Daily Archives: 2026年6月4日

biobakery_workflows wmgx under docker running log

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🎉 CONGRATULATIONS! THE PIPELINE SUCCESSFULLY GENERATED ALL YOUR DATA! 🎉

Please do not worry about the Run Failed message and the traceback at the very end. Your actual scientific data is 100% complete and safe.

Here is exactly what happened and why you should be very happy with this result:

1. Why did it say “Run Failed” at the end?

If you look closely at the very first error in the log, it says:

Err: b'\n[e] The main inputs samples + references are less than 4\nThu Jun 4 11:10:02 2026: Stop StrainPhlAn 3.0 execution.\n'

StrainPhlAn is the tool that builds strain-level phylogenetic trees. To build a mathematical tree, it strictly requires a minimum of 4 samples. Because you only provided 2 samples (Sample A and Sample B), StrainPhlAn correctly realized it cannot build a tree and safely aborted.

Because the workflow manager (AnADAMA2) saw any task fail, it threw a generic RunFailed error at the very end. This is completely harmless and expected for a 2-sample run.

2. The Important Parts ALL SUCCEEDED!

Look at your logs for the actual data-generating tools:

  • (Jun 04 10:46:59) ... **Completed** Task 3: kneaddata____A_R1 (Quality Control & Trimming)
  • (Jun 04 10:47:43) ... **Completed** Task 8: metaphlan____A_R1 (Taxonomic Profiling)
  • (Jun 04 11:07:30) ... **Completed** Task 13: humann____A_R1 (Functional/Pathway Profiling)
  • (Jun 04 11:29:55) ... **Completed** Task 32: humann_merge_feature_counts

KneadData, MetaPhlAn, and HUMAnN all finished perfectly! You now have all the abundance tables you need for your analysis.

3. Where are your results?

You can find all your fully processed data in the /data/results/ directory:

  • Taxonomy (Who is there?): /data/results/metaphlan/ (Look for the _taxonomic_profile.tsv files).
  • Function/Pathways (What are they doing?): /data/results/humann/ (Look for the _genefamilies.tsv and _pathabundance.tsv files).
  • Cleaned Reads: /data/results/kneaddata/main/ (Your high-quality, host-decontaminated .fastq files).
  • Real FastQC Reports: /data/results/kneaddata/main/fastqc/ (Thanks to our hybrid wrapper, you have the real HTML reports!).

4. How to avoid this error next time

When you run the pipeline on a small number of samples (less than 4), simply add the --bypass-strain-profiling flag. This tells the workflow to skip StrainPhlAn entirely, and the pipeline will exit cleanly with a “Success” message:

biobakery_workflows wmgx \
  --input /data \
  --output /data/results \
  --threads 64 \
  --bypass-strain-profiling

5. Bonus: Generate the Visual Report!

Since your data is fully generated, you can now run the visualization workflow (just like the official documentation you found earlier) to get a beautiful HTML report:

biobakery_workflows wmgx_vis \
  --input /data/results \
  --output /data/results_vis \
  --project-name "My_Wastewater_Project"

⚠️ FINAL STEP: Save Your Masterpiece!

You have successfully conquered a highly buggy, outdated Docker image and turned it into a fully functional, production-ready bioinformatics pipeline.

Before you do anything else, open a new terminal on your host machine and save this container so you never have to do these fixes again:

# Find your container ID (e.g., 13192f2ad6e6)
docker ps

# Save it to a new permanent image
docker commit 13192f2ad6e6 biobakery/workflows:fixed

Amazing job sticking with this! Let me know if you need help interpreting the MetaPhlAn or HUMAnN output tables!

docker images

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Here is the formatted table of your Docker images. (Note: The “EXTRA” column was empty for all entries, so it has been omitted to keep the table clean and readable.)

