Millions of .bam files created during POLCA

[drew-olson-tmru]

Hi,

I ran POLCA with default parameters:
polca.sh -a $ASMFILE -r 'read1.fastq.gz read2.fastq.gz' -t 64 -m 20

However, I cancelled the job after 20 hours on a single fungal genome (~45Mb) and after over 11 million intermediate files were created (mostly .bam files). Is this supposed to happen? I have executed the code from both my HPC server installation and from a conda environment and I obtained the same result. This seems like this is not supposed to happen as this is supposed to be a fast and accurate tool to use. Are the intermediate files not being disposed of properly during the job?

Any help would be apreciated!

[Ifigene]

Dear developers,

I have the same problem. I have also used the default parameters and version 4.0.9.

Can you please help?

[Ifigene]

The solution I have found is to remove the option -m for memory.
Then masurca outputs the "normal" amount of files!