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No more space error on classifier about ampliseq HOT 7 CLOSED

nf-core commented on May 25, 2024

No more space error on classifier

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Comments (7)

apeltzer commented on May 25, 2024 4

Found the problem in the Docker thing as well after ~10 hours of debugging and without help at the QIIME2 user forum.

docker.temp = 'auto'
    env {
      JOBLIB_TEMP_FOLDER="/tmp"
    }

Nobody tells you about this here:

https://forum.qiime2.org/t/error-no-28-out-of-memory/5758
https://forum.qiime2.org/t/error-no-28-no-space-left-on-device-with-feature-classifier-sklearn/5961
https://forum.qiime2.org/t/error-in-filtering-using-dada2/3543

@KochTobi and I found this here:

https://scikit-learn.org/stable/modules/generated/sklearn.utils.Parallel.html

and that the scikit learn application apparently looks for the env variable JOBLIB_TEMP_FOLDER first, setting this fixed to /tmp and using nextflows docker.temp = 'auto' resolved the issue.

That means, we'Ll have working CI tests today!!!!

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apeltzer commented on May 25, 2024 1

It even runs through entirely without a single error message.

=======================================================
Pipeline Name  : nf-core/rrna-ampliseq
Pipeline Version: 1.0dev
Run Name       : cheesy_coulomb
Reads          : data/*_L001_R{1,2}_001.fastq.gz
Data Type      : Paired-End
Max Memory     : 6 GB
Max CPUs       : 2
Max Time       : 2d
Output dir     : ./results
Working dir    : /home/alex/IDEA/nf-core/rrna-ampliseq/work
Container Engine: singularity
Container      : nfcore/rrna-ampliseq:latest
Current home   : /home/alex
Current user   : alex
Current path   : /home/alex/IDEA/nf-core/rrna-ampliseq
Script dir     : /home/alex/IDEA/nf-core/rrna-ampliseq
Config Profile : test,singularity
=========================================
[warm up] executor > local
[11/ed9b34] Cached process > get_software_versions
[8d/ab2a66] Cached process > output_documentation
[7e/7b98fb] Cached process > metadata_category_all (1)
[30/a8b348] Cached process > metadata_category_pairwise (1)
[c7/254f41] Cached process > fastqc (1_S103)
[6f/0948dd] Cached process > fastqc (1a_S103)
[6d/3a1a3c] Cached process > trimming (2_S115)
[03/385ca3] Cached process > trimming (1a_S103)
[7f/648968] Cached process > trimming (2a_S115)
[60/b91fd1] Cached process > fastqc (2a_S115)
[37/35e535] Cached process > trimming (1_S103)
[cc/5e3356] Cached process > fastqc (2_S115)
[9e/71976f] Cached process > qiime_import
[61/037f86] Cached process > qiime_demux_visualize
[74/df79da] Cached process > multiqc
[40/71b95b] Cached process > dada_trunc_parameter
[49/3a2962] Cached process > dada_single
[5c/2e4105] Submitted process > classifier (1)
[3f/937df3] Submitted process > filter_taxa (1)
[05/470625] Submitted process > RelativeAbundanceASV (1)
[6e/30bc88] Submitted process > RelativeAbundanceReducedTaxa (1)
[f3/3619b3] Submitted process > export_filtered_dada_output (1)
[82/49c195] Submitted process > tree (1)
[e3/b2432f] Submitted process > ancom (1)
[1a/f08022] Submitted process > barplot (1)
[da/aad654] Submitted process > combinetable (1)
[a3/20e214] Submitted process > report_filter_stats (1)
[01/69a2c5] Submitted process > diversity_core (1)
[5f/af8a16] Submitted process > alpha_rarefaction (1)
[47/28fc6c] Submitted process > beta_diversity_ordination (1)
[33/35de42] Submitted process > beta_diversity (1)
[f4/e7c281] Submitted process > alpha_diversity (1)
[nf-core/rrna-ampliseq] Pipeline Complete

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