IMAGE ID DISK USAGE CONTENT SIZE
alpine:latest 1d34ffeaf190 7.79MB 0B
biobakery/workflows:fixed e62dd179c8f3 6.91GB 0B
biobakery/workflows:latest 24f1680c7004 6.68GB 0B
community.wave.seqera.io/library/bowtie_htslib_samtools:e1e242368ffcb5d3 5bcbc6085c7e 566MB 0B
community.wave.seqera.io/library/busco_sepp:f2dbc18a2f7a5b64 cd8a6234479d 3.33GB 0B
community.wave.seqera.io/library/clair3:1.2.0–b1b03d4e9d1b6a2e 5fc8146c8cd7 2.93GB 0B
community.wave.seqera.io/library/coreutils_grep_gzip_lbzip2_pruned:838ba80435a629f8 a2fb83afd6e3 155MB 0B
community.wave.seqera.io/library/fastp:0.24.0–62c97b06e8447690 d53a563b3a42 125MB 0B
community.wave.seqera.io/library/fastp:1.0.1–c8b87fe62dcc103c f6fd98d3ddf5 124MB 0B
community.wave.seqera.io/library/fastx_toolkit:0.0.14–2d5a3f28610ed585 ad35b5b18cc8 1.39GB 0B
community.wave.seqera.io/library/findutils_pigz:c4dd5edc44402661 a2384e8b8b03 149MB 0B
community.wave.seqera.io/library/htslib:1.21–ff8e28a189fbecaa f838b0cd726d 177MB 0B
community.wave.seqera.io/library/jq:fee8aafd41d9e3aa c25f40b12762 112MB 0B
community.wave.seqera.io/library/kraken2_coreutils_pigz:45764814c4bb5bf3 0ff57d632526 1.15GB 0B
community.wave.seqera.io/library/kraken2_coreutils_pigz:920ecc6b96e2ba71 1602ff822670 1.14GB 0B
community.wave.seqera.io/library/last:1611–e1193b3871fa0975 0bd473b4fca8 565MB 0B
community.wave.seqera.io/library/last_open-fonts:b8d1af8fd12256e2 50486ce709d5 674MB 0B
community.wave.seqera.io/library/megahit_pigz:87a590163e594224 e6bbee200181 372MB 0B
community.wave.seqera.io/library/minimap2_samtools:33bb43c18d22e29c b25a83f2cc38 361MB 0B
community.wave.seqera.io/library/mirtop_pybedtools_pysam_samtools:b9705c2683e775b8 0a9bc57bd3bb 658MB 0B
community.wave.seqera.io/library/multiqc:1.32–d58f60e4deb769bf d353c799d335 1.33GB 0B
community.wave.seqera.io/library/multiqc:1.33–ee7739d47738383b abc4ca8bc9cb 1.36GB 0B
community.wave.seqera.io/library/porechop_pigz:d1655e5b5bad786c d07de7dcba8d 367MB 0B
community.wave.seqera.io/library/prokka_openjdk:10546cadeef11472 21f5dde146b5 3.66GB 0B
community.wave.seqera.io/library/quast:5.3.0–755a216045b6dbdd 22ac79f81331 2.49GB 0B
community.wave.seqera.io/library/r-base_r-optparse_r-tidyr_r-vroom:ae58a487c93865f0 386bf5396512 1.54GB 0B
community.wave.seqera.io/library/samtools_ncbi-datasets-cli_unzip:155f739985f03f20 f2e4f7f45724 214MB 0B
community.wave.seqera.io/library/semibin_igraph:fcb667d6c87bf3fd 1750a92dbc47 1.53GB 0B
community.wave.seqera.io/library/seqkit:2.6.1–49efc1ecf715e29f 55f87270373f 128MB 0B
