WARNING: Use of uninitialized value

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

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

1 Like

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

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.