Dear all, I'm transitioning from khmer-0.7.1 to khmer-2.0 and my pipepline (PE Illumina raw reads->Trimomatic->interleave-reads.py->extract-paired-reads.py->normalize-by-mean.py) fails to recognise the reads as paired reads at the digital normalization step, as suggested by the following error message from normalize-by-median.py in paired mode :
making countgraph ** ERROR: Unpaired reads when require_paired is set! ** Failed on interleaved_trimmed_WTCHG_322035_270_1.fastq: ** Exiting!
I went to the script but can't find where the problem apart from maybe this is_paired variable(?) from line 100 onwards.
i found some information (http://lists.idyll.org/pipermail/khmer/2015-December/000766.html) regarding is_pair from the interleave-reads.py script and it seems that it requires the reads to be sorted /1 then /2, which they are in my files.
But I'm not sure if this is anyhow related with is_paired from normalize-by-median.py, and I can't find any more information as to why normalize-by-median.py might not recognize my input file as paired reads. Does anyone have any idea what I might be doing wrong (Im sure there's plenty), and what I could try to solve this issue?
Please let me know if I should be providing more/less information (or different information) ; this is my first on such forums. Many thanks Clement