Couldnt create consensus markers

Microbial community profiling StrainPhlAn
1

For strainphlan4 -

I was unable to create the consensus markers and kept seeing this error:

(ERR): bowtie2-align exited with value 137
Traceback (most recent call last):
File “/opt/conda/bin/read_fastx.py”, line 10, in
sys.exit(main())
File “/opt/conda/lib/python3.10/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 “/opt/conda/lib/python3.10/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 “/opt/conda/lib/python3.10/site-packages/metaphlan/utils/read_fastx.py”, line 108, in read_and_write_raw_int
_ = sys.stdout.write(
BrokenPipeError: [Errno 32] Broken pipe
Killed
(ERR): bowtie2-align exited with value 137

[main_samview] fail to read the header from “consensus_markers/tmpj636h4jv/FB03960356_MQ2867_WGS_R1…sam”.

help!

Thanks

2

Hello, could you specify precisely what command you are running? Looks like you are running metaphlan script. There’s a “Killed” among the output and also the exit code 137 looks like you are running out of memory.