sarek ERROR ~ Cannot invoke method startsWith() on null object

ERROR ~ Cannot invoke method startsWith() on null object

Open adbeggs opened this issue 1 year ago • 6 comments

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

Jun 26 '23 07:06 adbeggs

Can you share the content of nextflow-bear.config too?

Jun 26 '23 07:06 maxulysse

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'
}

Jun 26 '23 07:06 adbeggs

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?

Jun 26 '23 07:06 adbeggs

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

Jul 01 '23 16:07 FriederikeHanssen

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

Oct 13 '23 06:10 FriederikeHanssen

@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.

Feb 22 '24 00:02 SpikyClip

sarek sarek copied to clipboard

ERROR ~ Cannot invoke method startsWith() on null object

Description of the bug

Command used and terminal output

Relevant files

System information

sarek
sarek copied to clipboard