Hi I m getting a weird error where apparently my NA s are no nf-core #bacass

Hi, I’m getting a weird error where apparently my ...

Mark Pampuch

12/11/2024, 11:44 AM

Hi, I’m getting a weird error where apparently my NA’s are not being recognized in my samplesheet it seems.

Not a valid path value: 'NA'

(see thread for details)

Mark Pampuch

12/11/2024, 11:45 AM

samplesheet.tsv

file

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ID  R1  R2  LongFastQ Fast5 GenomeSize
S01_S003  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/01_S003.fastq.gz  NA  NA
S02_S005  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/02_S005.fastq.gz  NA  NA
S03_S006  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/03_S006.fastq.gz  NA  NA
S04_S008  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/04_S008.fastq.gz  NA  NA
S05_S009  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/05_S009.fastq.gz  NA  NA
S06_S011  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/06_S011.fastq.gz  NA  NA
S07_S012  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/07_S012.fastq.gz  NA  NA
S08_S013  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/08_S013.fastq.gz  NA  NA
S09_S028  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/09_S028.fastq.gz  NA  NA
S10_S029  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/10_S029.fastq.gz  NA  NA
S11_S031  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/11_S031.fastq.gz  NA  NA
S12_S045  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/12_S045.fastq.gz  NA  NA
S13_S051  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/13_S051.fastq.gz  NA  NA
S14_kaust071  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/14_kaust071.fastq.gz  NA  NA
S15_kaust066  NA  NA  /biocorelab/BCLCustomers/lauersk/GridION/20241118_P41U1_KSAlib-rapid-barcode/20241118_P41U1_KSAlib-rapid-barcode/20241118_1601_X1_FAX02488_fafcfcf9/processed/fastq/15_kaust066.fastq.gz  NA  NA

My command

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nextflow run nf-core/bacass -r 2.4.0 -c nextflow.config -profile singularity --input samplesheet.tsv --kraken2db /ibex/ai/reference/KSL/kraken2/kraken2_dbs/scripts_download/k2_nt_20230502.tar.gz --kmerfinderdb '/ibex/reference/KSL/kmerfinder/bacteria' --ncbi_assembly_metadata ASSEMBLY-REPORTS/assembly_summary_refseq.txt --outdir outputs/2024-12-11_15-KSA-samples__new-kmer-database

My output

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N E X T F L O W   ~  version 24.04.4
 
Launching `<https://github.com/nf-core/bacass>` [modest_torvalds] DSL2 - revision: be9c064f57 [2.4.0]
 
 
------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/bacass 2.4.0
------------------------------------------------------
Input/output options
  input                 : samplesheet.tsv
  outdir                : outputs/2024-12-11_15-KSA-samples__new-kmer-database
 
Contamination Screening
  kraken2db             : /ibex/ai/reference/KSL/kraken2/kraken2_dbs/scripts_download/k2_nt_20230502.tar.gz
  kmerfinderdb          : /ibex/reference/KSL/kmerfinder/bacteria
  ncbi_assembly_metadata: ASSEMBLY-REPORTS/assembly_summary_refseq.txt
 
Assembly parameters
  canu_mode             : -nanopore
 
Annotation
  dfast_config          : /home/pampum/.nextflow/assets/nf-core/bacass/assets/test_config_dfast.py
 
Core Nextflow options
  revision              : 2.4.0
  runName               : modest_torvalds
  containerEngine       : singularity
  launchDir             : /ibex/user/pampum/2024-11-26_KSA-lib-ONT-assemblies
  workDir               : /ibex/user/pampum/2024-11-26_KSA-lib-ONT-assemblies/work
  projectDir            : /home/pampum/.nextflow/assets/nf-core/bacass
  userName              : pampum
  profile               : singularity
  configFiles           :
 
!! Only displaying parameters that differ from the pipeline defaults !!
------------------------------------------------------* The pipeline
  <https://doi.org/10.5281/zenodo.2669428>
 
* The nf-core framework
    <https://doi.org/10.1038/s41587-020-0439-x>
 
* Software dependencies
    <https://github.com/nf-core/bacass/blob/master/CITATIONS.md>
 
[-        ] NFCORE_BACASS:BACASS:CAT_FASTQ                                      -
[-        ] NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW             -
[-        ] NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP                  -
[-        ] NFCORE_BACASS:BACASS:CAT_FASTQ                                      -
[-        ] NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW             -
[-        ] NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTP                  -
[-        ] NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_TRIM            -
[-        ] NFCORE_BACASS:BACASS:NANOPLOT                                       -
[-        ] NFCORE_BACASS:BACASS:PYCOQC                                         -
[-        ] NFCORE_BACASS:BACASS:UNICYCLER                                      -
[-        ] NFCORE_BACASS:BACASS:KRAKEN2_DB_PREPARATION                         -
[-        ] NFCORE_BACASS:BACASS:KRAKEN2                                        -
[-        ] NFCORE_BACASS:BACASS:KRAKEN2_LONG                                   -
[-        ] NFCORE_BACASS:BACASS:KMERFINDER_SUBWORKFLOW:KMERFINDER              -
[-        ] NFCORE_BACASS:BACASS:KMERFINDER_SUBWORKFLOW:KMERFINDER_SUMMARY      -
[-        ] NFCORE_BACASS:BACASS:KMERFINDER_SUBWORKFLOW:FIND_DOWNLOAD_REFERENCE -
[-        ] NFCORE_BACASS:BACASS:QUAST                                          -
[-        ] NFCORE_BACASS:BACASS:QUAST_BYREFSEQID                               -
[-        ] NFCORE_BACASS:BACASS:GUNZIP                                         -
[-        ] NFCORE_BACASS:BACASS:PROKKA                                         -
[-        ] NFCORE_BACASS:BACASS:MULTIQC_CUSTOM                                 -                                                                      Execution cancelled -- Finishing pending tasks before exit
-[nf-core/bacass] Pipeline completed with errors-                                                                                                      Pulling Singularity image <https://depot.galaxyproject.org/singularity/nanoplot:1.41.6--pyhdfd78af_0> [cache /ibex/user/pampum/2024-11-26_KSA-lib-ONT-assemblies/work/singularity/depot.galaxyproject.org-singularity-nanoplot-1.41.6--pyhdfd78af_0.img]                                                        Pulling Singularity image <https://depot.galaxyproject.org/singularity/ubuntu:20.04> [cache /ibex/user/pampum/2024-11-26_KSA-lib-ONT-assemblies/work/singularity/depot.galaxyproject.org-singularity-ubuntu-20.04.img]
WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /ibex/user/pampum/2024-11-26_KSA-lib-ONT-assemblies/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location
ERROR ~ Error executing process > 'NFCORE_BACASS:BACASS:FASTQ_TRIM_FASTP_FASTQC:FASTQC_RAW (13)'
 
Caused by:
  Not a valid path value: 'NA'
 
 
 
Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
 
-- 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

Daniel Straub

12/17/2024, 1:21 PM

You are attempting to use a short read first assembler (unicycler) without short reads. Sort of intuitive that this will crash. Use a different assembler with https://nf-co.re/bacass/2.4.0/parameters/#assembler

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