Errors running genome polishing with Arrow

Question

[YocelynGG]

Dear Biostars community,

I am performing a genome polishing using Arrow, but I am getting errors immediately I launch the script. I have tried to use Arrow though gcpp version 2.0.2-2.0.2 (installed via bioconda), and using variantCaller version 2.3.3

Using gcpp, I got the error above:

-|- FATAL -|- Run -|- 0x2b79f87c8300|| -|- gcpp ERROR: map::at

My code:

gcpp -j 20 file_align.bam -r genome_flye_assembly.fasta -o file_arrow.gff -o file_arrow.fa -o file_arrow.fq --algorithm arrow

Using variantCaller algorithm=arrow, I got the error above:

Invalid literal for int() with base 16

My code:

variantCaller -j 20 file_align.bam --referenceFilename file_flye_assembly.fasta -o file_arrow.gff -o file_arrow.fasta -o file_arrow.fq --algorithm arrow

I generated the PacBio genome assembly with Flye and the alignment bam file was generated using pbmm2.

There is not a report for this at the pbbioconda repository.

I tried so many options, I wonder if someone cal help to figure out and solve these errors.