"scan" error

[ilikvlad]

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?

[12:05:37] /ocean/projects/mcb190015p/ilikvlad/anaconda3/envs/minimap2_2.18/bin/minimap2 .. ok
[12:05:37] samtools .. ok
[12:05:37] prepping .. done
[12:05:38] mode: -x asm5 ( bp) "-x asm5"
[12:05:38] mapping .. done
[12:05:42] plotting
Error in scan(file = file, what = what, sep = sep, quote = quote, dec = dec,  : 
  line 2 did not have 18 elements
Calls: read.table -> scan
Execution halted
 failed

Thank you,

Vladislav

[thackl]

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?

[ilikvlad]

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:

results.zip

Thank you for helping me with this!