The bioBakery help forum

Error using bowtie2 in humann2

This is the output I receive when trying to run the tutorial from:

I don’t understand why I keep getting these errors

Building Bowtie2 indexes
Fatal error running ‘bowtie2-build --quiet --threads 4 -f /home/j/jronho/jmarquis/anaconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna /home/j/jronho/jmarquis/anaconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901’
Error message: ‘Command ‘[‘bowtie2-build’, ‘–quiet’, ‘–threads’, ‘4’, ‘-f’, ‘/home/j/jronho/jmarquis/anaconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901.fna’, ‘/home/j/jronho/jmarquis/anaconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901’]’ returned non-zero exit status 232.’

Hi, Thank you for posting the sub-command that generated the error message. I have not seen bowtie2 exit with an error code of 232 before so I am not sure exactly what it might be. Can you run that exact command directly and see if bowtie2 prints any information to standard error to help debug what might be going on?

Thank you,
Lauren