EnriqueDoster
commented
2 weeks ago Hi @ahayyes , thanks for pointing this out! Looks like the issue was a version difference between multiQC changed how the output files were named. Earlier, I made an update to make it work with the newer version of multiQC, but now I made another change that should make it work with any version. So please download the latest AMR++ code and try again!
I have installed AMR++ on our local computing cluster. I have been trying to get it running on our cluster, and have run into a problem with the multiqc part of the pipeline.
I currently am running this - nextflow run main_AMR++.nf -profile singularity --pipeline standard_AMR_wKraken --output test_AMR++_output -w work_AMR++
within a slurm script, loading python, multiqc, nextflow, and AMR++ as modules prior to asking the nextflow command.
However, it fails with the multiqc step. I have tried altering my multiqc config file as suggested as a fix here but this has not fixed the problem.
The error code is below:
Caused by: Process
STANDARD_AMRplusplus_wKraken:FASTQ_QC_WF:multiqc (Running multiQC)terminated with an error exit status (1)Command executed:
cp multiqc/ . multiqc -v data --interactive -f --cl-config "max_table_rows: 3000" mv AMR-Bioinformatic-pipeline_multiqc_report_data/multiqc_general_stats.txt .
Command exit status: 1
Command output: (empty)
Command error:
[2024-06-10 14:43:08,302] multiqc [DEBUG ] This is MultiQC v1.14 [2024-06-10 14:43:08,305] multiqc [DEBUG ] Loading config settings from: multiqc_config.yaml [2024-06-10 14:43:08,305] multiqc [DEBUG ] New config: {'title': 'AMR++ Bioinformatic pipeline', 'subtitle': 'A pipeline mea$ [2024-06-10 14:43:08,305] multiqc [DEBUG ] Found command line config: {'max_table_rows': 3000} [2024-06-10 14:43:08,305] multiqc [DEBUG ] New config: {'max_table_rows': 3000} [2024-06-10 14:43:08,305] multiqc [DEBUG ] Command used: /opt/conda/bin/multiqc -v data1 data2 data3 --interactive -f --cl-c$ [2024-06-10 14:43:08,556] multiqc [WARNING] MultiQC Version v1.22.2 now available! [2024-06-10 14:43:08,556] multiqc [DEBUG ] Working dir : /nobackup/beegfs/workspace/ah1336/AMRplusplus/work_AMR++/71/8d39097$ [2024-06-10 14:43:08,556] multiqc [DEBUG ] Template : default [2024-06-10 14:43:08,556] multiqc [DEBUG ] Running Python 3.9.16 | packaged by conda-forge | (main, Feb 1 2023, 21:39:03) $ [2024-06-10 14:43:08,556] multiqc [INFO ] Report title: AMR++ Bioinformatic pipeline [2024-06-10 14:43:08,557] multiqc [DEBUG ] Analysing modules: custom_content, ccs, ngsderive, purple, conpair, lima, peddy, $ [2024-06-10 14:43:08,557] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp63a3bwem [2024-06-10 14:43:08,766] multiqc [INFO ] Search path : data1 [2024-06-10 14:43:08,766] multiqc [INFO ] Search path : data2 [2024-06-10 14:43:08,766] multiqc [INFO ] Search path : data3 | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 12/12 [2024-06-10 14:43:09,750] multiqc [DEBUG ] Summary of files that were skipped by the search: [skipped_module_specific_max_fi$ | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 12/12 [2024-06-10 14:43:09,750] multiqc [DEBUG ] Summary of files that were skipped by the search: [skipped_module_specific_max_fi$ [2024-06-10 14:43:10,360] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.7.1 [2024-06-10 14:43:10,362] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.7.1 [2024-06-10 14:43:10,362] multiqc [DEBUG ] No samples found: custom_content [2024-06-10 14:43:10,385] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2024-06-10 14:43:10,493] multiqc [INFO ] Compressing plot data [2024-06-10 14:43:10,564] multiqc Type': 'AMR++'}, {'Project Type': 'FastQC analysis'}], 'custom_logo_url': 'https://www.meglab.org/', 'custom_logo_title':$ [2024-06-10 14:43:08,305] multiqc [DEBUG ] Found command line config: {'max_table_rows': 3000} [2024-06-10 14:43:08,305] multiqc [DEBUG ] New config: {'max_table_rows': 3000} [2024-06-10 14:43:08,305] multiqc [DEBUG ] Command used: /opt/conda/bin/multiqc -v data1 data2 data3 --interactive -f --cl-c$ [2024-06-10 14:43:08,556] multiqc [WARNING] MultiQC Version v1.22.2 now available! [2024-06-10 14:43:08,556] multiqc [DEBUG ] Working dir : /nobackup/beegfs/workspace/ah1336/AMRplusplus/work_AMR++/71/8d39097$ [2024-06-10 14:43:08,556] multiqc [DEBUG ] Template : default [2024-06-10 14:43:08,556] multiqc [DEBUG ] Running Python 3.9.16 | packaged by conda-forge | (main, Feb 1 2023, 21:39:03) $ [2024-06-10 14:43:08,556] multiqc [INFO ] Report title: AMR++ Bioinformatic pipeline [2024-06-10 14:43:08,557] multiqc [DEBUG ] Analysing modules: custom_content, ccs, ngsderive, purple, conpair, lima, peddy, $ [2024-06-10 14:43:08,557] multiqc [DEBUG ] Using temporary directory for creating report: /tmp/tmp63a3bwem [2024-06-10 14:43:08,766] multiqc [INFO ] Search path : data1 [2024-06-10 14:43:08,766] multiqc [INFO ] Search path : data2 [2024-06-10 14:43:08,766] multiqc [INFO ] Search path : data3 | searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 12/12 [2024-06-10 14:43:09,750] multiqc [DEBUG ] Summary of files that were skipped by the search: [skipped_module_specific_max_fi$ [2024-06-10 14:43:10,360] multiqc.plots.bargraph [DEBUG ] Using matplotlib version 3.7.1 [2024-06-10 14:43:10,362] multiqc.plots.linegraph [DEBUG ] Using matplotlib version 3.7.1 [2024-06-10 14:43:10,362] multiqc [DEBUG ] No samples found: custom_content [2024-06-10 14:43:10,385] multiqc.modules.fastqc.fastqc [INFO ] Found 6 reports [2024-06-10 14:43:10,493] multiqc [INFO ] Compressing plot data [2024-06-10 14:43:10,564] multiqc [INFO ] Report : multiqc_report.html [2024-06-10 14:43:10,564] multiqc [INFO ] Data : multiqc_data [2024-06-10 14:43:10,564] multiqc [DEBUG ] Moving data file from '/tmp/tmp63a3bwem/multiqc_data' to 'multiqc_data' [2024-06-10 14:43:10,852] multiqc [INFO ] MultiQC complete mv: cannot stat 'AMR-Bioinformatic-pipeline_multiqc_report_data/multiqc_general_stats.txt': No such file or directory
Work dir: /nobackup/beegfs/workspace/ah1336/AMRplusplus/work_AMR++/71/8d390975cdd097e0fa949296fdebdd
Hopefully you can help!