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biobakery / MetaPhlAn

MetaPhlAn is a computational tool for profiling the composition of microbial communities from metagenomic shotgun sequencing data
http://segatalab.cibio.unitn.it/tools/metaphlan/index.html
MIT License
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MetaPhlAn3: IndexError: list index out of range #181

Closed y1025i closed 2 years ago

y1025i commented 2 years ago

Hi, I use MetaPhlAn3 to which I downloaded through conda install.

Command: metaphlan R19003012LD01-XG9021.merge.fastq --input_type fastq -o R19003012LD01-XG9021.metaphlan.profile

I got an error:

Traceback (most recent call last): File "/lustre/zhangy/software/miniconda3/bin/metaphlan", line 8, in sys.exit(main()) File "/lustre/zhangy/software/miniconda3/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 "/lustre/zhangy/software/miniconda3/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

Can anyone help me solve this problem ? Thank you!

github-actions[bot] commented 2 years ago

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