Open ilikvlad opened 3 years ago
Hi Vladislav,
sorry, just returned from vacation. I don't know what happened there. There should be a .paf
file in the folder where you ran the script. Can you send the first lines of that file?
Hello @thackl
sure, I attach the paf file and error message again. I am trying to compare two nematode genomes (244 vs. 236 Mb):
The original command was:
bin/minidot -M $PROJECT/anaconda3/envs/minimap2_2.18/bin/minimap2 -m "-x asm20 -t 10" \
-S -o results.pdf data/necator_aroian_longread_flye_charcoaled_07.15.2021.fa data/necator_americanus.PRJNA72135.WBPS15.genomic.fa.clean.fa ;
error message was:
-S [10:47:09] /ocean/projects/mcb190015p/ilikvlad/anaconda3/envs/minimap2_2.18/bin/minimap2 .. ok [10:47:09] samtools .. ok [10:47:09] prepping .. done [10:47:31] mode: -x asm20 -t 10 ( bp) "-x asm20 -t 10" [10:47:31] mapping .. done [10:51:21] plotting Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec, : line 89 did not have 18 elements Calls: read.table -> scan Execution halted failed
and the paf file is attached here:
Thank you for helping me with this!
Hello,
I've been trying to run minidot on two different sequences (ca. the same size), using minimap2 and I am getting this error. Do you have an idea what to do with this?
Thank you,
Vladislav