No error for running MetaPhlAn3, but nothing in the output file - profile.txt

Microbial community profiling MetaPhlAn
1

Hi all,

I ran MetaPhlAn3 for one metagenomics sample at the back end with the command:

metaphlan sample1.fa --input_type fasta --nproc 30 > sample1_profile.txt

No error was reported and there were 2 output files. However, nothing was written to the output file - sample1_profile.txt

-rwxr–r-- 1 claire claire 16507925362 Feb 25 22:39 sample1.fa*
-rw-r–r-- 1 claire claire 134433986 Mar 1 00:30 sample1.fa.bowtie2out.txt
-rw-r–r-- 1 claire claire 0 Mar 1 00:18 sample1_profile.txt

According to the nohup.out, there is no error. Strangely, the content inside the nohup.txt seem to be the “real” output for profile.txt.
nohup.txt (58.3 KB)

image
image1508×817 61.3 KB

Any comments or suggestions on this issue would be highly appreciated.

Best regards,
Claire

2

Hi @fbeghini ,

Not sure whether I’m tagging the right person. Just wondering you have any idea how to solve the issue?

Best regards,
Claire

3

Hi @Claire
You should be able to solve this problem by using the -o parameter instead of >
E.g: metaphlan sample1.fa --input_type fasta --nproc 30 -o sample1_profile.txt