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ERROR ~ Cannot invoke method startsWith() on null object #1134

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adbeggs opened this issue Jun 26, 2023 · 7 comments
Open

ERROR ~ Cannot invoke method startsWith() on null object #1134

adbeggs opened this issue Jun 26, 2023 · 7 comments
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bug Something isn't working moreinfo

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@adbeggs
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adbeggs commented Jun 26, 2023

Description of the bug

I've just upgraded sarek from 3.14 to the latest version. When I run it now it crashes out almost immediately with:

ERROR ~ Cannot invoke method startsWith() on null object

Command used and terminal output

nextflow run nf-core/sarek -config ~/nextflow-bear.config --input samplesheet.csv --outdir results/ --genome GATK.GRCh38 -resume --tools strelka,manta,tiddit,cnvkit,vep --umi_read_structure "+T 18M11S+T"

N E X T F L O W  ~  version 23.04.2
Launching `https://github.com/nf-core/sarek` [stupefied_carlsson] DSL2 - revision: ed1cc84993 [master]


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

  nf-core/sarek v3.2.3-ged1cc84
------------------------------------------------------
Core Nextflow options
  revision                  : master
  runName                   : stupefied_carlsson
  containerEngine           : singularity
  launchDir                 : /rds/projects/b/beggsa-hpbcancer/BILCAP3/panelseq/DNA
  workDir                   : /rds/projects/b/beggsa-hpbcancer/BILCAP3/panelseq/DNA/work
  projectDir                : /rds/homes/b/beggsa/.nextflow/assets/nf-core/sarek
  userName                  : beggsa
  profile                   : standard
  configFiles               : /rds/homes/b/beggsa/.nextflow/assets/nf-core/sarek/nextflow.config, /rds/homes/b/beggsa/nextflow-bear.config

Input/output options
  input                     : samplesheet.csv
  outdir                    : results/

Main options
  intervals                 : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/intervals/wgs_calling_regions_noseconds.hg38.bed
  tools                     : strelka,manta,tiddit,cnvkit,vep

FASTQ Preprocessing
  umi_read_structure        : +T 18M11S+T

Variant Calling
  cf_chrom_len              : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/Length/Homo_sapiens_assembly38.len
  pon                       : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz
  pon_tbi                   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000g_pon.hg38.vcf.gz.tbi

Reference genome options
  ascat_genome              : hg38
  ascat_alleles             : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_alleles_hg38.zip
  ascat_loci                : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/G1000_loci_hg38.zip
  ascat_loci_gc             : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/GC_G1000_hg38.zip
  ascat_loci_rt             : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/ASCAT/RT_G1000_hg38.zip
  bwa                       : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAIndex/
  bwamem2                   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/BWAmem2Index/
  chr_dir                   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/Chromosomes
  dbsnp                     : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz
  dbsnp_tbi                 : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/dbsnp_146.hg38.vcf.gz.tbi
  dbsnp_vqsr                : --resource:dbsnp,known=false,training=true,truth=false,prior=2.0 dbsnp_146.hg38.vcf.gz
  dict                      : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.dict
  dragmap                   : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/dragmap/
  fasta                     : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta
  fasta_fai                 : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Sequence/WholeGenomeFasta/Homo_sapiens_assembly38.fasta.fai
  germline_resource         : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz
  germline_resource_tbi     : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/af-only-gnomad.hg38.vcf.gz.tbi
  known_indels              : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz
  known_indels_tbi          : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/{Mills_and_1000G_gold_standard.indels.hg38,beta/Homo_sapiens_assembly38.known_indels}.vcf.gz.tbi
  known_indels_vqsr         : --resource:gatk,known=false,training=true,truth=true,prior=10.0 Homo_sapiens_assembly38.known_indels.vcf.gz --resource:mills,known=false,training=true,truth=true,prior=10.0 Mills_and_1000G_gold_standard.indels.hg38.vcf.gz
  known_snps                : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz
  known_snps_tbi            : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/GATKBundle/1000G_omni2.5.hg38.vcf.gz.tbi
  known_snps_vqsr           : --resource:1000G,known=false,training=true,truth=true,prior=10.0 1000G_omni2.5.hg38.vcf.gz
  mappability               : s3://ngi-igenomes/igenomes/Homo_sapiens/GATK/GRCh38/Annotation/Control-FREEC/out100m2_hg38.gem
  snpeff_db                 : 105
  snpeff_genome             : GRCh38
  snpeff_version            : 5.1
  vep_genome                : GRCh38
  vep_species               : homo_sapiens
  vep_cache_version         : 108
  vep_version               : 108.2
  igenomes_base             : s3://ngi-igenomes/igenomes

Institutional config options
  config_profile_description: The Francis Crick Institute CAMP HPC cluster profile provided by nf-core/configs.
  config_profile_contact    : Chris Cheshire (@chris-cheshire)
  config_profile_url        : https://www.crick.ac.uk/research/platforms-and-facilities/scientific-computing/technologies

Max job request options
  max_cpus                  : 32
  max_memory                : 128 GB
  max_time                  : 96.h

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

* The pipeline
  https://doi.org/10.12688/f1000research.16665.2
  https://doi.org/10.5281/zenodo.4468605

* 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
------------------------------------------------------
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -

[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
[-        ] process > NFCORE_SAREK:SAREK:PREPARE_... -
WARN: There's no process matching config selector: NFCORE_SAREK:SAREK:CRAM_QC_NO_MD:SAMTOOLS_STATS -- Did you mean: NFCORE_SAREK:SAREK:CRAM_QC_RECAL:SAMTOOLS_STATS?
ERROR ~ Cannot invoke method startsWith() on null object

 -- Check script '/rds/homes/b/beggsa/.nextflow/assets/nf-core/sarek/./workflows/sarek.nf' at line: 1356 or see '.nextflow.log' file for more details
-[nf-core/sarek] Pipeline completed with errors-

Relevant files

samplesheet.csv

System information

nextflow version 23.04.2.5870
HPOC
Slurm
Singularity
RedHat Enterprise 8.6
@adbeggs adbeggs added the bug Something isn't working label Jun 26, 2023
@maxulysse
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Can you share the content of nextflow-bear.config too?

@adbeggs
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adbeggs commented Jun 26, 2023 •
edited
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Sure:

//Profile config names for nf-core/configs


singularity {
  enabled = true
  autoMounts = true
}

process {
  executor = 'slurm'
}

params {
  max_memory = 128.GB
  max_cpus = 32
  max_time = '96.h'
}

@adbeggs
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adbeggs commented Jun 26, 2023

Hmm I see exactly the same on 3.1.4 when I removed the latest version and download the last version it worked on.. must be the sample sheet but it looks okay to me?

@FriederikeHanssen
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looks weird indeed, can you try by providing the full path to the files as well as removing the last line? It is empty

@FriederikeHanssen
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Please open an issue with the demultiplex pipeline here: https://github.com/nf-core/demultiplex/issues

@SpikyClip
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@adbeggs are any of your fastqs or input files empty? If so that is the cause, or at least, it was in my case. See this issue.

@RafigaM
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RafigaM commented Nov 18, 2024

Dear all, I get the same error. How was that solved before?

Thank you.

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@maxulysse @FriederikeHanssen @adbeggs @RafigaM @SpikyClip