metagenome-atlas / atlas

ATLAS - Three commands to start analyzing your metagenome data
https://metagenome-atlas.github.io/
BSD 3-Clause "New" or "Revised" License
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Error in localrule parse_vamb_output: #698

Closed the-eon-flux closed 9 months ago

the-eon-flux commented 11 months ago
Error in rule parse_vamb_output:
    jobid: 0
    input: Intermediate/cobinning/healthy/vamb_output, Intermediate/cobinning/Pneumonia/vamb_output
    output: Binning/vamb/vamb_clusters.tsv.gz, SRR8369372/binning/vamb/cluster_attribution.tsv, SRR8369373/binning/vamb/cluster_attribution.tsv, SRR8369375/binning/vamb/cluster_attribution.tsv, SRR8369376/binning/vamb/cluster_attribution.tsv, SRR8369377/binning/vamb/cluster_attribution.tsv, SRR8369378/binning/vamb/cluster_attribution.tsv, SRR8369379/binning/vamb/cluster_attribution.tsv, SRR8369380/binning/vamb/cluster_attribution.tsv, SRR8369381/binning/vamb/cluster_attribution.tsv, SRR8369382/binning/vamb/cluster_attribution.tsv, SRR8369383/binning/vamb/cluster_attribution.tsv, SRR8369384/binning/vamb/cluster_attribution.tsv, SRR8369385/binning/vamb/cluster_attribution.tsv, SRR8369386/binning/vamb/cluster_attribution.tsv, SRR8369388/binning/vamb/cluster_attribution.tsv, SRR8369389/binning/vamb/cluster_attribution.tsv, SRR8369390/binning/vamb/cluster_attribution.tsv, SRR8369391/binning/vamb/cluster_attribution.tsv, SRR8369393/binning/vamb/cluster_attribution.tsv, SRR8369394/binning/vamb/cluster_attribution.tsv, SRR8369395/binning/vamb/cluster_attribution.tsv, SRR8369396/binning/vamb/cluster_attribution.tsv, SRR8369397/binning/vamb/cluster_attribution.tsv, SRR8369398/binning/vamb/cluster_attribution.tsv, SRR8369399/binning/vamb/cluster_attribution.tsv, SRR8369402/binning/vamb/cluster_attribution.tsv, SRR8369404/binning/vamb/cluster_attribution.tsv, SRR8369405/binning/vamb/cluster_attribution.tsv, SRR8369406/binning/vamb/cluster_attribution.tsv, SRR8369408/binning/vamb/cluster_attribution.tsv, SRR8369409/binning/vamb/cluster_attribution.tsv, SRR8369410/binning/vamb/cluster_attribution.tsv, SRR8369411/binning/vamb/cluster_attribution.tsv, SRR8369412/binning/vamb/cluster_attribution.tsv, SRR8369413/binning/vamb/cluster_attribution.tsv, SRR8369414/binning/vamb/cluster_attribution.tsv, SRR8369417/binning/vamb/cluster_attribution.tsv, SRR8369419/binning/vamb/cluster_attribution.tsv, SRR8369421/binning/vamb/cluster_attribution.tsv, SRR8369423/binning/vamb/cluster_attribution.tsv, SRR8369426/binning/vamb/cluster_attribution.tsv, SRR8369427/binning/vamb/cluster_attribution.tsv, SRR8369428/binning/vamb/cluster_attribution.tsv, SRR8369432/binning/vamb/cluster_attribution.tsv, SRR8369433/binning/vamb/cluster_attribution.tsv, SRR8369434/binning/vamb/cluster_attribution.tsv, SRR8369436/binning/vamb/cluster_attribution.tsv, SRR8369438/binning/vamb/cluster_attribution.tsv, SRR8369441/binning/vamb/cluster_attribution.tsv, SRR8369443/binning/vamb/cluster_attribution.tsv, SRR8369444/binning/vamb/cluster_attribution.tsv, SRR8369445/binning/vamb/cluster_attribution.tsv, SRR8369447/binning/vamb/cluster_attribution.tsv, SRR8369449/binning/vamb/cluster_attribution.tsv, SRR8369451/binning/vamb/cluster_attribution.tsv, SRR8369454/binning/vamb/cluster_attribution.tsv, SRR8369455/binning/vamb/cluster_attribution.tsv, SRR8369456/binning/vamb/cluster_attribution.tsv, SRR8369457/binning/vamb/cluster_attribution.tsv, SRR8369458/binning/vamb/cluster_attribution.tsv, SRR8369459/binning/vamb/cluster_attribution.tsv, SRR8369460/binning/vamb/cluster_attribution.tsv, SRR8369462/binning/vamb/cluster_attribution.tsv, SRR8369464/binning/vamb/cluster_attribution.tsv, SRR8369465/binning/vamb/cluster_attribution.tsv, SRR8369468/binning/vamb/cluster_attribution.tsv, SRR8369469/binning/vamb/cluster_attribution.tsv, SRR8369470/binning/vamb/cluster_attribution.tsv, SRR8369471/binning/vamb/cluster_attribution.tsv, SRR8369472/binning/vamb/cluster_attribution.tsv, SRR8369473/binning/vamb/cluster_attribution.tsv, SRR8369474/binning/vamb/cluster_attribution.tsv, SRR8369475/binning/vamb/cluster_attribution.tsv, SRR8369479/binning/vamb/cluster_attribution.tsv, SRR8369482/binning/vamb/cluster_attribution.tsv, SRR8369483/binning/vamb/cluster_attribution.tsv, SRR8369