fasterq-dump fails due to output file naming error

[dmalzl]

I am currently trying to download a couple of raw sequencing data files using sra-tools prefetch and fasterq-dump. Prefetch works fine but I get a weird error when trying to convert the generated *.sra file to fastq with fasterq-dump. The data is paired-end and the actual path should be /scratch/daniel.malzl/work/aa/7ab6e5d29db7a0352a1f1cd4af2af3/SRX10737613_SRR14385311 but judging by the error message there seems to be some bug in the renaming code because it says the following:

        Error: fasterq-dump cannot create this file: '/scratch/daniel_1.malzl/work/aa/7ab6e5d29db7a0352a1f1cd4af2af3/SRX10737613_SRR14385311'

        Error: fasterq-dump cannot create this file: '/scratch/daniel_2.malzl/work/aa/7ab6e5d29db7a0352a1f1cd4af2af3/SRX10737613_SRR14385311'
spots read      : 174,563,529
reads read      : 349,127,058

=============================================================
An error occurred during processing.
A report was generated into the file '/users/daniel.malzl/ncbi_error_report.txt'.
If the problem persists, you may consider sending the file
to 'sra-tools@ncbi.nlm.nih.gov' for assistance.
=============================================================

fasterq-dump quit with error code 3

so it seems to insert the read1, read2 suffixes into the path causing the path to be invalid.

The version I am using is 3.0.8.

[dmalzl]

the executed command was this

fasterq-dump \
    --split-files --include-technical \
    --threads 6 \
    --outfile SRX10737613_SRR14385311 \
     \
    SRR14385311

[wraetz]

It looks like the tool is confused about the output-file. Try this command: 'fasterq-dump --split-files --include-technical SRR14385311' The --threads 6 is not necessary, it is the default. The --outfile is not neccessary, the tool will create the output-filename from the accession. I think it is confused because you included the experiment in the output-file. It should not be confused about that. I will have to investigate why this happens. In the mean time try the shortened command.

[dmalzl]

Thanks for the swift response and the workaround. I'll try to modify the code of the pipeline I am using. However, to me it looks like the path gets split at the . character somewhen in the process where the _1, _2 suffix is inserted and then concatenated again. So it might be the . confusing it but I try and report back

[wraetz]

by the way... what is the version of fasteq-dump you are using?

[dmalzl]

the version is 3.0.8

[dmalzl]

Just to let you know. This does not occur in version 2.11.0

[drpatelh]

Thanks for reporting @dmalzl ! And thanks for investigating @wraetz 🙏🏽

I have managed to reproduce the issue and the problem is indeed the fact that a . exists in the path where the output files will be written.

1. Defined a Conda environment called env.yml with the dependencies below (you can exclude pigz if you like):

name: sra-tools-3.0.8
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - conda-forge::pigz=2.6
  - bioconda::sra-tools=3.0.8

2. Created the environment

conda env create -f env.yml

3. ✅ Run with a path without a .

mkdir testwithoutdot
cd testwithoutdot

prefetch SRR12848126

fasterq-dump \
        --split-files --include-technical \
        --outfile SRX9315476_SRR12848126 \
        SRR12848126

2024-01-05T11:41:39 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-01-05T11:41:39 prefetch.3.0.8: 1) Downloading 'SRR12848126'...
2024-01-05T11:41:39 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-01-05T11:41:39 prefetch.3.0.8:  Downloading via HTTPS...
2024-01-05T11:41:40 prefetch.3.0.8:  HTTPS download succeed
2024-01-05T11:41:40 prefetch.3.0.8:  'SRR12848126' is valid
2024-01-05T11:41:40 prefetch.3.0.8: 1) 'SRR12848126' was downloaded successfully
2024-01-05T11:41:41 prefetch.3.0.8: 'SRR12848126' has 1 unresolved dependency
2024-01-05T11:41:41 prefetch.3.0.8: 2) Downloading 'ncbi-acc:NC_000069.6?vdb-ctx=refseq'...
2024-01-05T11:41:41 prefetch.3.0.8:  Downloading via HTTPS...
2024-01-05T11:41:43 prefetch.3.0.8:  HTTPS download succeed
2024-01-05T11:41:43 prefetch.3.0.8: 2) 'ncbi-acc:NC_000069.6?vdb-ctx=refseq' was downloaded successfully
spots read      : 1,517
reads read      : 3,034
reads written   : 2,982

4. :x: Run with a path that contains a .

mkdir test.withdot
cd test.withdot

prefetch SRR12848126

fasterq-dump \
        --split-files --include-technical \
        --outfile SRX9315476_SRR12848126 \
        SRR12848126

2024-01-05T11:37:35 prefetch.3.0.8: Current preference is set to retrieve SRA Normalized Format files with full base quality scores.
2024-01-05T11:37:35 prefetch.3.0.8: 1) Downloading 'SRR12848126'...
2024-01-05T11:37:35 prefetch.3.0.8: SRA Normalized Format file is being retrieved, if this is different from your preference, it may be due to current file availability.
2024-01-05T11:37:35 prefetch.3.0.8:  Downloading via HTTPS...
2024-01-05T11:37:36 prefetch.3.0.8:  HTTPS download succeed
2024-01-05T11:37:36 prefetch.3.0.8:  'SRR12848126' is valid
2024-01-05T11:37:36 prefetch.3.0.8: 1) 'SRR12848126' was downloaded successfully
2024-01-05T11:37:37 prefetch.3.0.8: 'SRR12848126' has 1 unresolved dependency
2024-01-05T11:37:37 prefetch.3.0.8: 2) Downloading 'ncbi-acc:NC_000069.6?vdb-ctx=refseq'...
2024-01-05T11:37:37 prefetch.3.0.8:  Downloading via HTTPS...
2024-01-05T11:37:55 prefetch.3.0.8:  HTTPS download succeed
2024-01-05T11:37:55 prefetch.3.0.8: 2) 'ncbi-acc:NC_000069.6?vdb-ctx=refseq' was downloaded successfully

        Error: fasterq-dump cannot create this file: '/home/harshil/test_2.withdot/SRX9315476_SRR12848126'

        Error: fasterq-dump cannot create this file: '/home/harshil/test_1.withdot/SRX9315476_SRR12848126'
spots read      : 1,517
reads read      : 3,034

=============================================================
An error occurred during processing.
A report was generated into the file '/home/harshil/ncbi_error_report.txt'.
If the problem persists, you may consider sending the file
to 'sra-tools@ncbi.nlm.nih.gov' for assistance.
=============================================================

fasterq-dump quit with error code 3

[adamrtalbot]

The problem is this function here, which splits on any period found and creates a new filename. It should split on the final period only, or even better use some form of path handling (not 100% familiar with code).

https://github.com/ncbi/sra-tools/blob/8575947cb74af06760b670ddc58aa318149769a6/tools/external/fasterq-dump/sbuffer.c#L146-L172