Metaphlan: running on rnaseq data

Dear all,

I am running metaphlan through the docker biobakery/metaphlan image with the following command:

metaphlan reads.fq --input_type fastq --nproc 32 --add_viruses > profile.txt

I receive the following error:

File “/usr/local/bin/metaphlan”, line 11, in
File “/usr/local/lib/python3.6/dist-packages/metaphlan/”, line 991, in main
min_alignment_len=pars[‘min_alignment_len’], read_min_len=pars[‘read_min_len’], min_mapq_val=pars[‘min_mapq_val’])
File “/usr/local/lib/python3.6/dist-packages/metaphlan/”, line 429, in run_bowtie2
nreads = int(read_fastx_stderr[0])
IndexError: list index out of range

How can I solve it?

Hi. I have the same problem! were you able to figure this out?