484/binning/vamb/cluster_attribution.tsv, SRR8369485/binning/vamb/cluster_attribution.tsv, SRR8369486/binning/vamb/cluster_attribution.tsv, SRR8369487/binning/vamb/cluster_attribution.tsv, SRR8369488/binning/vamb/cluster_attribution.tsv, SRR8369489/binning/vamb/cluster_attribution.tsv, SRR8369490/binning/vamb/cluster_attribution.tsv, SRR8369491/binning/vamb/cluster_attribution.tsv, SRR8369492/binning/vamb/cluster_attribution.tsv, SRR8369493/binning/vamb/cluster_attribution.tsv, SRR8369494/binning/vamb/cluster_attribution.tsv, SRR8369495/binning/vamb/cluster_attribution.tsv, SRR8369496/binning/vamb/cluster_attribution.tsv, SRR8369497/binning/vamb/cluster_attribution.tsv, SRR8369498/binning/vamb/cluster_attribution.tsv, SRR8369499/binning/vamb/cluster_attribution.tsv, SRR8369501/binning/vamb/cluster_attribution.tsv, SRR8369502/binning/vamb/cluster_attribution.tsv, SRR8369503/binning/vamb/cluster_attribution.tsv, SRR8369504/binning/vamb/cluster_attribution.tsv, SRR8369506/binning/vamb/cluster_attribution.tsv, SRR8369507/binning/vamb/cluster_attribution.tsv, SRR8369508/binning/vamb/cluster_attribution.tsv, SRR8369509/binning/vamb/cluster_attribution.tsv, SRR8369510/binning/vamb/cluster_attribution.tsv, SRR8369511/binning/vamb/cluster_attribution.tsv, SRR8369512/binning/vamb/cluster_attribution.tsv, SRR8369513/binning/vamb/cluster_attribution.tsv, SRR8369518/binning/vamb/cluster_attribution.tsv, SRR8369519/binning/vamb/cluster_attribution.tsv, SRR8369520/binning/vamb/cluster_attribution.tsv, SRR8369523/binning/vamb/cluster_attribution.tsv, SRR8369524/binning/vamb/cluster_attribution.tsv, SRR8369525/binning/vamb/cluster_attribution.tsv, SRR8369527/binning/vamb/cluster_attribution.tsv, SRR8369528/binning/vamb/cluster_attribution.tsv, SRR8369531/binning/vamb/cluster_attribution.tsv, SRR8369533/binning/vamb/cluster_attribution.tsv, SRR8369534/binning/vamb/cluster_attribution.tsv, SRR8369535/binning/vamb/cluster_attribution.tsv, SRR8369536/binning/vamb/cluster_attribution.tsv, SRR8369537/binning/vamb/cluster_attribution.tsv, SRR8369538/binning/vamb/cluster_attribution.tsv, SRR8369539/binning/vamb/cluster_attribution.tsv, SRR8369540/binning/vamb/cluster_attribution.tsv, SRR8369541/binning/vamb/cluster_attribution.tsv, SRR8369542/binning/vamb/cluster_attribution.tsv, SRR8369545/binning/vamb/cluster_attribution.tsv, SRR8369546/binning/vamb/cluster_attribution.tsv, SRR8369547/binning/vamb/cluster_attribution.tsv, SRR8369548/binning/vamb/cluster_attribution.tsv, SRR8369549/binning/vamb/cluster_attribution.tsv, SRR8369550/binning/vamb/cluster_attribution.tsv, SRR8369551/binning/vamb/cluster_attribution.tsv, SRR8369552/binning/vamb/cluster_attribution.tsv, SRR8369553/binning/vamb/cluster_attribution.tsv, SRR8369555/binning/vamb/cluster_attribution.tsv, SRR8369556/binning/vamb/cluster_attribution.tsv, SRR8369557/binning/vamb/cluster_attribution.tsv, SRR8369558/binning/vamb/cluster_attribution.tsv, SRR8369559/binning/vamb/cluster_attribution.tsv, SRR8369560/binning/vamb/cluster_attribution.tsv, SRR8369561/binning/vamb/cluster_attribution.tsv, SRR8369562/binning/vamb/cluster_attribution.tsv, SRR8369563/binning/vamb/cluster_attribution.tsv, SRR8369564/binning/vamb/cluster_attribution.tsv, SRR8369567/binning/vamb/cluster_attribution.tsv, SRR8369570/binning/vamb/cluster_attribution.tsv, SRR8369571/binning/vamb/cluster_attribution.tsv, SRR8369573/binning/vamb/cluster_attribution.tsv, SRR8369574/binning/vamb/cluster_attribution.tsv, SRR8369575/binning/vamb/cluster_attribution.tsv, SRR8369576/binning/vamb/cluster_attribution.tsv, SRR8369577/binning/vamb/cluster_attribution.tsv, SRR8369580/binning/vamb/cluster_attribution.tsv, SRR8369582/binning/vamb/cluster_attribution.tsv, SRR8369584/binning/vamb/cluster_attribution.tsv, SRR8369586/binning/vamb/cluster_attribution.tsv, SRR8369587/binning/vamb/cluster_attribution.tsv, SRR8369588/binning/vamb/cluster_attribution.tsv, SRR8369589/binning/vamb/cluster_attribution.tsv, SRR8369590/binning/vamb/cluster_attribution.tsv, SRR8369591/binning/vamb/cluster_attribution.tsv, SRR8369592/binning/vamb/cluster_attribution.tsv, SRR8369593/binning/vamb/cluster_attribution.tsv, SRR8369594/binning/vamb/cluster_attribution.tsv, SRR8369596/binning/vamb/cluster_attribution.tsv, SRR8369