Error executing process > 'mod:modkit_phase (1)' #184
Comments
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Please also find the log file here |
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@cihaterdogan could you please share the content of folder: In particular, can you share the content of |
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Hi @RenzoTale88, |
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Ok no worries, I'll close this ticket then. We just released v2.2.2, so if you come across the issue again please re-open this issue with the new comment. |
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Hi @RenzoTale88 I am using v2.2.2 but I have exactly the same error. |
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@agatafant we will need more investigation into this then. Can you please share the nextflow log? |
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Can you please check the content of the following files: |
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command.env command.err is empty thanks |
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Thanks for confirming this. |
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I had to run -resume because:
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The issue with this is that it will not retry the sample-probs process, and therefore will fail again with the same error. Can you try removing the following file and try again? |
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@agatafant can you provide more details on how you generated the input BAM? |
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As you suggested I removed /archive/s2/genomics/afant/NANOPORE_analysis/PDM0001NBLDN1R/pipe_wf_human_variation_threshold_latest/work/97/8923b6fe6fde356317df755ccedf3f/.command.env, I have launched again the pipeline with -resume but I have obtained same error. |
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@agatafant I was mostly interested in knowing which remora model(s) did you use. Did you use a single model, multiple models, etc |
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dorado basecaller -x cuda:all --reference /archive/s1/sconsRequirements/databases/reference/resources_broad_hg38_v0_Homo_sapiens_assembly38.fasta /archive/s2/genomics/afant/PCG_Nanopore/out_PCG_PDM_PDM0001NBLDN1R/dorado0.6.0/[email protected] /archive/genomic_data/Collaboration/PCG_ParkinsonDiseaseMilano/FAST5/PCG_PDM_PDM0001NBLDN1R/PDM0001NBLDN1R/20240409_1716_1G_PAS38058_469a1fd2/pod5/ --modified-bases-models /archive/s2/genomics/afant/PCG_Nanopore/out_PCG_PDM_PDM0001NBLDN1R/dorado0.6.0/[email protected]_6mA@v2,/archive/s2/genomics/afant/PCG_Nanopore/out_PCG_PDM_PDM0001NBLDN1R/dorado0.6.0/[email protected]_5mC_5hmC@v1 |
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Ok this confirms the issue, i.e. the workflow currently can't handle multiple modified bases, and causes to compute multiple filtering thresholds. We will work on a patch, and notify when ready. |
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Ok great, thank you. In the meanwhile I re-obtain the BAM with only one modified bases |
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@agatafant we just released wf-human-variation v2.2.4, that should support multiple modification types (e.g. modA and modC). Can you try with this release and let us know if it works for you? |
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Thank you @RenzoTale88. I still have this problem when launching the pipeline: I have to remove folder ~/.nextflow/assets/epi2me-labs otherwise it fails with: But since I have to modify some options in nextflow.config I have to stop the pipeline (is there a better way to do this?), modify the config and then resume, but when resuming it fails again with: |
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Hi @agatafant try do first drop the workflow: And then try the analysis again, specifying version 2.2.4: |
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Hi, I have launched the pipeline, but it continues failing because of: attached the log |
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From what I can see, you are using a PBS distributed system right? If so, you need to discuss with your IT support to define an appropriate configuration for your system to avoid this issue. |
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@agatafant did you manage to run the workflow successfully? |
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No, I sadly removed --mod option in order to run the pipeline successfully |
Operating System
Other Linux (please specify below)
Other Linux
Red Hat Enterprise Linux 8.9
Workflow Version
v2.2.0
Workflow Execution
Command line (Cluster)
Other workflow execution
No response
EPI2ME Version
No response
CLI command run
module load singularity/3.7.2
module load java/15.0.2
export NXF_SINGULARITY_CACHEDIR=Path/.singularity
export SINGULARITY_TMPDIR=Path/.singularity
export NXF_HOME=Path
OUTPUT=s4059246577_results
./nextflow run epi2me-labs/wf-human-variation
-w ${OUTPUT}/workspace
-profile singularity
--bam 'data/s4059246577_merged.bam'
--basecaller_cfg '[email protected]'
--mod
--ref 'hg38/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna'
--sample_name 's4059246577'
--sv
--snp
--str
--cnv
--phased
--threads 16
--bam_min_coverage 5
--out_dir ${OUTPUT}
Workflow Execution - CLI Execution Profile
None
What happened?
I was running the wf-human-variation pipeline as a job (with Slurm) on my institution's clusters using the above command. But got the following error
ERROR ~ Error executing process > 'mod:modkit_phase (1)'
Caused by:
Process
mod:modkit_phase (1)terminated with an error exit status (2)Command executed:
modkit pileup
chrY_hp.bam
s4059249500
--ref GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
--partition-tag HP
--interval-size 1000000
--prefix s4059249500.wf_mods.chrY
--log-filepath modkit.log
--region chrY
--filter-threshold 0.78125 0.8613281
--threads 4 --combine-strands --cpg
Compress all
for i in
ls s4059249500/; doroot_name=$( basename $i '.bed' )
# modkit saves the file as params.sample_name.wf_mods_haplotype.bed
# create a new name with the patter params.sample_name.wf_mods.haplotype.bedmethyl
new_name=$( echo ${root_name} | sed 's/wf_mods_/wf_mods./' )
mv s4059249500/${root_name}.bed s4059249500/${new_name}.bedmethyl
bgzip s4059249500/${new_name}.bedmethyl
done
Command exit status:
2
Command output:
(empty)
Command error:
error: unexpected argument '0.8613281' found
Usage: modkit pileup [OPTIONS] <IN_BAM> <OUT_BED>
For more information, try '--help'.
Relevant log output
Application activity log entry
No response
Were you able to successfully run the latest version of the workflow with the demo data?
yes
Other demo data information
No response
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