# BrokenPipeError MetaPhlAn 3.0.7

**URL:** <https://forum.biobakery.org/t/brokenpipeerror-metaphlan-3-0-7/1476>\
**Category:** MetaPhlAn\
**Created:** [December 28, 2020, 10:01am UTC](https://forum.biobakery.org/t/brokenpipeerror-metaphlan-3-0-7/1476 "2020-12-28T10:01:15Z")\
**Posts on this page:** 2\
**Page:** 1

<div class="post-metadata">

**Author:** ![Keepi983](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/keepi983/32/540_2.png) [@Keepi983](https://forum.biobakery.org/u/Keepi983)\
**Post date:** [December 28, 2020, 10:01am UTC](https://forum.biobakery.org/t/brokenpipeerror-metaphlan-3-0-7/1476/1 "2020-12-28T10:01:15Z")

</div>

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

---

<div class="post-metadata">

**Author:** ![fbeghini](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/fbeghini/32/81_2.png) [@fbeghini](https://forum.biobakery.org/u/fbeghini)\
**Post date:** [December 30, 2020, 10:29am UTC](https://forum.biobakery.org/t/brokenpipeerror-metaphlan-3-0-7/1476/2 "2020-12-30T10:29:24Z")

</div>

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.