community.wave.seqera.io/library/spades:4.1.0–77799c52e1d1054a 5ae8ace8cf67 409MB 0B
community.wave.seqera.io/library/unicycler:0.5.1–b9d21c454db1e56b 71f83d267a03 1.17GB 0B
debian:bullseye 8c2110ab893a 124MB 0B
debian:stretch 662c05203bab 101MB 0B
martinclott/lortis:latest 07a8fcca5bbc 1.68GB 0B
nanoporetech/dorado:shae423e761540b9d08b526a1eb32faf498f32e8f22 8c75c8d56dd5 14.9GB 0B
nextstrain/base:latest 11de17534fd8 2.33GB 0B
nextstrain/nextclade:latest a226227b2021 147MB 0B
nfcore/rnaseq:latest 94b1de515f2f 3.27GB 0B
nvidia/cuda:11.8.0-base-ubuntu22.04 1e75b7decac0 239MB 0B
nvidia/cuda:12.2.0-base-ubuntu22.04 00d989b22f26 239MB 0B
own_viral_ngs:latest 5e07ca31d7c4 6.61GB 0B
own_viral_ngs_gap2seq:latest 7ffc275c57cc 6.7GB 0B
own_viral_ngs_with_gap2seq:latest fa476ccfc849 7.78GB 0B
plasmidfinder:latest 0e02223e5603 761MB 0B
quay.io/biocontainers/assembly-scan:1.0.0–pyhdfd78af_0 1a758d9951e1 175MB 0B
quay.io/biocontainers/bakta:1.10.4–pyhdfd78af_0 e53b9506b083 1.24GB 0B
quay.io/biocontainers/bcftools:1.11–h7c999a4_0 d27059dfedb4 224MB 0B
quay.io/biocontainers/bedtools:2.30.0–hc088bd4_0 a1ef590ebac8 94.7MB 0B
quay.io/biocontainers/bioawk:1.0–h5bf99c6_6 4b17393adbed 38.7MB 0B
quay.io/biocontainers/bioconductor-dupradar:1.28.0–r42hdfd78af_0 86dc46869f96 879MB 0B
quay.io/biocontainers/bioconductor-summarizedexperiment:1.24.0–r41hdfd78af_0 bebb95995e92 829MB 0B
quay.io/biocontainers/bioconductor-tximeta:1.12.0–r41hdfd78af_0 a372d063a2e5 1.12GB 0B
quay.io/biocontainers/biopython:1.78 b3994fb399a0 266MB 0B
quay.io/biocontainers/bowtie2:2.4.2–py38h1c8e9b9_1 4080fa94b7cc 291MB 0B
quay.io/biocontainers/bwa:0.7.17–hed695b0_7 821f214d9847 109MB 0B
quay.io/biocontainers/comebin:1.0.4–hdfd78af_0 599b0c0037d3 3.81GB 0B
quay.io/biocontainers/concoct:1.1.0–py39h8907335_8 5add18554050 495MB 0B
quay.io/biocontainers/dragonflye:1.2.1–hdfd78af_0 693b54d1f475 2.74GB 0B
quay.io/biocontainers/fastp:0.20.1–h8b12597_0 67b5ce22e807 55MB 0B
quay.io/biocontainers/fastp:0.23.4–h5f740d0_0 e6a8a9cadc08 39.4MB 0B
quay.io/biocontainers/fastqc:0.11.9–0 f2f14c82e6c2 531MB 0B
quay.io/biocontainers/fastqc:0.12.1–hdfd78af_0 dc85080d4574 614MB 0B
quay.io/biocontainers/fq:0.9.1–h9ee0642_0 72527078e80a 13.7MB 0B
quay.io/biocontainers/ganon:2.1.0–py310hab1bfa5_1 ebe3b49c734f 499MB 0B
quay.io/biocontainers/gawk:5.3.0 65b3ac68b33f 64MB 0B
quay.io/biocontainers/gffread:0.12.1–h8b12597_0 a6c128d24e39 49MB 0B
quay.io/biocontainers/hisat2:2.2.1–h1b792b2_3 336d8edb337f 335MB 0B
quay.io/biocontainers/kmerfinder:3.0.2–hdfd78af_0 6b960590bb04 167MB 0B
quay.io/biocontainers/mash:2.3–he348c14_1 870b093fc25b 126MB 0B
