GEMmaker not pulling test files (failed to pull sample URLs)

[feltus]

Description of the bug

The 'nextflow run systemsgenetics/gemmaker -profile test,singularity' test run is broken. Did they chage the data access URL at NCBI again?

Command used and terminal output

[ffeltus@node0865 SRX218012]$ nextflow run systemsgenetics/gemmaker -profile test,singularity
N E X T F L O W  ~  version 23.10.0
Launching `https://github.com/systemsgenetics/gemmaker` [exotic_hopper] DSL2 - revision: c7fe33612e [master]


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                                        ,--./,-.
        ___     __   __   __   ___     /,-._.--~'
  |\ | |__  __ /  ` /  \ |__) |__         }  {
  | \| |       \__, \__/ |  \ |___     \`-._,-`-,
                                        `._,._,'
  systemsgenetics/gemmaker v2.1.1
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Core Nextflow options
  revision                  : master
  runName                   : exotic_hopper
  containerEngine           : singularity
  launchDir                 : /home/ffeltus/test/results/Samples/SRX218012
  workDir                   : /home/ffeltus/test/results/Samples/SRX218012/work
  projectDir                : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker
  userName                  : ffeltus
  profile                   : test,singularity
  configFiles               : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/nextflow.config

Input/output options
  input                     : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/demo/*{1,2}.fastq
  pipeline                  : hisat2
  sras                      : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/demo/SRA_IDs.txt
  skip_samples              : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/demo/samples2skip.txt
  failed_run_report_template: /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/failed_sra_runs.template.html
  multiqc_config_file       : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/multiqc_config.yaml
  multiqc_custom_logo       : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/systemsgenetics-gemmaker_logo.png

Kallisto Pipeline
  kallisto_index_path       : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/demo/references/CORG.transcripts.Kallisto.indexed
  kallisto_bootstrap_samples: 0

Salmon Pipeline
  salmon_index_path         : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/demo/references/CORG.transcripts.Salmon.indexed

Hisat Pipeline
  hisat2_base_name          : CORG
  hisat2_index_dir          : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/demo/references/CORG.genome.Hisat2.indexed
  hisat2_gtf_file           : /home/ffeltus/.nextflow/assets/systemsgenetics/gemmaker/assets/demo/references/CORG.transcripts.gtf

Reference genome options
  igenomes_ignore           : true

Generic options
  publish_dir_mode          : link

Max job request options
  max_cpus                  : 2
  max_memory                : 6 GB
  max_time                  : 2d

Institutional config options
  config_profile_name       : Test profile
  config_profile_description: Minimal test dataset to check pipeline function

!! Only displaying parameters that differ from the pipeline defaults !!
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If you use systemsgenetics/gemmaker for your analysis please cite:

* The pipeline
  https://doi.org/10.5281/zenodo.3620945

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

* Software dependencies
  https://github.com/systemsgenetics/gemmaker/blob/master/CITATIONS.md
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[-        ] process > GEMmaker:get_software_versions -
[-        ] process > GEMmaker:get_software_versions -
executor >  local (1)
executor >  local (1)
executor >  local (2)
executor >  local (2)
executor >  local (3)
executor >  local (4)
executor >  local (4)
executor >  local (4)
[-        ] process > GEMmaker:get_software_versions     -
[2c/74029e] process > GEMmaker:retrieve_sra_metadata     [100%] 1 of 1 ?
[e8/a5963e] process > GEMmaker:download_runs (SRX218012) [100%] 1 of 1 ?
[-        ] process > GEMmaker:fastq_dump                -
[-        ] process > GEMmaker:fastq_merge               -
[-        ] process > GEMmaker:fastqc_1                  -
[-        ] process > GEMmaker:trimmomatic               -
[-        ] process > GEMmaker:fastqc_2                  -
[-        ] process > GEMmaker:hisat2                    -
[-        ] process > GEMmaker:samtools_sort             -
[-        ] process > GEMmaker:samtools_index            -[-        ] process > GEMmaker:stringtie                 -[-        ] process > GEMmaker:stringtie_fpkm_tpm        -
[43/5ffabd] process > GEMmaker:next_sample (SRX218012)   [100%] 1 of 1 ?[-        ] process > GEMmaker:multiqc                   -[-        ] process > GEMmaker:create_gem                -[bc/f29c25] process > GEMmaker:failed_run_report         [100%] 1 of 1 ?[-        ] process > GEMmaker:clean_work_files          -[-        ] process > GEMmaker:clean_work_dirs           -Pulling Singularity image docker://systemsgenetics/gemmaker:2.1.0 [cache /home/ffeltus/test/results/Samples/SRX218012/work/singularity/systemsgenetics-gemmaker-2.1.0.img]WARN: Singularity cache directory has not been defined -- Remote image will be stored in the path: /home/ffeltus/test/results/Samples/SRX218012/work/singularity -- Use the environment variable NXF_SINGULARITY_CACHEDIR to specify a different location



[ffeltus@node0865 SRX218012]$ cat SRX218012.failed_runs.download.txt
{
    "SRR649944": "Failed to fetch sample url."
}[ffeltus@node0865 SRX218012]$ history

Relevant files

No response

System information

No response