WARNING: Use of uninitialized value

Microbial community profiling MetaPhlAn
1

Hi community!!! @fbeghini
I using Metaphlan3. While running it I am getting the following warning message. But also, I am getting bowtie2out.txt and profile.txt output files. Why such error is coming? How can I fix it? Should I rely on the output data?

My command:
for f in ERR273*; do metaphlan $f --input_type fastq --nproc 32 --ignore_eukaryotes --ignore_archaea > ${f%.fastq.gz}_profile.txt; done

WARNING meassage:

Use of uninitialized value $bt2_args[2] in join or string at /home/ubuntu/anaconda3/envs/biobakery3/bin/bowtie2 line 423.

Use of uninitialized value $bt2_args[3] in join or string at /home/ubuntu/anaconda3/envs/biobakery3/bin/bowtie2 line 459.

Thanks and Regards,
DC7

2

See https://github.com/biobakery/MetaPhlAn/issues/101#issuecomment-646657221

1 Like
3

Thanks @fbeghini. According to your comment in the discussion, this WARNING does not affect the output. So, I will proceed with the output files. But, is there any problem if I don’t use the --no-unal flag and just use the above mentioned command?

Thanks,
DC7

4

It’s better to leave the internal command as it is since the sam output handling is done under the assumption that the non-aligned reads are not present.