Hi,
I’m trying to run metaphlan with my custom database.
I added a lot of fasta files and also updated dictionary (pickle file).
With the custom database files, I execute metaphlan. Then bowtie2 index files were created with file extention as .bt2l…
Then the error message came out as below :
No MetaPhlAn BowTie2 database found (–index option)!
Expecting location bowtie2db
Exiting…
===================
I thought the problem might come from the fiile extension for large bowtie index.
So, I tried to switch the file extension of bowtie file as .bt2 (just using mv ***.bt2l ***.bt2)
However, after rerun metaphlan with switched extension of bowtie2 index.
Another error came out.
=======================
First record in reference index file was not marked as ‘first’
Error: Encountered internal Bowtie 2 exception (#1)
Command: /home/miniconda2/envs/newshot/bin/bowtie2-align-s --wrapper basic-0 --quiet --very->sensitive -x /home/miniconda2/envs/newshot/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v30_CHOCOPhlAn_NEW -p 4 -f --passthrough -U -
(ERR): bowtie2-align exited with value 1
Traceback (most recent call last):
File “/home/miniconda2/envs/newshot/bin/read_fastx.py”, line 10, in
sys.exit(main())
File “/home/miniconda2/envs/newshot/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/miniconda2/envs/newshot/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/miniconda2/envs/newshot/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
So, I think the problem caused by reading of created large index bowtie2 file (.bt2l)…
Can anyone help me?
Thanks,
Kim