Metaphlan4_Broken pipe error

Microbial community profiling MetaPhlAn
1

while running MetaPhlan 4 , I am getting the following error. I have about 200 gb space in my computer…if it is a memory issue.

bowtie2-align exited with value 137
Traceback (most recent call last):
File “/home/poppy/miniconda3/envs/mpa/bin/read_fastx.py”, line 10, in
sys.exit(main())
File “/home/poppy/miniconda3/envs/mpa/lib/python3.7/site-packages/metaphlan/utils/read_fastx.py”, line 168, in main
f_nreads, f_avg_read_length = read_and_write_raw(f, opened=False, min_len=min_len, prefix_id=prefix_id)
File “/home/poppy/miniconda3/envs/mpa/lib/python3.7/site-packages/metaphlan/utils/read_fastx.py”, line 130, in read_and_write_raw
nreads, avg_read_length = read_and_write_raw_int(inf, min_len=min_len, prefix_id=prefix_id)
File “/home/poppy/miniconda3/envs/mpa/lib/python3.7/site-packages/metaphlan/utils/read_fastx.py”, line 109, in read_and_write_raw_int
print_record(description + “__{}{}{}”.format(prefix_id, ‘.’ if prefix_id else ‘’, idx), sequence, qual, fmt))
BrokenPipeError: [Errno 32] Broken pipe

2

Hi @shreya
It seems more a problem of RAM than storage space. How much ram is available in your machine for running metaphlan 4 ?

3

Hello @aitor.blancomiguez, I see the same error message but the HPC I have access to has 35 gb of RAM.

4

While I have access to at least 35Gb of RAM the pod I am using in a HPC resource limited me to only accessing 4Gb of RAM. Once I increased the limits I no longer experienced the error.