ERROR: max count before zero is less than min required count (4) duplicates removed

[didillysquat]

Running preseq from the latest release preseq-3.1.2.tar.gz

lc_extrap give the following error:

Singularity> preseq lc_extrap -P scaf1.1m.bam
ERROR:	max count before zero is less than min required count (4) duplicates removed

However, converting the .bam to .bed first and then running lc_extrap on the .bed file completes as expected:

Singularity> bedtools bamtobed -i scaf1.1m.bam > scaf1.1m.bed
Singularity> preseq lc_extrap -P scaf1.1m.bed > lc_extrap.out

Any idea what's going wrong?

Example .bam and .bed files attached. bams.zip

[idot]

I have the same issue. I use the preseq from bioconda which was built with --enable-hts .

wget https://depot.galaxyproject.org/singularity/preseq%3A3.1.2--h06ef8b0_1
singularity exec preseq:3.1.2--h06ef8b0_1 preseq  lc_extrap -pe -output 187530_T1.ccurve.txt  187530_T1.bam
ERROR:	max count before zero is less than min required count (4) duplicates removed

see also #49

(I also tried preseq:3.1.2--hfb6f838_0)

[z-spider]

need -B or --bam，then we will encounter this problem: #57 but, -B option is not what was causing the issue.

preseq try to merge the paired-end reads, but there are multiple alignments in the bam. -v option can show that. use samtools to fileter multiple alignments can fix it.

All the best.