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Problem with intervals file #1690

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Eduardo-Auer opened this issue Oct 20, 2024 · 3 comments
Open

Problem with intervals file #1690

Eduardo-Auer opened this issue Oct 20, 2024 · 3 comments

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@Eduardo-Auer
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Description of the bug

I think the problem might be the format (using .list or .bed formats) that I used to use in intervals parameter and I do not know the correct format (even after reading the help in sarek page). I need to use these intervals because my data are WES and I created an bed file from Illumina Exome Targeted Regions bed file. I will upload the files (my google drive link) that I used as intervals (exome_intervals.list, exome_intervals.bed) and the Illumina Exome Targeted Regions bed file (Illumina_Exome_TargetedRegions_v1.2.hg38.bed). Could someone help me?

Command used

nextflow run nf-core/sarek -r 3.4.4 -profile conda --input /home/eduardo/gargantua/samplesheet.csv -work-dir /home/eduardo/gargantua/temp --step mapping --aligner bwa-mem2 --concatenate_vcfs false --joint_germline false --fasta /home/eduardo/sequencing_resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna --fasta_fai /home/eduardo/sequencing_resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai --wes --intervals /home/eduardo/gargantua/exome_intervals.list --dbsnp /home/eduardo/sequencing_resources/GRCh38.dbSNP156_chr_included.vcf.gz --dbsnp_tbi /home/eduardo/sequencing_resources/GRCh38.dbSNP156_chr_included.vcf.gz.tbi --known_indels /home/eduardo/sequencing_resources/Homo_sapiens_assembly38.known_indels.vcf.gz,/home/eduardo/sequencing_resources/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz --known_indels_tbi /home/eduardo/sequencing_resources/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi,/home/eduardo/sequencing_resources/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi --skip_tools bcftools,multiqc,fastqc --genome null --igenomes_ignore --outdir home/eduardo/gargantua/results/

Terminal output

This example is for only .list file and the same error happens with .bed file

[](N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/nf-core/sarek` [exotic_solvay] DSL2 - revision: 5cc30494a6 [3.4.4]

WARN: Access to undefined parameter `monochromeLogs` -- Initialise it to a default value eg. `params.monochromeLogs = some_value`


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
      ____
    .´ _  `.
   /  |\`-_ \      __        __   ___     
  |   | \  `-|    |__`  /\  |__) |__  |__/
   \ |   \  /     .__| /¯¯\ |  \ |___ |  \
    `|____\´

  nf-core/sarek v3.4.4-g5cc3049
------------------------------------------------------
Core Nextflow options
  revision             : 3.4.4
  runName              : exotic_solvay
  launchDir            : /home/eduardo/gargantua
  workDir              : /home/eduardo/gargantua/temp
  projectDir           : /home/eduardo/.nextflow/assets/nf-core/sarek
  userName             : eduardo
  profile              : conda
  configFiles          : 

Input/output options
  input                : /home/eduardo/gargantua/samplesheet.csv
  outdir               : home/eduardo/gargantua/results/

Main options
  wes                  : true
  intervals            : /home/eduardo/gargantua/exome_intervals.list
  skip_tools           : bcftools,multiqc,fastqc

Preprocessing
  aligner              : bwa-mem2

Reference genome options
  genome               : null
  dbsnp                : /home/eduardo/sequencing_resources/GRCh38.dbSNP156_chr_included.vcf.gz
  dbsnp_tbi            : /home/eduardo/sequencing_resources/GRCh38.dbSNP156_chr_included.vcf.gz.tbi
  fasta                : /home/eduardo/sequencing_resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna
  fasta_fai            : /home/eduardo/sequencing_resources/GCA_000001405.15_GRCh38_no_alt_analysis_set.fna.fai
  known_indels         : /home/eduardo/sequencing_resources/Homo_sapiens_assembly38.known_indels.vcf.gz,/home/eduardo/sequencing_resources/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  known_indels_tbi     : /home/eduardo/sequencing_resources/Homo_sapiens_assembly38.known_indels.vcf.gz.tbi,/home/eduardo/sequencing_resources/Mills_and_1000G_gold_standard.indels.hg38.vcf.gz.tbi
  igenomes_ignore      : true

Generic options
  validationLenientMode: true

!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------
If you use nf-core/sarek for your analysis please cite:

* The pipeline
  https://doi.org/10.12688/f1000research.16665.2
  https://doi.org/10.1093/nargab/lqae031
  https://doi.org/10.5281/zenodo.3476425

