schmeing

The python code uses np.int32 to read in the files from minimap2, so for these large draft genomes you need to replace these with np.int64 or int. Then I hope...

The first thing would be to check if it is purely an error during plotting. You can remove the plotting by removing `-s pass${i}/gapless_stats.pdf` from the `gapless.py scaffold` command. The...

Thx for the detailed information. The negative number should not be there as a result of the fit. The program cannot successfully run through like this with out without plotting....

I am still facing issues with the VPN and cannot run anything, but thinking about it some more, I realized that maybe it is not the fit that goes wrong,...

Thank you! The numbers in the dataframe seem to be good. Thus, I introduced bounds to the optimization and this should fix the issue. It requires Scipy 1.7.0 now, so...

Sorry, for being unclear scipy >= 1.7.0 is required. So, it should work for you. Providing the information to the program which contigs are allowed to be connected is currently...

With the latest commit the memory requirement of the step that crashed for you should be considerably reduced. To split the job into subgenomes, I would recommend to align the...

In the gapless.py there is a parameter org_scaffold_trust that is by default set to "basic". If you set it to "blind", it should only fill gaps. I did not pull...

Thank you for reporting this. The divisions by zero worry me and that the graph is inconsistent should never happen, so this is clearly a bug. To fix this we...

I strongly assume that the crash is caused by the `-o /mnt/project/IPV2/gapless/gapless/final_output_assembly/` after the read file specification `porechop_output.fastq.gz`. `sh gapless.sh -j 40 -i genome.fasta -o /mnt/project/IPV2/gapless/gapless/final_output_assembly/ -t nanopore porechop_output.fastq.gz` is...