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

[Some Kid]

Hello all,

I tried using Binsanity-profile on this infant gut dataset from 2013 (the Sharon et al. one) but I'm not sure where in the protocol I went wrong, or even if it matters.

I entered:
Binsanity-profile -i 03_CONTIGS/contigs.fa -s 04_MAPPING/ -c Binsanity_out/MEGAHIT_coverage --transform scale -T 1 -o Binsanity_out_2/

And every single file in there seemed to work, but they all had this error at the end of what looks like the normal feedback, so I'll paste the first block here.

        ******************************************************
                    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_out_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 : 04_MAPPING/SRR492065.bam

The bit I'm  confused about is that end statement. How should I be storing my files so that they're in a paired-end library? Does that mess up how the program operates? Is there a place I can learn the differences between library types?

Thank you for your time.

[Elaina Graham]

Hello,

This is a new issue for me. How did you produce your bam file?

-Elaina

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[Some Kid]

Hello,

I am using the workflow from the anvi'o website; I started with their  assembly-based metagenomics workflow and then made it partway through another tutorial that came afterwards. The last command I used on the data before binsanity-profile was anvi-merge.

I may have done something out of order, or perhaps out of ignorance -- I am new to bioinformatics; I may have thought something was arbitrary when it was not.

Thank you for your time,
Ken