Claire Lemaitre

Hi, This issue comes from the `bitmap` function, used to save the figure in a png file, which requires Ghostscript to be installed on your machine. If Ghostscript is not...

Hi, Yes, the positions indicated in the vcf file are the positions in the chromosome of the insertion sites. It can be slightly different from the exact simulation points, because...

Hi, 92 is not a multiple of 32, try with 96 instead. Note that by default DSK is compiled to handle kmer-sizes up to 127. (default `-DKSIZE_LIST="32 64 96 128"`)...

Hi, Indeed, this is an extremely large running time estimation ! The running time depends mainly on the number of gap-fllings to perform (number of contigs in the input contig...

Hi Avery, thanks for using MindTheGap. Given the large number of gap-fillings to perform (38,000 contigs implies almost 80,000 gap-fillings to perform), the observed running time may not be unusual....

Hi @tuck82er, Glad it helps and I hope you will get interesting with MindTheGap. In case you did not know, we have also developed a full pipeline to assemble specific...

Hi, This error occurs when the program does not find the files at the indicated path. Here, your input file contains only file names (and not absolute paths for instance),...

> Are there specific requirements for the contigs headers? My contigs' headers are like this: >000000000011. Is there a possibility that simka didn't recognize my fasta files? No, headers can...

Hi, This simple test should normally take less than a minute. Can you test it when limiting the number of processes for the merging task, for instance : ``` ./simple_test.sh...

Dear Hans, Thank you for pointing out this behavior. Since the last release, SimkaMin is supposed to output fully symmetrical matrices, with the same values in the upper and lower...