597/binning/vamb/cluster_attribution.tsv, SRR8369598/binning/vamb/cluster_attribution.tsv, SRR8369599/binning/vamb/cluster_attribution.tsv, SRR8369600/binning/vamb/cluster_attribution.tsv, SRR8369601/binning/vamb/cluster_attribution.tsv, SRR8369602/binning/vamb/cluster_attribution.tsv, SRR8369603/binning/vamb/cluster_attribution.tsv, SRR8369605/binning/vamb/cluster_attribution.tsv, SRR8369606/binning/vamb/cluster_attribution.tsv, SRR8369607/binning/vamb/cluster_attribution.tsv, SRR8369608/binning/vamb/cluster_attribution.tsv, SRR8369610/binning/vamb/cluster_attribution.tsv, SRR8369612/binning/vamb/cluster_attribution.tsv, SRR8369613/binning/vamb/cluster_attribution.tsv, SRR8369614/binning/vamb/cluster_attribution.tsv, SRR8369615/binning/vamb/cluster_attribution.tsv, SRR8369616/binning/vamb/cluster_attribution.tsv, SRR8369617/binning/vamb/cluster_attribution.tsv, SRR8369618/binning/vamb/cluster_attribution.tsv, SRR8369619/binning/vamb/cluster_attribution.tsv, SRR8369620/binning/vamb/cluster_attribution.tsv, SRR8369621/binning/vamb/cluster_attribution.tsv, SRR8369622/binning/vamb/cluster_attribution.tsv, SRR8369623/binning/vamb/cluster_attribution.tsv, SRR8369624/binning/vamb/cluster_attribution.tsv, SRR8369625/binning/vamb/cluster_attribution.tsv, SRR8369626/binning/vamb/cluster_attribution.tsv, SRR8369627/binning/vamb/cluster_attribution.tsv, SRR8369628/binning/vamb/cluster_attribution.tsv, SRR8369629/binning/vamb/cluster_attribution.tsv, SRR8369630/binning/vamb/cluster_attribution.tsv, SRR8369631/binning/vamb/cluster_attribution.tsv, SRR8369633/binning/vamb/cluster_attribution.tsv, SRR8369634/binning/vamb/cluster_attribution.tsv, SRR8369635/binning/vamb/cluster_attribution.tsv, SRR8369638/binning/vamb/cluster_attribution.tsv, SRR8369639/binning/vamb/cluster_attribution.tsv, SRR8369640/binning/vamb/cluster_attribution.tsv, SRR8369641/binning/vamb/cluster_attribution.tsv, SRR8369642/binning/vamb/cluster_attribution.tsv, SRR8369643/binning/vamb/cluster_attribution.tsv, SRR8369644/binning/vamb/cluster_attribution.tsv, SRR8369645/binning/vamb/cluster_attribution.tsv, SRR8369647/binning/vamb/cluster_attribution.tsv, SRR8369649/binning/vamb/cluster_attribution.tsv, SRR8369650/binning/vamb/cluster_attribution.tsv, SRR8369651/binning/vamb/cluster_attribution.tsv, SRR8369652/binning/vamb/cluster_attribution.tsv, SRR8369653/binning/vamb/cluster_attribution.tsv, SRR8369654/binning/vamb/cluster_attribution.tsv, SRR8369656/binning/vamb/cluster_attribution.tsv, SRR8369657/binning/vamb/cluster_attribution.tsv, SRR8369658/binning/vamb/cluster_attribution.tsv, SRR8369659/binning/vamb/cluster_attribution.tsv, SRR8369662/binning/vamb/cluster_attribution.tsv, SRR8369663/binning/vamb/cluster_attribution.tsv, SRR8369664/binning/vamb/cluster_attribution.tsv, SRR8369665/binning/vamb/cluster_attribution.tsv, SRR8369666/binning/vamb/cluster_attribution.tsv, SRR8369667/binning/vamb/cluster_attribution.tsv, SRR8369668/binning/vamb/cluster_attribution.tsv, SRR8369669/binning/vamb/cluster_attribution.tsv, SRR8369670/binning/vamb/cluster_attribution.tsv, SRR8369671/binning/vamb/cluster_attribution.tsv, SRR8369672/binning/vamb/cluster_attribution.tsv, SRR8369673/binning/vamb/cluster_attribution.tsv, SRR8369674/binning/vamb/cluster_attribution.tsv, SRR8369677/binning/vamb/cluster_attribution.tsv, SRR8369679/binning/vamb/cluster_attribution.tsv, SRR8369682/binning/vamb/cluster_attribution.tsv, SRR8369683/binning/vamb/cluster_attribution.tsv, SRR8369684/binning/vamb/cluster_attribution.tsv, SRR8369686/binning/vamb/cluster_attribution.tsv, SRR8369687/binning/vamb/cluster_attribution.tsv, SRR8369688/binning/vamb/cluster_attribution.tsv, SRR8369689/binning/vamb/cluster_attribution.tsv, SRR8369690/binning/vamb/cluster_attribution.tsv, SRR8369691/binning/vamb/cluster_attribution.tsv, SRR8369693/binning/vamb/cluster_attribution.tsv, SRR8369694/binning/vamb/cluster_attribution.tsv, SRR8369696/binning/vamb/cluster_attribution.tsv, SRR8369698/binning/vamb/cluster_attribution.tsv, SRR8369702/binning/vamb/cluster_attribution.tsv
    log: logs/cobinning/vamb_parse_output.log (check log file(s) for error details)
    conda-env: /lisc/scratch/hygiene/P1_Catalog_Project/Resources/ATLASDB/conda_envs/eec97627e0168911f89cd4541f94e683_