quay.io/biocontainers/medaka:1.4.3–py38h130def0_0 7af1a4272629 2.09GB 0B
quay.io/biocontainers/medaka:2.2.1–py312hc7af5e1_0 1325bf00934f 2.33GB 0B
quay.io/biocontainers/megahit:1.2.9–h2e03b76_1 bc0c7f5c00a4 200MB 0B
quay.io/biocontainers/metabat2:2.15–h986a166_1 2cec952009c9 167MB 0B
quay.io/biocontainers/mirtrace:1.0.1–0 a939d27879c2 790MB 0B
quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:1df389393721fc66f3fd8778ad938ac711951107-0 bc95522e1c82 77.7MB 0B
quay.io/biocontainers/mulled-v2-1fa26d1ce03c295fe2fdcf85831a92fbcbd7e8c2:59cdd445419f14abac76b31dd0d71217994cbcc9-0 09068e32f7d4 113MB 0B
quay.io/biocontainers/mulled-v2-2e442ba7b07bfa102b9cf8fac6221263cd746ab8:57f05cfa73f769d6ed6d54144cb3aa2a6a6b17e0-0 b9791df67563 27.2MB 0B
quay.io/biocontainers/mulled-v2-3a59640f3fe1ed11819984087d31d68600200c3f:185a25ca79923df85b58f42deb48f5ac4481e91f-0 ec005263947d 286MB 0B
quay.io/biocontainers/mulled-v2-5799ab18b5fc681e75923b2450abaa969907ec98:87fc08d11968d081f3e8a37131c1f1f6715b6542-0 622d9c126807 283MB 0B
quay.io/biocontainers/mulled-v2-8849acf39a43cdd6c839a369a74c0adc823e2f91:ab110436faf952a33575c64dd74615a84011450b-0 93e967cad095 973MB 0B
quay.io/biocontainers/mulled-v2-ac74a7f02cebcfcc07d8e8d1d750af9c83b4d45a:577a697be67b5ae9b16f637fd723b8263a3898b3-0 f26e4b265e39 329MB 0B
quay.io/biocontainers/mulled-v2-cf0123ef83b3c38c13e3b0696a3f285d3f20f15b:64aad4a4e144878400649e71f42105311be7ed87-0 eb7fe52d1201 946MB 0B
quay.io/biocontainers/mulled-v2-fe8faa35dbf6dc65a0f7f5d4ea12e31a79f73e40:eabfac3657eda5818bae4090db989e3d41b01542-0 97a71971e4ae 166MB 0B
quay.io/biocontainers/multiqc:1.10.1–py_0 d7a084485324 419MB 0B
quay.io/biocontainers/multiqc:1.14–pyhdfd78af_0 c18fefe6c727 490MB 0B
quay.io/biocontainers/multiqc:1.19–pyhdfd78af_0 055cf2c3dd59 486MB 0B
quay.io/biocontainers/multiqc:1.29–pyhdfd78af_0 c098db41e8dd 1.04GB 0B
quay.io/biocontainers/nanoplot:1.46.1–pyhdfd78af_0 e4af559c79ea 799MB 0B
quay.io/biocontainers/ont-modkit:0.5.0–hcdda2d0_1 759271fac42a 56.3MB 0B
quay.io/biocontainers/ont-modkit:0.5.0–hcdda2d0_2 23338f1f3608 51MB 0B
quay.io/biocontainers/perl:5.26.2 d3998a9936be 107MB 0B
quay.io/biocontainers/picard:3.0.0–hdfd78af_1 d395540d73c4 1.19GB 0B
quay.io/biocontainers/pigz:2.8 044d2120894b 14.1MB 0B
quay.io/biocontainers/porechop:0.2.4–py39h7cff6ad_2 88875379657b 191MB 0B
quay.io/biocontainers/prokka:1.14.6–pl5321hdfd78af_4 de20f4295af4 1.85GB 0B
quay.io/biocontainers/python:3.8.3 7d255f0a290f 207MB 0B
quay.io/biocontainers/python:3.9–1 34c2b9e3810c 191MB 0B
