The bioBakery help forum

BrokenPipeError MetaPhlAn 3.0.7

Downloaded the database and built bowtie index. Tried to run MetaPhlAn on a sample .fasta file. Encountered the following error while running MetaPhlAn 3.0.7 on a .fasta file.

Error reading _ebwt[] array: no more data
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/priya/anaconda3/bin/bowtie2-align-s --wrapper basic-0 --quiet --very-sensitive -x /home/priya/anaconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_201901 -p 4 -f --passthrough -U -
(ERR): bowtie2-align exited with value 1
Traceback (most recent call last):
File “/home/priya/anaconda3/bin/read_fastx.py”, line 10, in
sys.exit(main())
File “/home/priya/anaconda3/lib/python3.7/site-packages/metaphlan/utils/read_fastx.py”, line 155, in main
f_nreads, f_avg_read_length = read_and_write_raw(f, opened=False, min_len=min_len)
File “/home/priya/anaconda3/lib/python3.7/site-packages/metaphlan/utils/read_fastx.py”, line 118, in read_and_write_raw
nreads, avg_read_length = read_and_write_raw_int(inf, min_len=min_len)
File “/home/priya/anaconda3/lib/python3.7/site-packages/metaphlan/utils/read_fastx.py”, line 101, in read_and_write_raw_int
_ = sys.stdout.write(print_record(description, sequence, qual, fmt))
BrokenPipeError: [Errno 32] Broken pipe

I’d suggest to remove the bowtie2 index from /home/priya/anaconda3/lib/python3.7/site-packages/metaphlan/metaphlan_databases/ and re-build it using bowtie2-build. It seems that the index you have is corrupted.