Removing output files of failed job parse_vamb_output since they might be corrupted:
Binning/vamb/vamb_clusters.tsv.gz, SRR8369372/binning/vamb/cluster_attribution.tsv, SRR8369373/binning/vamb/cluster_attribution.tsv, SRR8369375/binning/vamb/cluster_attribution.tsv, SRR8369376/binning/vamb/cluster_attribution.tsv, SRR8369377/binning/vamb/cluster_attribution.tsv, SRR8369378/binning/vamb/cluster_attribution.tsv, SRR8369379/binning/vamb/cluster_attribution.tsv, SRR8369380/binning/vamb/cluster_attribution.tsv, SRR8369381/binning/vamb/cluster_attribution.tsv, SRR8369382/binning/vamb/cluster_attribution.tsv, SRR8369383/binning/vamb/cluster_attribution.tsv, SRR8369384/binning/vamb/cluster_attribution.tsv, SRR8369385/binning/vamb/cluster_attribution.tsv, SRR8369386/binning/vamb/cluster_attribution.tsv, SRR8369388/binning/vamb/cluster_attribution.tsv, SRR8369389/binning/vamb/cluster_attribution.tsv, SRR8369390/binning/vamb/cluster_attribution.tsv, SRR8369391/binning/vamb/cluster_attribution.tsv, SRR8369393/binning/vamb/cluster_attribution.tsv, SRR8369394/binning/vamb/cluster_attribution.tsv, SRR8369395/binning/vamb/cluster_attribution.tsv, SRR8369397/binning/vamb/cluster_attribution.tsv, SRR8369398/binning/vamb/cluster_attribution.tsv, SRR8369399/binning/vamb/cluster_attribution.tsv, SRR8369402/binning/vamb/cluster_attribution.tsv, SRR8369404/binning/vamb/cluster_attribution.tsv, SRR8369405/binning/vamb/cluster_attribution.tsv, SRR8369406/binning/vamb/cluster_attribution.tsv, SRR8369408/binning/vamb/cluster_attribution.tsv, SRR8369409/binning/vamb/cluster_attribution.tsv, SRR8369410/binning/vamb/cluster_attribution.tsv, SRR8369411/binning/vamb/cluster_attribution.tsv, SRR8369412/binning/vamb/cluster_attribution.tsv, SRR8369413/binning/vamb/cluster_attribution.tsv, SRR8369414/binning/vamb/cluster_attribution.tsv, SRR8369417/binning/vamb/cluster_attribution.tsv, SRR8369419/binning/vamb/cluster_attribution.tsv, SRR8369421/binning/vamb/cluster_attribution.tsv, SRR8369423/binning/vamb/cluster_attribution.tsv, SRR8369426/binning/vamb/cluster_attribution.tsv, SRR8369427/binning/vamb/cluster_attribution.tsv, SRR8369428/binning/vamb/cluster_attribution.tsv, SRR8369432/binning/vamb/cluster_attribution.tsv, SRR8369433/binning/vamb/cluster_attribution.tsv, SRR8369434/binning/vamb/cluster_attribution.tsv, SRR8369436/binning/vamb/cluster_attribution.tsv, SRR8369438/binning/vamb/cluster_attribution.tsv, SRR8369441/binning/vamb/cluster_attribution.tsv, SRR8369444/binning/vamb/cluster_attribution.tsv, SRR8369445/binning/vamb/cluster_attribution.tsv, SRR8369447/binning/vamb/cluster_attribution.tsv, SRR8369449/binning/vamb/cluster_attribution.tsv, SRR8369451/binning/vamb/cluster_attribution.tsv, SRR8369454/binning/vamb/cluster_attribution.tsv, SRR8369455/binning/vamb/cluster_attribution.tsv, SRR8369456/binning/vamb/cluster_attribution.tsv, SRR8369457/binning/vamb/cluster_attribution.tsv, SRR8369458/binning/vamb/cluster_attribution.tsv, SRR8369459/binning/vamb/cluster_attribution.tsv, SRR8369460/binning/vamb/cluster_attribution.tsv, SRR8369462/binning/vamb/cluster_attribution.tsv, SRR8369464/binning/vamb/cluster_attribution.tsv, SRR8369465/binning/vamb/cluster_attribution.tsv, SRR8369468/binning/vamb/cluster_attribution.tsv, SRR8369470/binning/vamb/cluster_attribution.tsv, SRR8369471/binning/vamb/cluster_attribution.tsv, SRR8369472/binning/vamb/cluster_attribution.tsv, SRR8369473/binning/vamb/cluster_attribution.tsv, SRR8369474/binning/vamb/cluster_attribution.tsv, SRR8369479/binning/vamb/cluster_attribution.tsv, SRR8369482/binning/vamb/cluster_attribution.tsv, SRR8369483/binning/vamb/cluster_attribution.tsv, SRR8369484/binning/vamb/cluster_attribution.tsv, SRR8369485/binning/vamb/cluster_attribution.tsv, SRR8369486/binning/vamb/cluster_attribution.tsv, SRR8369487/binning/vamb/cluster_attribution.tsv, SRR8369488/binning/vamb/cluster_attribution.tsv, SRR8369489/binning/vamb/cluster_attribution.tsv, SRR8369490/binning/vamb/cluster_attribution.tsv, SRR8369491/binning/vamb/cluster_attribution.tsv, SRR8369492/binning/vamb/cluster_attribution.tsv, SRR8369493/binning/vamb/cluster_attribution.tsv, SRR8369494/binning/vamb/cluster_attribution.tsv, SRR8369495/binning/vamb/cluster_attribution.tsv, SRR8369496/binning/vamb/cluster_attribution.tsv, SRR8369497/binning/vamb/cluster_attribution.tsv, SRR8369498/binning/vamb/cluster_attribution.tsv, SRR8369499/binning/vamb/cluster_attribution.tsv, SRR8369501/binning/vamb/cluster_attribution.tsv, SRR8369502/binning/vamb/cluster_attribution.tsv, SRR8369503/binning/vamb/cluster_attribution.tsv, SRR8369504/binning/vamb/cluster_attribution.tsv, SRR8369506/binning/vamb/cluster_attribution.tsv, SRR8369507/binning/vamb/cluster_attribution.tsv, SRR8369508/binning/vamb/cluster_attribution.tsv, SRR8369509/binning/vamb/cluster_attribution.tsv, SRR8369510/binning/vamb/cluster_attribution.tsv, SRR8369511/binning/vamb/cluster_attribution.tsv, SRR8369512/binning/vamb/cluster_attribution.tsv, SRR8369513/binning/vamb/cluster_attribution.tsv, SRR8369518/binning/vamb/cluster_attribution.tsv, SRR8369519/binning/vamb/cluster_attribution.tsv, SRR8369520/binning/vamb/cluster_attribution.tsv, SRR8369523/binning/vamb/cluster_attribution.tsv, SRR8369525/binning/vamb/cluster_attribution.tsv, SRR8369527/binning/vamb/cluster_attribution.tsv, SRR8369528/binning/vamb/cluster_attribution.tsv, SRR8369531/binning/vamb/cluster_attribution.tsv, SRR8369533/binning/vamb/cluster_attribution.tsv, SRR8369534/binning/vamb/cluster_attribution.tsv, SRR8369535/binning/vamb/cluster_attribution.tsv, SRR8369536/binning/vamb/cluster_attribution.tsv, SRR8369537/binning/vamb/cluster_attribution.tsv, SRR8369538/binning/vamb/cluster_attribution.tsv, SRR8369539/binning/vamb/cluster_attribution.tsv, SRR8369540/binning/vamb/cluster_attribution.tsv, SRR8369541/binning/vamb/cluster_attribution.tsv, SRR8369542/binning/vamb/cluster_attribution.tsv, SRR8369545/binning/vamb/cluster_attribution.tsv, SRR8369547/binning/vamb/cluster_attribution.tsv, SRR8369548/binning/vamb/cluster_attribution.tsv, SRR8369549/binning/vamb/cluster_attribution.tsv, SRR8369550/binning/vamb/cluster_attribution.tsv, SRR8369551/binning/vamb/cluster_attribution.tsv, SRR8369552/binning/vamb/cluster_attribution.tsv, SRR8369553/binning/vamb/cluster_attribution.tsv, SRR8369555/binning/vamb/cluster_attribution.tsv, SRR8369556/binning/vamb/cluster_attribution.tsv, SRR8369557/binning/vamb/cluster_attribution.tsv, SRR8369558/binning/vamb/cluster_attribution.tsv, SRR8369559/binning/vamb/cluster_attribution.tsv, SRR8369560/binning/vamb/cluster_attribution.tsv, SRR8369561/binning/vamb/cluster_attribution.tsv, SRR8369562/binning/vamb/cluster_attribution.tsv, SRR8369563/binning/vamb/cluster_attribution.tsv, SRR8369564/binning/vamb/cluster_attribution.tsv, SRR8369567/binning/vamb/cluster_attribution.tsv, SRR8369570/binning/vamb/cluster_attribution.tsv, SRR8369571/binning/vamb/cluster_attribution.tsv, SRR8369573/binning/vamb/cluster_attribution.tsv, SRR8369574/binning/vamb/cluster_attribution.tsv, SRR8369575/binning/vamb/cluster_attribution.tsv, SRR8369576/binning/vamb/cluster_attribution.tsv, SRR8369577/binning/vamb/cluster_attribution.tsv, SRR8369580/binning/vamb/cluster_attribution.tsv, SRR8369582/binning/vamb/cluster_attribution.tsv, SRR8369584/binning/vamb/cluster_attribution.tsv, SRR8369586/binning/vamb/cluster_attribution.tsv, SRR8369587/binning/vamb/cluster_attribution.tsv, SRR8369588/binning/vamb/cluster_attribution.tsv, SRR8369589/binning/vamb/cluster_attribution.tsv, SRR8369590/binning/vamb/cluster_attribution.tsv, SRR8369591/binning/vamb/cluster_attribution.tsv, SRR8369592/binning/vamb/cluster_attribution.tsv, SRR8369593/binning/vamb/cluster_attribution.tsv, SRR8369594/binning/vamb/cluster_attribution.tsv, SRR8369596/binning/vamb/cluster_attribution.tsv, SRR8369597/binning/vamb/cluster_attribution