.0. See https://numba.readthedocs.io/en/stable/reference/deprecation.html#deprecation-of-object-mode-fall-back-behaviour-when-using-jit for details.[0m @numba.jit() [03:44:37 - workflow_glue] Starting entrypoint. Traceback (most recent call last): File "/usr2/collab/isarfraz/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow-glue", line 7, in cli() File "/usr2/collab/isarfraz/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/init.py", line 72, in cli args.func(args) File "/usr2/collab/isarfraz/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/tag_bam.py", line 107, in main add_tags(args.tags, args.in_bam, args.out_bam, args.chrom, args.flip) File "/usr2/collab/isarfraz/.nextflow/assets/epi2me-labs/wf-single-cell/bin/workflow_glue/tag_bam.py", line 80, in add_tags align.set_tag('CR', row['CR'], value_type="Z") File "pysam/libcalignedsegment.pyx", line 2316, in pysam.libcalignedsegment.AlignedSegment.set_tag File "pysam/libcalignedsegment.pyx", line 2400, in pysam.libcalignedsegment.AlignedSegment.set_tag File "pysam/libcutils.pyx", line 134, in pysam.libcutils.force_bytes TypeError: Argument must be string, bytes or unicode.
Work dir: /restricted/projectnb/camplab/home/isarfraz/Nanopore/20231027_Oxford_Nanpore/wf-single-cell/results_1415/workspace/72/d91b6b46cf4680d8cf981ddd800546
Tip: you can replicate the issue by changing to the process work dir and entering the command
bash .command.run
Thank you for looking into this!
Operating System
Linux
Other Linux
No response
Workflow Version
v0.3.0
Workflow Execution
EPI2ME Desktop application
EPI2ME Version
No response
CLI command run
Workflow Execution - CLI Execution Profile
None
What happened?
Error from add_tag as shown below:
Relevant log output
Application activity log entry
No response