ajeffs
commented
1 month ago Adding verbose multiqc output:
multiqc -v mgikit-examples/test/
/// MultiQC 🔍 v1.25.1
[2024-10-09 15:12:16] multiqc.core.tmp_dir [DEBUG ] Using new temporary directory: /tmp/tmp4ihj0ptn
[2024-10-09 15:12:16] root [DEBUG ] Logging to file: /tmp/tmp4ihj0ptn/multiqc.log
[2024-10-09 15:12:16] multiqc.core.update_config [DEBUG ] This is MultiQC v1.25.1
[2024-10-09 15:12:16] multiqc.core.update_config [DEBUG ] Running Python 3.12.3 (main, Sep 11 2024, 14:17:37) [GCC 13.2.0]
[2024-10-09 15:12:16] urllib3.connectionpool [DEBUG ] Starting new HTTPS connection (1): api.multiqc.info:443
[2024-10-09 15:12:17] urllib3.connectionpool [DEBUG ] https://api.multiqc.info:443 "GET /version?version_multiqc=1.25.1&version_python=3.12.3&operating_system=Linux&is_docker=False&is_singularity=False&is_conda=False&is_ci=False&is_notebook=False HTTP/1.1" 200 182
[2024-10-09 15:12:17] multiqc.core.version_check [DEBUG ] Latest MultiQC version is v1.25.1, released 2024-10-01
[2024-10-09 15:12:17] multiqc.multiqc [DEBUG ] Working dir : /home/ajeffs/mgikit-multiqc
[2024-10-09 15:12:17] multiqc.multiqc [DEBUG ] Template : default
[2024-10-09 15:12:17] multiqc.multiqc [DEBUG ] Command used: /home/ajeffs/.local/bin/multiqc -v mgikit-examples/test/
[2024-10-09 15:12:17] multiqc.core.file_search [INFO ] Search path: /home/ajeffs/mgikit-multiqc/mgikit-examples/test
[2024-10-09 15:12:17] multiqc.core.file_search [DEBUG ] Analysing modules: mgikit, custom_content, ccs, ngsderive, purple, conpair, isoseq, lima, peddy, somalier, methylqa, mosdepth, phantompeakqualtools, qualimap, bamdst, preseq, hifiasm, quast, qorts, rna_seqc, rockhopper, rsem, rseqc, busco, bustools, goleft_indexcov, gffcompare, disambiguate, supernova, deeptools, sargasso, verifybamid, mirtrace, happy, mirtop, glimpse, gopeaks, homer, hops, macs2, theta2, snpeff, gatk, htseq, bcftools, featurecounts, fgbio, dragen, dragen_fastqc, dedup, pbmarkdup, damageprofiler, mapdamage, biobambam2, jcvi, mtnucratio, picard, vep, bakta, prokka, qc3C, nanoq, nanostat, samblaster, samtools, bamtools, sambamba, ngsbits, pairtools, sexdeterrmine, seqera_cli, eigenstratdatabasetools, jellyfish, vcftools, longranger, stacks, varscan2, snippy, umicollapse, umitools, truvari, megahit, ganon, bbmap, bismark, biscuit, diamond, hicexplorer, hicup, hicpro, salmon, kallisto, slamdunk, star, hisat2, tophat, bowtie2, bowtie1, hostile, cellranger, snpsplit, odgi, vg, pangolin, nextclade, freyja, humid, kat, leehom, librarian, nonpareil, adapterremoval, bbduk, clipandmerge, cutadapt, flexbar, sourmash, kaiju, kraken, malt, motus, trimmomatic, sickle, skewer, sortmerna, biobloomtools, fastq_screen, afterqc, fastp, fastqc, sequali, filtlong, prinseqplusplus, pychopper, porechop, pycoqc, minionqc, anglerfish, multivcfanalyzer, clusterflow, checkqc, bcl2fastq, bclconvert, interop, ivar, flash, seqyclean, optitype, whatshap, spaceranger, xenome, xengsort, metaphlan, seqwho, software_versions
searching | ━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━━ 100% 5/5
[2024-10-09 15:12:17] multiqc.report [DEBUG ] Summary of files that were skipped by the search: |skipped_no_match: 3|, |skipped_module_specific_max_filesize: 2|
[2024-10-09 15:12:17] multiqc.core.exec_modules [DEBUG ] Running module: custom_content
[2024-10-09 15:12:17] multiqc.core.exec_modules [DEBUG ] No samples found: custom_content
[2024-10-09 15:12:17] multiqc.core.exec_modules [DEBUG ] Running module: htseq
[2024-10-09 15:12:17] multiqc.core.exec_modules [DEBUG ] No samples found: htseq
[2024-10-09 15:12:17] multiqc.core.software_versions [DEBUG ] Reading software versions from config.software_versions
[2024-10-09 15:12:17] multiqc.multiqc [WARNING] No analysis results found. Cleaning up…
Hi,
Thanks for mgikit, really useful tool!
I've installed mgikit-multiqc without any issue as far as I can tell (substituting python3 for python because of a "Command 'python' not found error with 'python setup.py install') :
'multiqc -h' shows mgikit-multiqc options:
So I understand that to mean that the mgikit-multiqc plugin is installed and seen by multiqc.
However, when running multiqc none of the mgikit report files are recognised as valid results:
Any feedback on what might me happening here, and what I might have done wrong, would be very much appreciated!
All the best,
Aaron.