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epi2me-labs / wf-artic

ARTIC SARS-CoV-2 workflow and reporting
https://labs.epi2me.io/
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Problems process pipeline:runArtic #98

Closed Bioloko closed 1 year ago

Bioloko commented 1 year ago

Operating System

macOS

Other Linux

No response

Workflow Version

fails with more than one version

Workflow Execution

Command line

EPI2ME Version

No response

CLI command run

nextflow run epi2me-labs/wf-artic --fastq /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass --sample_sheet /Users/agaliana/Documents/Analisis_temporal/CORONA_230928/fastq_pass/148_sec_pend.csv --scheme_name SARS-CoV-2 --scheme_version Midnight-IDT/V1 --out_dir /Users/agaliana/wf-ARTIC/CORONA_230928 --update_data --report_detailed true --medaka_variant_model r1041_e82_400bps_fast_g632

Workflow Execution - CLI Execution Profile

standard (default)

What happened?

The pipeline fails when starts pipeline:runArtic steps.

Relevant log output

Workflow execution completed unsuccessfully!
The exit status of the task that caused the workflow execution to fail was: 4.

The full error message was:

Error executing process > 'pipeline:runArtic (1)'

Caused by:
  Process `pipeline:runArtic (1)` terminated with an error exit status (4)

Command executed:

  run_artic.sh         818566 seqs.fastq.gz 150 1200         r1041_e82_400bps_fast_g632 SARS-CoV-2 SARS-CoV-2         Midnight-IDT/V1 4 0 200
  bcftools stats 818566.pass.named.vcf.gz > 818566.pass.named.stats

Command exit status:
  4

Command output:
  Moving input: 'seqs.fastq.gz' to '818566/818566.fastq.gz'
  818566_818566.fastq   40809
   - artic guppyplex finished
  Suppress variant 23599

  Running hacked up minion.py

Command error:
  [11:12:18 - TrimOlap] MN908947.3:25468.1-25780.0 and MN908947.3:26748.0-27041.0 cannot be concatenated as there is no overlap and they do not abut.
  [11:12:18 - TrimOlap] MN908947.3:27569.2-27885.0 and MN908947.3:28678.0-29028.0 cannot be concatenated as there is no overlap and they do not abut.
  [11:12:20 - ValidArgs] Reads will be filtered to only those with RG tag: 1
  [11:12:20 - Annotate] Getting chrom coordinates
  [11:12:22 - Annotate] Processing chunk with coordinates: MN908947.3:34-29737
  [11:12:22 - BAMFile] Creating pool of 16 BAM file sets.
  Suppress variant 23599

