virusbreakend samtools check should require recent samtools version

[MjelleLab]

Got this error. Maybe related to the samtools error further up? Please see code below:

Fri Nov 5 14:55:19 MET 2021: Aligning viral reads ./sample.virusbreakend.vcf.virusbreakend.working/unadjusted/unmapped.bam.viral.bam
[M::bwa_idx_load_from_disk] read 0 ALT contigs
[M::bwa_idx_load_from_disk] read 0 ALT contigs
fixmate: invalid option -- 'm'
Usage: samtools fixmate <in.nameSrt.bam> <out.nameSrt.bam>
Options:
-r Remove unmapped reads and secondary alignments
-p Disable FR proper pair check
-c Add template cigar ct tag
--input-fmt-option OPT[=VAL]
Specify a single input file format option in the form
of OPTION or OPTION=VALUE
-O, --output-fmt FORMAT[,OPT[=VAL]]...
Specify output format (SAM, BAM, CRAM)
--output-fmt-option OPT[=VAL]
Specify a single output file format option in the form
of OPTION or OPTION=VALUE
--reference FILE
Reference sequence FASTA FILE [null]

As elsewhere in samtools, use '-' as the filename for stdin/stdout. The input
file must be grouped by read name (e.g. sorted by name). Coordinated sorted
input is not accepted.
[M::process] read 51031 sequences (7705681 bp)...
[M::mem_process_seqs] Processed 51031 reads in 3.632 CPU sec, 0.470 real sec
[M::process] read 529802 sequences (80000102 bp)...
[M::process] read 529802 sequences (80000102 bp)...
[M::mem_pestat] # candidate unique pairs for (FF, FR, RF, RR): (0, 19, 0, 0)
[M::mem_pestat] skip orientation FF as there are not enough pairs
[M::mem_pestat] analyzing insert size distribution for orientation FR...
[M::mem_pestat] (25, 50, 75) percentile: (342, 403, 514)
[M::mem_pestat] low and high boundaries for computing mean and std.dev: (1, 858)
[M::mem_pestat] mean and std.dev: (421.11, 96.77)
[M::mem_pestat] low and high boundaries for proper pairs: (1, 1030)
[M::mem_pestat] skip orientation RF as there are not enough pairs
[M::mem_pestat] skip orientation RR as there are not enough pairs
[M::mem_process_seqs] Processed 529802 reads in 35.460 CPU sec, 4.568 real sec
Fri Nov 5 14:55:25 MET 2021: Failure running aligning viral reads

[MjelleLab]

removing -m from the virusbreakend file solved this.

[MjelleLab]

But now I got this error:

Fri Nov 5 16:03:23 MET 2021: Aligning viral reads ./sample.virusbreakend.vcf.virusbreakend.working/unadjusted/unmapped.bam.viral.bam
[main] unrecognized command 'coverage'
Fri Nov 5 16:05:16 MET 2021: Exit status 0 for samtools coverage $prefix_unadjusted.merged.bam > $prefix_unadjusted.merged.bam.coverage

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See log file ./sample.virusbreakend.vcf.virusbreakend.working/virusbreakend.20211105_160323.mh-ikom01.1138.log for underlying error

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[MjelleLab]

Solved by updating samtools