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

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)

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

Best regards,

Hi @fbeghini ,

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

Best regards,

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