.tsv, SRR8369598/binning/vamb/cluster_attribution.tsv, SRR8369599/binning/vamb/cluster_attribution.tsv, SRR8369601/binning/vamb/cluster_attribution.tsv, SRR8369602/binning/vamb/cluster_attribution.tsv, SRR8369603/binning/vamb/cluster_attribution.tsv, SRR8369605/binning/vamb/cluster_attribution.tsv, SRR8369606/binning/vamb/cluster_attribution.tsv, SRR8369607/binning/vamb/cluster_attribution.tsv, SRR8369608/binning/vamb/cluster_attribution.tsv, SRR8369610/binning/vamb/cluster_attribution.tsv, SRR8369612/binning/vamb/cluster_attribution.tsv, SRR8369613/binning/vamb/cluster_attribution.tsv, SRR8369614/binning/vamb/cluster_attribution.tsv, SRR8369615/binning/vamb/cluster_attribution.tsv, SRR8369616/binning/vamb/cluster_attribution.tsv, SRR8369617/binning/vamb/cluster_attribution.tsv, SRR8369618/binning/vamb/cluster_attribution.tsv, SRR8369619/binning/vamb/cluster_attribution.tsv, SRR8369620/binning/vamb/cluster_attribution.tsv, SRR8369621/binning/vamb/cluster_attribution.tsv, SRR8369622/binning/vamb/cluster_attribution.tsv, SRR8369623/binning/vamb/cluster_attribution.tsv, SRR8369624/binning/vamb/cluster_attribution.tsv, SRR8369625/binning/vamb/cluster_attribution.tsv, SRR8369626/binning/vamb/cluster_attribution.tsv, SRR8369627/binning/vamb/cluster_attribution.tsv, SRR8369628/binning/vamb/cluster_attribution.tsv, SRR8369629/binning/vamb/cluster_attribution.tsv, SRR8369630/binning/vamb/cluster_attribution.tsv, SRR8369631/binning/vamb/cluster_attribution.tsv, SRR8369633/binning/vamb/cluster_attribution.tsv, SRR8369634/binning/vamb/cluster_attribution.tsv, SRR8369635/binning/vamb/cluster_attribution.tsv, SRR8369638/binning/vamb/cluster_attribution.tsv, SRR8369639/binning/vamb/cluster_attribution.tsv, SRR8369640/binning/vamb/cluster_attribution.tsv, SRR8369641/binning/vamb/cluster_attribution.tsv, SRR8369642/binning/vamb/cluster_attribution.tsv, SRR8369643/binning/vamb/cluster_attribution.tsv, SRR8369644/binning/vamb/cluster_attribution.tsv, SRR8369645/binning/vamb/cluster_attribution.tsv, SRR8369647/binning/vamb/cluster_attribution.tsv, SRR8369649/binning/vamb/cluster_attribution.tsv, SRR8369650/binning/vamb/cluster_attribution.tsv, SRR8369651/binning/vamb/cluster_attribution.tsv, SRR8369652/binning/vamb/cluster_attribution.tsv, SRR8369653/binning/vamb/cluster_attribution.tsv, SRR8369654/binning/vamb/cluster_attribution.tsv, SRR8369656/binning/vamb/cluster_attribution.tsv, SRR8369657/binning/vamb/cluster_attribution.tsv, SRR8369658/binning/vamb/cluster_attribution.tsv, SRR8369659/binning/vamb/cluster_attribution.tsv, SRR8369662/binning/vamb/cluster_attribution.tsv, SRR8369663/binning/vamb/cluster_attribution.tsv, SRR8369664/binning/vamb/cluster_attribution.tsv, SRR8369665/binning/vamb/cluster_attribution.tsv, SRR8369666/binning/vamb/cluster_attribution.tsv, SRR8369667/binning/vamb/cluster_attribution.tsv, SRR8369668/binning/vamb/cluster_attribution.tsv, SRR8369669/binning/vamb/cluster_attribution.tsv, SRR8369670/binning/vamb/cluster_attribution.tsv, SRR8369671/binning/vamb/cluster_attribution.tsv, SRR8369672/binning/vamb/cluster_attribution.tsv, SRR8369673/binning/vamb/cluster_attribution.tsv, SRR8369674/binning/vamb/cluster_attribution.tsv, SRR8369679/binning/vamb/cluster_attribution.tsv, SRR8369682/binning/vamb/cluster_attribution.tsv, SRR8369683/binning/vamb/cluster_attribution.tsv, SRR8369684/binning/vamb/cluster_attribution.tsv, SRR8369686/binning/vamb/cluster_attribution.tsv, SRR8369687/binning/vamb/cluster_attribution.tsv, SRR8369688/binning/vamb/cluster_attribution.tsv, SRR8369689/binning/vamb/cluster_attribution.tsv, SRR8369690/binning/vamb/cluster_attribution.tsv, SRR8369691/binning/vamb/cluster_attribution.tsv, SRR8369693/binning/vamb/cluster_attribution.tsv, SRR8369694/binning/vamb/cluster_attribution.tsv, SRR8369696/binning/vamb/cluster_attribution.tsv, SRR8369698/binning/vamb/cluster_attribution.tsv, SRR8369702/binning/vamb/cluster_attribution.tsv

