I get the same error. Any workarounds?
(biobakery3) user@server:~/ncbi/dbGaP-20066/sra$ humann --threads 20 --input test.fastq --output testout
Output files will be written to: /local/home/robinm/ncbi/dbGaP-20066/sra/testout
Removing spaces from identifiers in input file …
CRITICAL ERROR: Can not call software version for bowtie2
(biobakery3) user@server:~/ncbi/dbGaP-20066/sra$ bowtie2 --version
/local/home/robinm/miniconda2/envs/biobakery3/bin/bowtie2-align-s version
64-bit
Built on
Sat Jun 6 20:17:22 UTC 2020
Compiler: gcc version 7.5.0 (crosstool-NG 1.24.0.123_1667d2b)
Options: -O3 -msse2 -funroll-loops -g3 -fvisibility-inlines-hidden -std=c++17 -fmessage-length=0 -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /local/home/robinm/miniconda2/envs/biobakery3/include -fdebug-prefix-map=/opt/conda/conda-bld/bowtie2_1591474367590/work=/usr/local/src/conda/bowtie2-2.4.1 -fdebug-prefix-map=/local/home/robinm/miniconda2/envs/biobakery3=/usr/local/src/conda-prefix -DPOPCNT_CAPABILITY -DWITH_TBB -std=c++11 -DNO_SPINLOCK -DWITH_QUEUELOCK=1
Sizeof {int, long, long long, void*, size_t, off_t}: {4,