Hello,
I am trying to run metaphlan3 but keep getting an error
i followed some of the old posts like installing libtbb or reinstalling bowtie2 and metaphlan3 etc.
nothing worked for me
Traceback (most recent call last):
File “/home/scebmeta/bin/miniconda3/envs/metaphlan3/bin/metaphlan”, line 10, in
sys.exit(main())
File “/home/scebmeta/bin/miniconda3/envs/metaphlan3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 1060, in main
min_alignment_len=pars[‘min_alignment_len’], read_min_len=pars[‘read_min_len’], min_mapq_val=pars[‘min_mapq_val’])
File “/home/scebmeta/bin/miniconda3/envs/metaphlan3/lib/python3.7/site-packages/metaphlan/metaphlan.py”, line 434, in run_bowtie2
nreads, avg_read_length = list(map(float, read_fastx_stderr[0].decode().split()))
IndexError: list index out of range
my command was, started only for one sample
bowtie2db="/media/scebmeta/SSD/DB/"
metaphlan KN100_R1.unmapped.fastq.gz KN100_R2.unmapped.fastq.gz --bowtie2db $bowtie2db --bt2_ps very-sensitive --ignore_eukaryotes --ignore_archaea --input_type fastq -t rel_ab_w_read_stats --bowtie2out profiled_very_sensitive/1x.bowtie2_out.bz2 --nproc $(nproc) -o profiled_very_sensitive/1x.txt
…
FYI: installed in a conda environment and downloaded the database in a separate folder
Please can you help me to solve this issue?
Thanks,
Khem