Notice '^M' character, which is apparently a carriage return symbol. There are no '^M's in 1.fna I must admit! So this "carriage return"s were generated while performing the PROKKA routine. I played around with the options and found out that the output for just
seems to be fine. Annotation finished successfully. So it seems to be an issue of specifying the strain and/or species and should be considered a bug. I hope it will be addressed in the future versions of PROKKA. Thank you for a very useful software, by the way!
Hello!
I used prokka for annotation of a genome. Here is my command:
prokka 1.fna --addgenes --addmrna --cpus 16 --genus Wolbachia --usegenus --species pipientis --strain wMelCSIt yields the well-known (#179) problem:
[16:06:23] Running: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.14.6 from https://github.com/tseemann/prokka' -Z PROKKA_12072021\/PROKKA_12072021\.err -i PROKKA_12072021\/PROKKA_12072021\.fsa 2> /dev/null [16:06:23] Deleting unwanted file: PROKKA_12072021/errorsummary.val [16:06:23] Deleting unwanted file: PROKKA_12072021/PROKKA_12072021.dr [16:06:23] Deleting unwanted file: PROKKA_12072021/PROKKA_12072021.fixedproducts [16:06:23] Deleting unwanted file: PROKKA_12072021/PROKKA_12072021.ecn [16:06:23] Deleting unwanted file: PROKKA_12072021/PROKKA_12072021.val [16:06:23] Repairing broken .GBK output that tbl2asn produces... [16:06:23] Running: sed 's/COORDINATES: profile/COORDINATES:profile/' < PROKKA_12072021\/PROKKA_12072021\.gbf > PROKKA_12072021\/PROKKA_12072021\.gbk sh: 1: cannot open PROKKA_12072021/PROKKA_12072021.gbf: No such file [16:06:23] Could not run command: sed 's/COORDINATES: profile/COORDINATES:profile/' < PROKKA_12072021\/PROKKA_12072021\.gbf > PROKKA_12072021\/PROKKA_12072021\.gbkDigging deep into PROKKA_12072021\/PROKKA_12072021.fsa reveals that it contains lines like that:
>JACSNK010000002.1 [gcode=11] [organism=Wolbachia pipientis] [strain=wMelCS^M]Notice '^M' character, which is apparently a carriage return symbol. There are no '^M's in 1.fna I must admit! So this "carriage return"s were generated while performing the PROKKA routine. I played around with the options and found out that the output for just
prokka 1.fna --addgenes --addmrna --cpus 16 --genus Wolbachia --usegenusseems to be fine. Annotation finished successfully. So it seems to be an issue of specifying the strain and/or species and should be considered a bug. I hope it will be addressed in the future versions of PROKKA. Thank you for a very useful software, by the way!