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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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Failed to run binner. Exiting... #273

Open Vikicai opened 4 years ago

Vikicai commented 4 years ago

Hi, I'm running into an issue when using the classify_bins tool and got this error:

########################################################################################################################
#####                                   ALIGN CONTIGS TO DATABASE WITH MEGABLAST                                   #####
########################################################################################################################

------------------------------------------------------------------------------------------------------------------------
-----            setting up ouput folder /mnt/worker/workplace-life/s05-03/Classify/ and merging contigs           -----
-----                                               from all bins...                                               -----
------------------------------------------------------------------------------------------------------------------------

Warning: /mnt/worker/workplace-life/s05-03/Classify/ already exists.

------------------------------------------------------------------------------------------------------------------------
-----                    aligning /mnt/worker/workplace-life/s05-03/Classify//all_contigs.fa to                    -----
-----          /mnt/worker/workplace-life/Database-metawrap/NCBI_nt database with MEGABLAST. This is the           -----
-----               longest step - please be patient. You may look at the classification progress in               -----
-----                      /mnt/worker/workplace-life/s05-03/Classify//megablast_out.raw.tab                       -----
------------------------------------------------------------------------------------------------------------------------

------------------------------------------------------------------------------------------------------------------------
-----                  removing unnecessary lines that lead to bad tax IDs (without a proper rank)                 -----
------------------------------------------------------------------------------------------------------------------------

------------------------------------------------------------------------------------------------------------------------
-----                                              making mapping file                                             -----
------------------------------------------------------------------------------------------------------------------------

########################################################################################################################
#####                              GET TAXONOMY FROM MEGABLAST OUTPUT WITH TAXATOR-TK                              #####
########################################################################################################################

------------------------------------------------------------------------------------------------------------------------
-----                                   pulling out classifications with taxator                                   -----
------------------------------------------------------------------------------------------------------------------------

------------------------------------------------------------------------------------------------------------------------
-----                           binning and consolidating classifications for each contig                          -----
------------------------------------------------------------------------------------------------------------------------

analyzing sample composition by signal counting... done: 5663 nested taxa with total support of 142350761 bp
noise removal... done: 0 taxa were removed
binning step...  done
mv: "binning.log" and"/mnt/worker/workplace-life/s05-03/Classify/binning.log" are the same file

************************************************************************************************************************
*****                                       Failed to run binner. Exiting...                                       *****
************************************************************************************************************************

real    1773m22.003s
user    1706m8.980s
sys 1m56.364s
ursky commented 4 years ago

I revisited the code and there was a bug in the code that I just patched up on the metawrap gihub page. Its never come up before because it only happens if the current working directory is the same as your output directory... im assuming that you ran metawrap with -o ., or something similar? In any case, to get the fix you can just replace the metawrap/bin/metawrap-modules/classify_bins.sh script that you are currently using to the one from this repository.

Vikicai commented 4 years ago

Thanks for your reply. I will try it again