ERROR ~ ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!

[avanthikav]

Description of the bug

Hello,

I am having trouble with the sample input file. I have .csv file with correct file names and format as described in the pipeline page (also attached here). I get the error: ERROR ~ ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist! when I run

nextflow run nf-core/cutandrun -r 3.2.2 --input /Users/avanthika/Documents/07252024_Hank_CUTnRUN_n60-425835535/H3K4Me3/metadata.csv --outdir ./results --genome mm10 -profile docker --max_memory 6GB

Staging foreign file: s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf
Staging foreign file: s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/WholeGenomeFasta/genome.fa
Staging foreign file: s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa
WARN: There's no process matching config selector: NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_.*
WARN: There's no process matching config selector: .PREPARE_GENOME:GUNZIP_.
ERROR ~ ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!
07252024_CHA1_S1_L001_R1_001.fastq.gz

Docker is running, I've checked the file names. I am new user and not exactly sure what I am missing here. Kindly let me know any suggestions on how to proceed.

Thank you!
Avanthika

Command used and terminal output

(nf-core) avanthika@PHS025541 ~ % nextflow run nf-core/cutandrun -r 3.2.2 --input /Users/avanthika/Documents/07252024_Hank_CUTnRUN_n60-425835535/H3K4Me3/metadata.csv --outdir ./results --genome mm10 -profile docker --max_memory 6GB

 N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/nf-core/cutandrun` [hopeful_coulomb] DSL2 - revision: 6e1125d4fe [3.2.2]

WARN: =============================================================================
  When using UCSC assemblies the 'gene_biotype' field is absent from the GTF file.
  Biotype QC will be skipped to circumvent the issue below:
  https://github.com/nf-core/rnaseq/issues/460

  If you would like to use the soft-masked Ensembl assembly instead please see:
  https://github.com/nf-core/rnaseq/issues/159#issuecomment-501184312
===================================================================================
WARN: =========================================================================================================
  dt_calc_all_matrix is switched on which will calculate a deeptools matrix for all samples.
  If you have a large sample count, this may affect pipeline performance and result in errors.
  Set this option to false to disable this feature and only calculate deeptools heatmaps for single samples
===============================================================================================================


------------------------------------------------------
                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  nf-core/cutandrun v3.2.2-g6e1125d
------------------------------------------------------
Core Nextflow options
  revision           : 3.2.2
  runName            : hopeful_coulomb
  containerEngine    : docker
  launchDir          : /Users/avanthika
  workDir            : /Users/avanthika/work
  projectDir         : /Users/avanthika/.nextflow/assets/nf-core/cutandrun
  userName           : avanthika
  profile            : docker
  configFiles        :

Input/output options
  input              : /Users/avanthika/Documents/07252024_Hank_CUTnRUN_n60-425835535/H3K4Me3/metadata.csv

Reference data options
  genome             : mm10
  bowtie2            : s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/Bowtie2Index/
  gtf                : s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf
  spikein_bowtie2    : s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/Bowtie2Index/
  spikein_fasta      : s3://ngi-igenomes/igenomes//Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/WholeGenomeFasta/genome.fa
  fasta              : s3://ngi-igenomes/igenomes//Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa

Pipeline Options
  macs_gsize         : 2700000000.0
  replicate_threshold: 1.0

Max job request options
  max_memory         : 6GB

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

  https://doi.org/10.5281/zenodo.5653535

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

* Software dependencies
  https://github.com/nf-core/cutandrun/blob/master/CITATIONS.md

WARN: =============================================================================
  No genome blacklist file specified, switching to dummy empty file...
===================================================================================
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GTF2BED                                                              -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GTF2BED                                                              -
executor >  local (1)
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GTF2BED                                                              -
executor >  local (1)
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GTF2BED                                                              -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT                                             -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SAMTOOLS_FAIDX                                                       -
executor >  local (1)
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:GTF2BED                                                              -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:ANNOTATION_BEDTOOLS_SORT                                             -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TABIX_BGZIPTABIX                                                     -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SAMTOOLS_FAIDX                                                       -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:TARGET_CHROMSIZES                                                    -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:SPIKEIN_CHROMSIZES                                                   -
[3a/8e29c7] NFCORE_CUTANDRUN:CUTANDRUN:INPUT_CHECK:SAMPLESHEET_CHECK (metadata.csv)                                        [  0%] 0 of 1
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:CAT_FASTQ                                                                           -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:FASTQC                                                            -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:FASTQC_TRIMGALORE:TRIMGALORE                                                        -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_TARGET_ALIGN                                                  -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BOWTIE2_SPIKEIN_ALIGN                                                 -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_SORT                                 -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:SAMTOOLS_INDEX                                -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS             -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT          -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS:BAM_STATS_SAMTOOLS:SAMTOOLS_IDXSTATS          -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_SORT                         -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:SAMTOOLS_INDEX                        -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_STATS     -
[-        ] NFCORE_CUTANDRUN:CUTANDRUN:ALIGN_BOWTIE2:BAM_SORT_STATS_SAMTOOLS_SPIKEIN:BAM_STATS_SAMTOOLS:SAMTOOLS_FLAGSTAT  -
Plus 59 more processes waiting for tasks…
Staging foreign file: s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Annotation/Genes/genes.gtf
Staging foreign file: s3://ngi-igenomes/igenomes/Escherichia_coli_K_12_MG1655/NCBI/2001-10-15/Sequence/WholeGenomeFasta/genome.fa
Staging foreign file: s3://ngi-igenomes/igenomes/Mus_musculus/UCSC/mm10/Sequence/WholeGenomeFasta/genome.fa
WARN: There's no process matching config selector: NFCORE_CUTANDRUN:CUTANDRUN:PREPARE_GENOME:UNTAR_.*
WARN: There's no process matching config selector: .*PREPARE_GENOME:GUNZIP_.*
ERROR ~ ERROR: Please check input samplesheet -> Read 1 FastQ file does not exist!
07252024_CHA1_S1_L001_R1_001.fastq.gz

 -- Check '.nextflow.log' file for details



(nf-core) avanthika@PHS025541 ~ % nextflow run hello


 N E X T F L O W   ~  version 24.04.4

Launching `https://github.com/nextflow-io/hello` [irreverent_keller] DSL2 - revision: afff16a9b4 [master]

executor >  local (4)
[6a/c595c6] sayHello (1) [100%] 4 of 4 ✔
Hola world!

Hello world!

Ciao world!

Bonjour world!

Relevant files

metadata.csv

Files in the folder: /Users/avanthika/Documents/07252024_Hank_CUTnRUN_n60-425835535/

07252024_CHA1_S1_L001_R1_001.fastq.gz
07252024_CHA1_S1_L001_R2_001.fastq.gz
07252024_CHA2_S2_L001_R1_001.fastq.gz
07252024_CHA2_S2_L001_R2_001.fastq.gz
07252024_CHA3_S3_L001_R1_001.fastq.gz
07252024_CHA3_S3_L001_R2_001.fastq.gz

System information

Nextflow version - version 24.04.4
Hardware - Mac
Executor - local
Container engine - docker
OS - MacOS 14.5 (23F79)
Version of nf-core/cutandrun - v3.2.2

[chris-cheshire]

Hi, its probably to do with the path of your fastq files. Are they in the same directory as where you are running the pipeline from? Its best to use absoulate paths when pointing towards input data as you should keep it seperate from your pipeline run directories anyway.