Fatal error running metaphlan

[Megan Folkerts]

Hello,

I am suddenly getting the following error when running metaphlan:

Fatal error running MetaPhlAn2. Total metagenome size was not estimated.

Please update read_fastx.py to the latest version.

I recently uninstalled and re-installed metaphlan using conda, and am running version 2.96. I noticed there was another user that reported this issue on the bitbucket help page, however there was no resolution. What is causing this?

Here's the exact command I'm running:

metaphlan2.py 113C22_S17_R1_001_kneaddata_paired_1.fastq,113C22_S17_R1_001_kneaddata_paired_2.fastq --input_type fastq --bowtie2db /home/mfolkerts/miniconda3/envs/metaphlan2/bin/metaphlan_databases/ --bowtie2out 113C22.bowtie2.bz2 -o 113C22_profile --nproc 8

Thanks,

Megan