Binsanity-profile truncates the name of the alignment file

[jolespin]

I'm using Binsanity v0.2.8

Apologies for all of the activity on here lately. I've been trying to integrate Binsanity into some of the pipelines at my institute. Thought it would to log some of the issues and questions instead of just forgetting about them.

(metagenomics_env) -bash-4.1$ Binsanity-profile -i scaffolds.fasta -s ./alignment_output/ -T 4 -o binsanity_output --ids ./alignment_output/contig_identifiers.list -c binsanity_output/output.cov

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

        ==========     _____ _    _ ____  _____  ______          _____
        =====         / ____| |  | |  _ \|  __ \|  ____|   /\   |  __ \
          =====      | (___ | |  | | |_) | |__) | |__     /  \  | |  | |
            ====      \___ \| |  | |  _ <|  _  /|  __|   / /\ \ | |  | |
              ====    ____) | |__| | |_) | | \ \| |____ / ____ \| |__| |
        ==========   |_____/ \____/|____/|_|  \_\______/_/    \_\_____/
      v1.6.4

//========================== featureCounts setting ===========================\\
||                                                                            ||
||             Input files : 1 BAM file                                       ||
||                           P alignment.bam                                  ||
||                                                                            ||
||             Output file : lignment.bam.readcounts                          ||
||                 Summary : lignment.bam.readcounts.summary                  ||
||              Annotation : lignment.bam.saf (SAF)                           ||
||      Dir for temp files : binsanity_output                                 ||
||                                                                            ||
||                 Threads : 4                                                ||
||                   Level : meta-feature level                               ||
||              Paired-end : no                                               ||
||      Multimapping reads : counted                                          ||
|| Multi-overlapping reads : counted                                          ||
||   Min overlapping bases : 1                                                ||
||                                                                            ||
\\============================================================================//

//================================= Running ==================================\\
||                                                                            ||
|| Load annotation file lignment.bam.saf ...                                  ||
||    Features : 29710                                                        ||
||    Meta-features : 29710                                                   ||
||    Chromosomes/contigs : 29710                                             ||
||                                                                            ||
|| Process BAM file alignment.bam...                                          ||
||    Paired-end reads are included.                                          ||
||    Assign alignments to features...                                        ||
||    Total alignments : 166130                                               ||
||    Successfully assigned alignments : 84217 (50.7%)                        ||
||    Running time : 0.01 minutes                                             ||
||                                                                            ||
||                                                                            ||
|| Summary of counting results can be found in file "binsanity_output/lignme  ||
|| nt.bam.readcounts.summary"                                                 ||
||                                                                            ||
\\============================================================================//

        ********************************************************
                        Coverage profile produced
        ********************************************************

(metagenomics_env) -bash-4.1$ ls binsanity_output/
lignment.bam.readcounts  lignment.bam.readcounts.summary  lignment.bam.saf  output.cov.cov  output.cov.cov.x100.lognorm

[edgraham]

I am not sure why this would be occuring, are you saying it is truncating the name in the output coverage file or in the featurecounts output? What is the initial name of the file and how is it changing that name?

It could be related to featureCounts (I am currently running v1.5.3) and have never had issues with truncated bam file names, but there may be another issue at play here.