Here is the relevant log output:

2023-09-24 10:27:54 Parse vamb output for bingroup healthy
2023-09-24 10:27:55 Found 1852 bins created by Vamb (above size limit)
E.g. ['SRR8369372:1922', 'SRR8369613:3775', 'SRR8369556:1841', 'SRR8369669:2710', 'SRR8369519:1707']
2023-09-24 10:27:55 Load vamb cluster file Intermediate/cobinning/healthy/vamb_output/clusters.tsv
2023-09-24 10:27:58 Parse vamb output for bingroup Pneumonia
2023-09-24 10:27:58 Found 958 bins created by Vamb (above size limit)
E.g. ['SRR8369580:802', 'SRR8369698:4160', 'SRR8369454:2041', 'SRR8369397:3135', 'SRR8369383:1394']
2023-09-24 10:27:58 Load vamb cluster file Intermediate/cobinning/Pneumonia/vamb_output/clusters.tsv
2023-09-24 10:27:59 Concatenate clusters of all bingroups
2023-09-24 10:28:00 Number of bins per sample and bingroup passing the size filter:
BinGroup   Sample
Pneumonia  SRR8369380    19
           SRR8369381    15
           SRR8369383    22
           SRR8369393    12
           SRR8369394     7
                         ..
healthy    SRR8369686     5
           SRR8369687    18
           SRR8369688    29
           SRR8369689    16
           SRR8369702     8
Name: BinId, Length: 239, dtype: int64
2023-09-24 10:28:00 Write reformated table to Binning/vamb/vamb_clusters.tsv.gz
2023-09-24 10:28:06 Write cluster_attribution for samples
2023-09-24 10:28:07 Uncaught exception: Traceback (most recent call last):
  File "/lisc/scratch/hygiene/P1_Catalog_Project/01_ATLAS/URT_B1/.snakemake/scripts/tmph5a6ip1y.parse_vamb.py", line 135, in <module>
    cl[["Contig", "SampleBin"]].to_csv(
  File "/lisc/scratch/hygiene/P1_Catalog_Project/Resources/ATLASDB/conda_envs/eec97627e0168911f89cd4541f94e683_/lib/python3.9/site-packages/pandas/core/generic.py", line 3387, in to_csv
    return DataFrameRenderer(formatter).to_csv(
  File "/lisc/scratch/hygiene/P1_Catalog_Project/Resources/ATLASDB/conda_envs/eec97627e0168911f89cd4541f94e683_/lib/python3.9/site-packages/pandas/io/formats/format.py", line 1083, in to_csv
    csv_formatter.save()
  File "/lisc/scratch/hygiene/P1_Catalog_Project/Resources/ATLASDB/conda_envs/eec97627e0168911f89cd4541f94e683_/lib/python3.9/site-packages/pandas/io/formats/csvs.py", line 228, in save
    with get_handle(
  File "/lisc/scratch/hygiene/P1_Catalog_Project/Resources/ATLASDB/conda_envs/eec97627e0168911f89cd4541f94e683_/lib/python3.9/site-packages/pandas/io/common.py", line 647, in get_handle
    handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'SRR8369705/binning/vamb/cluster_attribution.tsv'

