error when using KRAKEN

[itiago]

Hi Gherman, hope everything is OK.

I have updated metaWRAP, and am trying to use it to analise 5 metagenomes. I already used with success all commands till assembly, and now I was trying to use KRAKEN module but I have an error and then it crashes (error bellow) Hope you can help me. Kind regards Igor

(metawrap-env) deepbio@deepbio-virtual-machine:~/Documents/Metagenomes/Spain/All$ metawrap kraken -o KRAKEN -t 5 -s 1000000 CLEAN_READS/ES_*fastq ASSEMBLY/final_assembly.fasta
metawrap kraken -o KRAKEN -t 5 -s 1000000 CLEAN_READS/ES_ALFAGU_1.fastq CLEAN_READS/ES_ALFAGU_2.fastq CLEAN_READS/ES_AMAR_1.fastq CLEAN_READS/ES_AMAR_2.fastq CLEAN_READS/ES_EBD_1.fastq CLEAN_READS/ES_EBD_2.fastq CLEAN_READS/ES_EBPU_1.fastq CLEAN_READS/ES_EBPU_2.fastq CLEAN_READS/ES_HEDION_1.fastq CLEAN_READS/ES_HEDION_2.fastq ASSEMBLY/final_assembly.fasta

########################################################################################################################
#####                                          RUNNING KRAKEN ON ALL FILES                                         #####
########################################################################################################################

------------------------------------------------------------------------------------------------------------------------
-----             Now processing CLEAN_READS/ES_ALFAGU_1.fastq and CLEAN_READS/ES_ALFAGU_2.fastq with 5            -----
-----                                                   threads                                                    -----
------------------------------------------------------------------------------------------------------------------------

------------------------------------------------------------------------------------------------------------------------
-----                                     subsampling down to 1000000 reads...                                     -----
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/home/deepbio/miniconda2/envs/metawrap-env/bin/metawrap-modules/kraken.sh: line 123:  #combine: command not found
/home/deepbio/miniconda2/envs/metawrap-env/bin/metawrap-modules/kraken.sh: line 124:  #shuffle: command not found

[ursky]

Thanks for the report, Igor. All it is is some comment lines inside a bash condition statement - it should work normally, but not always, obviously. I've seen bash script interpreters on some systems choke up on this before, so I will remove those lines for future versions. But for now, just go into /home/deepbio/miniconda2/envs/metawrap-env/bin/metawrap-modules/kraken.sh and remove the comment lines 122-124. Should work then.

[itiago]

I'm running the command now, will update the result when it finishes. Thanks for the reply.