  Lines   total/split/realigned/skipped:    113/0/0/0
  Note: the --sample option not given, applying all records regardless of the genotype
  The site MN908947.3:9344 overlaps with another variant, skipping...
  The site MN908947.3:22577 overlaps with another variant, skipping...
  The site MN908947.3:23604 overlaps with another variant, skipping...
  The site MN908947.3:28877 overlaps with another variant, skipping...
  The site MN908947.3:28881 overlaps with another variant, skipping...
  Applied 108 variants
  /home/epi2melabs/conda/lib/python3.8/site-packages/clint/textui/prompt.py:68: SyntaxWarning: "is not" with a literal. Did you mean "!="?
    if prompt[-1] is not ' ':
  Running: minimap2 -a -x map-ont -t 4 SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.reference.fasta 818566_818566.fastq | samtools view -bS -F 4 - | samtools sort -o 818566.sorted.bam -
  Running: samtools index 818566.sorted.bam
  Running: align_trim 818566.sorted.bam SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.scheme.bed  --normalise 200 --start --report 818566.alignreport.txt 2> 818566.alignreport.er | samtools sort -T 818566 - -o 818566.trimmed.rg.sorted.bam
  Running: align_trim 818566.sorted.bam SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.scheme.bed  --normalise 200 --report 818566.alignreport.txt 2> 818566.alignreport.er | samtools sort -T 818566 - -o 818566.primertrimmed.rg.sorted.bam
  Running: samtools index 818566.trimmed.rg.sorted.bam
  Running: samtools index 818566.primertrimmed.rg.sorted.bam
  Running: medaka consensus --model r1041_e82_400bps_fast_g632 --threads 4Running hacked up minion.py
   --chunk_len 800 --chunk_ovlp 400 --RG 2 818566.trimmed.rg.sorted.bam 818566.2.hdf
  Running: medaka variant --gvcf SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.reference.fasta 818566.2.hdf 818566.2.vcf
  Running: medaka tools annotate --pad 25 --RG 2 818566.2.vcf SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.reference.fasta 818566.trimmed.rg.sorted.bam tmp.medaka-annotate.vcf
  Running: mv tmp.medaka-annotate.vcf 818566.2.vcf
  Running: medaka consensus --model r1041_e82_400bps_fast_g632 --threads 4 --chunk_len 800 --chunk_ovlp 400 --RG 1 818566.trimmed.rg.sorted.bam 818566.1.hdf
  Running: medaka variant --gvcf SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.reference.fasta 818566.1.hdf 818566.1.vcf
  Running: medaka tools annotate --pad 25 --RG 1 818566.1.vcf SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.reference.fasta 818566.trimmed.rg.sorted.bam tmp.medaka-annotate.vcf
  Running: mv tmp.medaka-annotate.vcf 818566.1.vcf
  Running: artic_vcf_merge 818566 SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.scheme.bed 2> 818566.primersitereport.txt 2:818566.2.vcf 1:818566.1.vcf
  Running: bgzip -f 818566.merged.vcf
  Running: tabix -p vcf 818566.merged.vcf.gz
  Running: bcftools filter -e "ALT='.'" 818566.merged.vcf.gz | bgzip > tmp.vcf.gz
  Running: mv 818566.merged.vcf.gz 818566.merged.gvcf.vcf.gz
  Running: mv 818566.merged.vcf.gz.tbi 818566.merged.gvcf.vcf.gz.tbi
  Running: mv tmp.vcf.gz 818566.merged.vcf.gz
  Running: tabix -p vcf 818566.merged.vcf.gz
  Running: artic-tools check_vcf --summaryOut 818566.vcfreport.txt 818566.merged.vcf.gz SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.scheme.bed 2> 818566.vcfcheck.log
  Running: artic_vcf_filter --medaka --min-depth 20 --min-qual 20 --nanopolish-qual-cov-ratio 3.0 818566.merged.vcf.gz 818566.pass.vcf 818566.fail.vcf
  Running: artic_make_depth_mask --depth 20 SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.reference.fasta 818566.primertrimmed.rg.sorted.bam 818566.coverage_mask.txt
  Running: artic_mask SARS-CoV-2/Midnight-IDT/V1/SARS-CoV-2.reference.fasta 818566.coverage_mask.txt 818566.fail.vcf 818566.preconsensus.fasta
  Running: bcftools norm --check-ref x --fasta-ref 818566.preconsensus.fasta -O z -o 818566.pass.vcf.gz 818566.pass.vcf
  Running: tabix -p vcf 818566.pass.vcf.gz
  Running: bcftools consensus -f 818566.preconsensus.fasta 818566.pass.vcf.gz -m 818566.coverage_mask.txt -o 818566.consensus.fasta
  Running: artic_fasta_header 818566.consensus.fasta "818566/ARTIC/medaka"
  sed: couldn't open temporary file ./sedUOF7KB: Permission denied

Work dir:
  /Users/agaliana/Documents/Analisis_temporal/work/c4/88ccc510dbfda8da992a54fd7191b8

Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line

Application activity log entry

No response

mattdmem commented 1 year ago

Hi @Bioloko,

To help me troubleshoot this problem - could you let me know if you're on a Mac with an "M" (ARM) processor?

Has the workflow run previously on the machine you're using, has something changed?

Thanks

Matt

Bioloko commented 1 year ago

i Matt,

Thank you for your response. No, its an intel Mac (3,2 GHz Intel Xeon W 16 nucleus).

Best

mattdmem commented 1 year ago

Thanks @Bioloko - and have you successfully run the workflow previously or was this your 1st attempt?

Bioloko commented 1 year ago

Sorry i forgot to answer the second question: Im using this worflow more than a year without problems. But since last week started with problems and i decided to update docker and pull the pipeline and got this message and the pipeline sotopped working :

epi2me-labs/wf-artic contains uncommitted changes -- cannot pull from repository

mattdmem commented 1 year ago

Ok let's get you a fresh repository and go from there. You should have the following directory:

~/.nextflow/assets/epi2me-labs/wf-artic

Delete it and try your nextflow command again. You could either run nextflow pull or you could just execute your command above to run the workflow and nextflow will do a pull anyway.

Bioloko commented 1 year ago

Hi Matt,

Sorry but i cant find any directory as you tell me (~/.nextflow/assets/epi2me-labs/wf-artic), even i cant find any with the name of epi2me-labs. If i remember well when i installed this pipeline i did a conda environment called wf-artic where nextflow was installed and no more i did (docker was installed before for other pipelines i was using).

mattdmem commented 1 year ago

Hi @Bioloko,

May I suggest that we try running the workflow through the EPI2ME labs application?

https://ont-exd-int-s3-euwst1-epi2me-labs.s3.amazonaws.com/installers/EPI2ME-x86-5.1.2-x64.pkg

Download and install and lets see if we can get wf-artic running in the app,

Matt

Bioloko commented 1 year ago

Hi Matt,

I run the workflow with one sample with EPI2ME as you mentioned and got the same error, now i can attach you the nextflow.log .

Best

nextflow.log

mattdmem commented 1 year ago

Hi @Bioloko - this is an issue with sed - I'm working on a fix now, we'll release a new version ASAP.

mattdmem commented 1 year ago

@Bioloko v0.3.32 is just releasing now - should be here soon - let me know if this fixes your issue with sed.