gravatar for ccelispuga

2 hours ago by

Hi all I am trying to run this code

parallel -j 1 'humann2 --threads 1 --input {} --output humann2_out/{/.}' ::: kneaddata_out/clean_seq/*fastq

But for some reason I kept getting an error

Error message returned from metaphlan2.py :
No MetaPhlAn BowTie2 database found (--index option)!
Expecting location /opt/miniconda2/bin/databases
Exiting...
Creating output directory: /Users/christinacelispuga/humann2_out/SRS148157_kneaddata
Output files will be written to: /Users/christinacelispuga/humann2_out/SRS148157_kneaddata

Running metaphlan2.py ........

CRITICAL ERROR: Error executing: /opt/miniconda2/bin/metaphlan2.py /Users/christinacelispuga/kneaddata_out/clean_seq/SRS148157_kneaddata.fastq -t rel_ab -o /Users/christinacelispuga/humann2_out/SRS148157_kneaddata/SRS148157_kneaddata_humann2_temp/SRS148157_kneaddata_metaphlan_bugs_list.tsv --input_type multifastq --bowtie2out /Users/christinacelispuga/humann2_out/SRS148157_kneaddata/SRS148157_kneaddata_humann2_temp/SRS148157_kneaddata_metaphlan_bowtie2.txt

Error message returned from metaphlan2.py :
No MetaPhlAn BowTie2 database found (--index option)!
Expecting location /opt/miniconda2/bin/databases
Exiting...

I have tried to re-install metaphlan as well as bowtie & nothing has worked

any suggestions how to fix?



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