Atlas, version 2.18.0

Additional context

The error is for a sample that I excluded from the analysis after there were no Bins for the same. It seems like this rule in the workflow is not updated to the removed sample. or maybe I am doing something wrong.

I tried the following things:

I was actually doing single-sample binning first and then I switched to co-binning by updating the BinGroup in samples.tsv file. Some of the samples failed in the initial binning step so I removed them later. But then the error that I am getting is for samples which I have excluded now.

Is there a quick fix to this? Or do I have to run ATLAS again from the beginning?

I think I made it too complicated with the binning and co-binning back to back. Any help from your side would be appreciated.

SilasK commented 11 months ago
  1. No you don't need run atlas from the beginning. Maybe only binning.

By excluding you mean deleting the line from the sample.tsv, isn't it?

What you probably need to do is to delete all files in Intermediate/cobinning And in Binning/

And Restart. Check with dryrun that you don't execute steps from assembly in or before.

Also there is I think a monor update to atlas

the-eon-flux commented 11 months ago

Yes, I am deleting the sample rows. I made another file excluded_samples.tsv and moved the sample rows there to keep a track.

Thank you for your help. I deleted all the files, and I am running binning now. It didn't show any assembly run jobs with --dry-run.

Will keep you posted if I get the same error.

the-eon-flux commented 11 months ago

Hey, thank you for your help!

It worked and I am running atlas genomes now.

It is interesting how without co-binning, 37 samples had failed earlier after binning. And now, only 20 samples failed binning. So I ended up removing fewer samples.

I have some bins with the co-binning group (Healthy or Pneumonia) as a suffix name.

Just a quick question. Are those 17 samples (that are not failing to be binned now), retained now because there are some bins in those samples with more coverage or something?

SilasK commented 10 months ago

Vamb get more bins in general. I think it also gets more bins from low quality samples.

I suggest you to quantify all samples once you have a final set of mags.

E.g. add the samples vack and run 'atlas run quantify_genomes'

Chack that binning is not triggered again.

the-eon-flux commented 9 months ago

Sorry for the late reply. You were right. Some bins are of lower quality but they are good enough. Thanks for your help!