Metaphlan single file processing error

Microbial community profiling MetaPhlAn
1

Hi all,
I am running metaphlan in conda environment in our HPC cluster. I am receiving the following error-

ValueError: End of file without quality information.

Background:

I have quality trimmed my metagenomics fastq files with bbduk and catenated the reverse and forward reads from Illumina HiSeq2500 V2 250x250bp runs.
When I am using the catenated fastq files as input, I receive the above error message.

My command:
bash
. ~/.bashrc
conda activate metaphlan
metaphlan --input_type fastq --bowtie2out 109Y --nproc 20 -o 109Y.tsv -s 109Y --biom 109Y --tmp_dir 109tmp cleaned_109Y.fq

Error details-

image
image1920×614 167 KB

Appreciate any lead on this end.
Thanks

2

Hi @arijitnus
It seems that the trimming step or the concatenation you performed had produced a problem in your FASTQ file (by the log it seems that one (or more) of the quality rows has been missed. I recommend you to check your FASTQ file to see if all 4 FASTq lines (FASTQ files explained) are present for each read.

3

Thanks, it turned out that the catenation was the problem. Now it is running.