ERROR: [ATAC] FASTQ read files are present in the input directory, but the name format is incorrect. Check parameters and/or see documentation for file naming guidelines.

[hariesramdhani]

Hello,

Thank you for the software. We're getting this error ERROR: [ATAC] FASTQ read files are present in the input directory, but the name format is incorrect. Check parameters and/or see documentation for file naming guidelines. when we're trying to run the command below

nextflow run BioRadOpenSource/omnition -params-file <HOME_DIR>/MutationProject/renamed_srr/atac_new.yaml -profile standard --force

This is how the <HOME_DIR>/MutationProject/renamed_srr/atac_new.yaml looks like

atac:
  input: "<HOME_DIR>/MutationProject/original_srr/new_folder"
  output: "<HOME_DIR>/MutationProject/original_srr/new_workflow_results"
  workflow: "full"
  reference:
    directory: "<HOME_DIR>/MutationProject/references/mouse"
    fasta: "<HOME_DIR>/MutationProject/references/mouse/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz"
    gtf: "<HOME_DIR>/MutationProject/references/mouse/Mus_musculus.GRCm39.106.gtf.gz"
    blocklist: "<HOME_DIR>/MutationProject/references/mouse/mm10-blocklist.bed"

These are the FASTQs inside of the input folder, they're supposed to be already in the correct naming convention

(OmnitionEnv) [r02cb24@maxlogin1(maxwell) new_workflow_results]$ ls <HOME_DIR>/MutationProject/original_srr/new_folder
ControlRep1GmpPos_S1_L001_R1_001.fastq.gz          ControlRep2LinNegCd11bPos_S1_L001_R1_001.fastq.gz  KORep2GmpPos_S1_L001_R1_001.fastq.gz
ControlRep1GmpPos_S1_L001_R2_001.fastq.gz          ControlRep2LinNegCd11bPos_S1_L001_R2_001.fastq.gz  KORep2GmpPos_S1_L001_R2_001.fastq.gz
ControlRep1LinNegCd11bPos_S1_L001_R1_001.fastq.gz  KORep1GmpPos_S1_L001_R1_001.fastq.gz               KORep2LinNegCd11bPos_S1_L001_R1_001.fastq.gz
ControlRep1LinNegCd11bPos_S1_L001_R2_001.fastq.gz  KORep1GmpPos_S1_L001_R2_001.fastq.gz               KORep2LinNegCd11bPos_S1_L001_R2_001.fastq.gz
ControlRep2GmpPos_S1_L001_R1_001.fastq.gz          KORep1LinNegCd11bPos_S1_L001_R1_001.fastq.gz
ControlRep2GmpPos_S1_L001_R2_001.fastq.gz          KORep1LinNegCd11bPos_S1_L001_R2_001.fastq.gz

Would appreciate any help on this, thanks in advance.

[Spencer-Cesar]

Hello!

Could you try the paths without the use of <HOME_DIR> in any of them?
Also what version of nextflow are you using?

[hariesramdhani]

Hello,

Thanks for the help. Sorry, I’m using the full path when running it, the <HOME_DIR> is only for the purpose of creating this issue. The Nextflow version is 22.04.0.

[Spencer-Cesar]

Could you try nextflow version v23.10.1 and let me know if you get the same error?

[CalumB96]

Hi @Spencer-Cesar I am working with @hariesramdhani and we have exactly the same error using Nextflow version 23.10.1:

$ nextflow -v
nextflow version 23.10.1.5891

As a simple example of the error, I have renamed the FASTQ files as follows:

• SampleName_S1_L001_R1_001.fastq.gz
• SampleName_S1_L001_R2_001.fastq.gz

The returned error in the log file is :

ERROR ~ ERROR: [ATAC] FASTQ read files are present in the input directory, but the name format is incorrect. Check parameters and/or see documentation for file naming guidelines.

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

Thanks for your help.

[Spencer-Cesar]

Hello @CalumB96!

Could you post the contents of your yaml file, run command, and the contents of the input directory?

Thanks!

[CalumB96]

Hi @Spencer-Cesar

The Yaml file is:

$ cat atac_new.yaml atac: workflow: "full" input: "<HOME_DIR>/MutationProject/original_srr/new_folder/fastq.dir" reference: directory: "<HOME_DIR>/MutationProject/references/mouse" fasta: "<HOME_DIR>/MutationProject/references/mouse/Mus_musculus.GRCm39.dna.primary_assembly.fa.gz" gtf: "<HOME_DIR>/MutationProject/references/mouse/Mus_musculus.GRCm39.106.gtf.gz" blocklist: "<HOME_DIR>/MutationProject/references/mouse/mm10-blocklist.bed"
Run command:

#! /usr/bin/bash

nextflow run BioRadOpenSource/omnition \
   -params-file <HOME_DIR>/MutationProject/original_srr/new_folder/atac_new.yaml \
   -profile standard --force

And the input directory:

$ cd new_folder/fastq.dir
[<HOME_DIR>/original_srr/new_folder/fastq.dir]$ ls
SampleName_S1_L001_R1_001.fastq.gz  SampleName_S1_L001_R2_001.fastq.gz

Edit:
The sample data were downloaded from "https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA944632&o=acc_s%3Aa"
We have renamed the sample SRR23860411 to the above and split based on the reads.
Thanks in advance!

[pschnepp]

Hi @CalumB96 ,

Did you ever find a solution to your issue? I can't see where the fastq files are named incorrectly. When I use the sample names in your example, it runs correctly for me. Is there any other files in the folder containing the fastq files? Nothing else can be in that folder but fastq files. Including the yaml file. I recommend saving the yaml file one folder up from the fastq folder.

Thanks