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bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
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Could not find node with taxonomic id TaxID in taxonomy, skipping record. #358

Open yulong0827 opened 3 years ago

yulong0827 commented 3 years ago

Hello everyone. I got a error when run metawrap1.3.2-mg in an independent conda environment, do you know how to solve the problem? Many thanks! The error is pasted as follows:

metawrap classify_bins -b ceshi -o BIN_CLASSIFICATIONce -t 32
metawrap classify_bins -b ceshi -o BIN_CLASSIFICATIONce -t 32

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

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-----               setting up ouput folder BIN_CLASSIFICATIONce and merging contigs from all bins...              -----
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-----           aligning BIN_CLASSIFICATIONce/all_contigs.fa to /home/liuyulong/NCBI_NT_DB database with           -----
-----                 MEGABLAST. This is the longest step - please be patient. You may look at the                 -----
-----                    classification progress in BIN_CLASSIFICATIONce/megablast_out.raw.tab                     -----
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-----                  removing unnecessary lines that lead to bad tax IDs (without a proper rank)                 -----
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-----                                              making mapping file                                             -----
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########################################################################################################################
#####                              GET TAXONOMY FROM MEGABLAST OUTPUT WITH TAXATOR-TK                              #####
########################################################################################################################

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-----                                   pulling out classifications with taxator                                   -----
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-----                           binning and consolidating classifications for each contig                          -----
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analyzing sample composition by signal counting... done: 1 nested taxa with total support of 0 bp
noise removal... done: 0 taxa were removed
binning step...  done

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-----                                 pulling out full taxonomy path with taxknife                                 -----
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**Could not find node with taxonomic id  in taxonomy, skipping record.
Could not find node with taxonomic id  in taxonomy, skipping record.
Could not find node with taxonomic id  in taxonomy, skipping record.
Could not find node with taxonomic id TaxID in taxonomy, skipping record.**

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-----                                    finding consensus taxonomy for each bin                                   -----
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bin.11.fa   
bin.13.fa   
bin.2.fa    
bin.8.fa    
bin.9.fa    

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-----           you will find the consensus taxonomy of each bin in BIN_CLASSIFICATIONce/bin_taxonomy.tab          -----
------------------------------------------------------------------------------------------------------------------------

########################################################################################################################
#####                             BIN CLASSIFICATION PIPELINE FINISHED SUCCESSFULLY!!!                             #####
########################################################################################################################

real    59m15.074s
user    763m34.648s
sys 15m11.908s

**The config-metawrap:**
# Paths to metaWRAP scripts (dont have to modify)
mw_path=$(which metawrap)
bin_path=${mw_path%/*}
SOFT=${bin_path}/metawrap-scripts
PIPES=${bin_path}/metawrap-modules

# CONFIGURABLE PATHS FOR DATABASES (see 'Databases' section of metaWRAP README for details)
# path to kraken standard database
KRAKEN_DB=~/KRAKEN_DB
KRAKEN2_DB=~/KRAKEN_DB2

# path to indexed human (or other host) genome (see metaWRAP website for guide). This includes .bitmask and .srprism files
BMTAGGER_DB=~/BMTAGGER_DB

# paths to BLAST databases
BLASTDB=~/NCBI_NT_DB
TAXDUMP=~/NCBI_TAX_DB
ursky commented 3 years ago

I don't see an actual error, just warnings for some IDs. Seems to have finished correctly.