* The nf-core framework
  https://doi.org/10.1038/s41587-020-0439-x

* Software dependencies
  https://github.com/nf-core/sarek/blob/master/CITATIONS.md
------------------------------------------------------
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE                                  -
[-        ] NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY                     -
[-        ] NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN                                  -
[-        ] NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX                                     -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS                         -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP                                        -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE                            -
executor >  local (1)
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE                                  -
[-        ] NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY                     -
[-        ] NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN                                  -
[-        ] NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX                                     -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS                         -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP                                        -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE                            -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS                                   -
executor >  local (3)
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE                                  -
[-        ] NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY                     -
[-        ] NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN                                  -
[-        ] NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX                                     -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS                         -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP                                        -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE                            -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS                                   -
executor >  local (4)
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE                                  -
[-        ] NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY                     -
[-        ] NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN                                  -
executor >  local (4)
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE                                  -
[-        ] NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY                     -
[-        ] NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN                                  -
executor >  local (4)
executor >  local (5)
executor >  local (5)
executor >  local (5)
executor >  local (5)
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX                                                                    -
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX                                                                    -
[-        ] NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE                                                                -
[6c/b0ee11] NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY (GCA_000001405.15_GRCh38_no_alt_analysis_set.fna) [100%] 1 of 1 ✔
[-        ] NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN                                                                -
[-        ] NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX                                                                   -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS                                                       -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP                                                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE                                                          -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS                                                                 -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS                                                               -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_PON                                                                        -
[-        ] NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED                                                          -
[-        ] NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT                                               -
[-        ] NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED                                            -
[-        ] NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_FQ_PAIR                                                              -
[-        ] NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R1_FQ                                                                -
[-        ] NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R2_FQ                                                                -
[-        ] NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP                                                 -
[-        ] NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP                                             -
[4f/3e1b79] NFCORE_SAREK:SAREK:FASTP (DAC021-L2)                                                                         [100%] 4 of 4 ✔
Plus 24 more processes waiting for tasks…
ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED'

Caused by:
  Failed to create Conda environment
    command: conda env create --prefix /home/eduardo/gargantua/temp/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27 --file /home/eduardo/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml
    status : 1
    message:
      Channels:
executor >  local (5)
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM1_INDEX                                                                    -
[-        ] NFCORE_SAREK:PREPARE_GENOME:BWAMEM2_INDEX                                                                    -
[-        ] NFCORE_SAREK:PREPARE_GENOME:DRAGMAP_HASHTABLE                                                                -
[6c/b0ee11] NFCORE_SAREK:PREPARE_GENOME:GATK4_CREATESEQUENCEDICTIONARY (GCA_000001405.15_GRCh38_no_alt_analysis_set.fna) [100%] 1 of 1 ✔
[-        ] NFCORE_SAREK:PREPARE_GENOME:MSISENSORPRO_SCAN                                                                -
[-        ] NFCORE_SAREK:PREPARE_GENOME:SAMTOOLS_FAIDX                                                                   -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_BCFTOOLS_ANNOTATIONS                                                       -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_DBSNP                                                                      -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_GERMLINE_RESOURCE                                                          -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_SNPS                                                                 -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_KNOWN_INDELS                                                               -
[-        ] NFCORE_SAREK:PREPARE_GENOME:TABIX_PON                                                                        -
[-        ] NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED                                                          -
[-        ] NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_SPLIT                                               -
[-        ] NFCORE_SAREK:PREPARE_INTERVALS:TABIX_BGZIPTABIX_INTERVAL_COMBINED                                            -
[-        ] NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_FQ_PAIR                                                              -
[-        ] NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R1_FQ                                                                -
[-        ] NFCORE_SAREK:SAREK:SPRING_DECOMPRESS_TO_R2_FQ                                                                -
[-        ] NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_MAP_MAP                                                 -
[-        ] NFCORE_SAREK:SAREK:CONVERT_FASTQ_INPUT:SAMTOOLS_VIEW_UNMAP_UNMAP                                             -
[4f/3e1b79] NFCORE_SAREK:SAREK:FASTP (DAC021-L2)                                                                         [100%] 4 of 4 ✔
Plus 24 more processes waiting for tasks…
ERROR ~ Error executing process > 'NFCORE_SAREK:PREPARE_INTERVALS:CREATE_INTERVALS_BED'

Caused by:
  Failed to create Conda environment
    command: conda env create --prefix /home/eduardo/gargantua/temp/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27 --file /home/eduardo/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml
    status : 1
    message:
      Channels:
       - conda-forge
       - bioconda
       - defaults
       - anaconda
      Platform: linux-64
      Collecting package metadata (repodata.json): ...working... done
      Solving environment: ...working... failed
      Channels:
       - conda-forge
       - bioconda
       - defaults
       - anaconda
      Platform: linux-64
      Collecting package metadata (repodata.json): ...working... done
      Solving environment: ...working... failed
      
      LibMambaUnsatisfiableError: Encountered problems while solving:
        - package gawk-5.1.0-h7b6447c_0 is excluded by strict repo priority



 -- Check '.nextflow.log' file for details
ERROR ~ Pipeline failed. Please refer to troubleshooting docs: https://nf-co.re/docs/usage/troubleshooting

 -- Check '.nextflow.log' file for details
-[nf-core/sarek] Pipeline completed with errors-)

Relevant files

Google drive files

System information

Ubuntu 24.04.1 LTS
mamba 1.5.8
conda 24.3.0
nextflow 24.04.4
sarek v3.4.4-g5cc3049
@FriederikeHanssen
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Contributor

I don't think this is an issue with the bed file itself but more an issue with conda. Do you have to run it with conda or are you able to use a container engine?

@Eduardo-Auer
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Author

Thank you for your response! Currently, I am confortable with mamba/conda because I can understand better and use without any issue until now. Before, I tried using/installing docker in my Ubuntu and I had so much problems that I gave up using docker. Is there any solution to use in mamba/conda environment?

@FriederikeHanssen
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Contributor

Not sure, there seems to be an issue with resolving the conda environment on your system. You could try creating it manually to better see what is going on:

Failed to create Conda environment
    command: conda env create --prefix /home/eduardo/gargantua/temp/conda/gawk-f9b4f646bf1b67e52890543d27cb2f27 --file /home/eduardo/.nextflow/assets/nf-core/sarek/./subworkflows/local/prepare_intervals/../../../modules/local/create_intervals_bed/environment.yml

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@FriederikeHanssen @Eduardo-Auer