Paired-end reads stored in a single-end read library

[dzolier]

QC'ed the reads with illumina-utils (specifically iu-filter-quality-minoche and iu-merge pairs in two different attempts), performed preliminary binning with MegaHIT; feedback at the end was as in the title. Example:

Binsanity-profile -i minoche_CONTIGS/contigs.fa -s minoche_MAPPING/ -c Binsanity_minoche/MEGAHIT_coverage --transform scale -T 1 -o Binsanity_minoche_2/

    ******************************************************
                Contigs formated to generate counts
    ******************************************************


    ==========     _____ _    _ ____  _____  ______          _____
    =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
      =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
        ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
          ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
    ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
      v2.0.2

//========================== featureCounts setting ===========================\
|| ||
|| Input files : 1 BAM file ||
|| ||
|| SRR492065.bam ||
|| ||
|| Output file : SRR492065.bam.readcounts ||
|| Summary : SRR492065.bam.readcounts.summary ||
|| Paired-end : no ||
|| Count read pairs : no ||
|| Annotation : SRR492065.bam.saf (SAF) ||
|| Dir for temp files : Binsanity_minoche_2 ||
|| ||
|| Threads : 1 ||
|| Level : meta-feature level ||
|| Multimapping reads : counted ||
|| Multi-overlapping reads : counted ||
|| Min overlapping bases : 1 ||
|| ||
\============================================================================//

//================================= Running ==================================\
|| ||
|| Load annotation file SRR492065.bam.saf ... ||
|| Features : 1546 ||
|| Meta-features : 1546 ||
|| Chromosomes/contigs : 1546 ||
|| ||
|| Process BAM file SRR492065.bam... ||
ERROR: Paired-end reads were detected in single-end read library : minoche_MAPPING/SRR492065.bam

[Harpreet525]

You will have to open your Binsanity-profile script and add the parameter "-p" in line 31 to allow the script to forward the command to featureCounts to be able to read paired-end reads. It will work.
Because the script of Binsanity-profile is not prompting the featureCounts script to read paired reads.