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thackl / minidot

Fast and pretty dotplots for whole genomes assemblies using minimap and R/ggplot2
MIT License
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Mapping error #14

Open Estherrr1997 opened 2 years ago

Estherrr1997 commented 2 years ago

Hi there,

I am using minidot to plot genome assemblies. I already mapped the assemblies using minimap2 and I would like to visualize the results using minidot. Although I seem to get an error when minidot tries to map the genomes, the error message:

admin_bi@GSYMK2:/media/admin_bi/DATA/Files_Esther/minimap2$ /media/admin_bi/DATA/Files_Esther/minidot/bin/minidot -M /media/admin_bi/DATA/Files_Esther/minimap2/minimap2 -m "-x asm20" -o blue_shark_cl_catshark.pdf /media/admin_bi/DATA/Files_Esther/assemblies/quast/bluesharkhifiasm_filtered_16mrt.fa /media/admin_bi/DATA/Files_Esther/assemblies/quast/NCBI/cloudy_catshark_GCA_003427355.1.fna

[15:08:31] /media/admin_bi/DATA/Files_Esther/minimap2/minimap2 .. ok [15:08:31] samtools .. ok [15:08:31] prepping .. done [15:09:40] mode: -x asm20 ( bp) "-x asm20" [15:09:40] mapping ../media/admin_bi/DATA/Files_Esther/minidot/bin/minidot: line 186: 346438 Aborted (core dumped) $MBIN $MOPT $TFA $TFA >> $PAF 2>> $TML failed [WARNING] failed to parse the first FASTA/FASTQ record. Continue anyway. minimap2: bseq.c:95: mm_bseq_read3: Assertion `ks->seq.l <= INT32_MAX' failed.

I don't really know what the warning says, could you help me with that?

Kind regards, Esther