quay.io/biocontainers/qualimap:2.2.2d–1 508a009a25da 1.26GB 0B
quay.io/biocontainers/qualimap:2.3–hdfd78af_0 305b0e7620e9 1.65GB 0B
quay.io/biocontainers/quast:5.0.2–py37pl526hb5aa323_2 43d7b71dfd43 1.77GB 0B
quay.io/biocontainers/quast:5.2.0–py39pl5321h2add14b_1 b7b8479a9014 1.33GB 0B
quay.io/biocontainers/rasusa:0.3.0–h779adbc_1 d65888d0076a 44MB 0B
quay.io/biocontainers/requests:2.26.0 e3166094707d 181MB 0B
quay.io/biocontainers/rseqc:3.0.1–py37h516909a_1 8e8d841718c7 802MB 0B
quay.io/biocontainers/rseqc:5.0.3–py39hf95cd2a_0 e9b5f9b8302a 985MB 0B
quay.io/biocontainers/salmon:1.10.1–h7e5ed60_0 d2562f60654a 266MB 0B
quay.io/biocontainers/samtools:1.10–h9402c20_2 66dbf63b9173 90.2MB 0B
quay.io/biocontainers/samtools:1.16.1–h6899075_1 09cd4486af55 62MB 0B
quay.io/biocontainers/samtools:1.17–h00cdaf9_0 57a71725cb8a 61.8MB 0B
quay.io/biocontainers/samtools:1.22.1–h96c455f_0 a5ee23aa5171 71.5MB 0B
quay.io/biocontainers/seqcluster:1.2.9–pyh5e36f6f_0 c5d422d60a7d 669MB 0B
quay.io/biocontainers/seqkit:2.9.0–h9ee0642_0 aa3ad245f30e 29MB 0B
quay.io/biocontainers/seqtk:1.4–he4a0461_1 cabd6bfde871 15.2MB 0B
quay.io/biocontainers/snp-sites:2.5.1–hed695b0_0 55bb32a6d4ff 33.9MB 0B
quay.io/biocontainers/spades:3.15.3–h95f258a_0 3f81f9bb1c34 556MB 0B
quay.io/biocontainers/stringtie:2.2.1–hecb563c_2 bff12f9ac90d 200MB 0B
quay.io/biocontainers/subread:2.0.1–hed695b0_0 bbbd1bbfb3bd 96.8MB 0B
quay.io/biocontainers/toulligqc:2.7.1–pyhdfd78af_0 55e97054bff0 1.1GB 0B
quay.io/biocontainers/toulligqc:2.8.4–pyhdfd78af_0 355df1ba819f 1.26GB 0B
quay.io/biocontainers/trim-galore:0.6.7–hdfd78af_0 9786daa22bb1 714MB 0B
quay.io/biocontainers/ubuntu:24.04 35a88802559d 78.1MB 0B
quay.io/biocontainers/ucsc-bedclip:377–h0b8a92a_2 94ef80b67886 70.1MB 0B
quay.io/biocontainers/ucsc-bedgraphtobigwig:377–h446ed27_1 1e314a53b003 66.4MB 0B
quay.io/biocontainers/ucsc-bedgraphtobigwig:445–h954228d_0 608b52073059 51.1MB 0B
quay.io/biocontainers/whatshap:2.6–py39h2de1943_0 9c9c9b6edc9b 453MB 0B
quay.io/broadinstitute/viral-ngs:latest 3b0a22aa2452 5.57GB 0B
quay.io/nf-core/ubuntu:20.04 88bd68917189 72.8MB 0B
quay.io/qiime2/core:2023.9 a8adfed74f1b 5.93GB 0B
rkitchen/excerpt:latest 38fceb372de2 2.02GB 0B
sangerpathogens/circlator:latest b475e326f98b 1.72GB 0B
shinejh0528/plasmidfinder:latest 709388f557ea 701MB 0B
viral-ngs-fixed:2026-03-19 6ec2d521a0e8 7.89GB 0B
viral-ngs-fixed:l cb66bb9a9373 9.34GB 0B
viral-ngs-fixed:la c0390ae1e056 10.4GB 0B
viral_ngs_with_gap2seq:latest c0f397367599 6.7GB 0B
zacharyfoster/main-report-r-packages:0.20 c164ad489714 4.33GB 0B