Closed feltus closed 2 months ago
The 'nextflow run systemsgenetics/gemmaker -profile test,singularity' test run is broken. Did they chage the data access URL at NCBI again?
[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] ------------------------------------------------------ ,--./,-. ___ __ __ __ ___ /,-._.--~' |\ | |__ __ / ` / \ |__) |__ } { | \| | \__, \__/ | \ |___ \`-._,-`-, `._,._,' systemsgenetics/gemmaker v2.1.1 ------------------------------------------------------ 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 !! ------------------------------------------------------ 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 ------------------------------------------------------ [- ] 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
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We don't seem to be able to reproduce this problem. Sorry it's been so long. If this is still an issue please respond.
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
Relevant files
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System information
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