Open ZJin2021 opened 1 month ago
I met the same issue too. Have you ever fixed it?
I met the same issue too. Have you ever fixed it?
I modified the code on line 560 of script util/buildSummary.pl
, and now it can be used normally.
die "missing type for $id ... <$type>\n" if ( !$type );
to
if ( !$type ){
next;
}
I met the same issue too. Have you ever fixed it?
I modified the code on line 560 of script
util/buildSummary.pl
, and now it can be used normally.die "missing type for $id ... <$type>\n" if ( !$type );
to
if ( !$type ){ next; }
Thank you!
Hi shujun! I have some genome
mod.EDTA.TEanno.sum
files that are empty, so I checked part of the EDTA process. I found thatbuildSummary.pl
script at line 560 will terminate when reading the.mod.EDTA.TEanno.out
file if $type is missing. I checked the.mod.EDTA.TEanno.split.bed
file, and the repeat sequence missing the $type is marked as "snRNA". I don't know if there are other types of repeat sequences that may lack the $type tag. What about changing the "die" at line 560 of thebuildSummary.pl
script to "next"? I am not sure if this will affect subsequent processes.perl EDTA-master/util/buildSummary.pl -maxDiv 40 -stats $genome.mod.stats $genome.mod.EDTA.TEanno.out > $genome.mod.EDTA.TEanno.sum 2> out.log
out.log
``mod.EDTA.TEanno.out
.mod.EDTA.TEanno.split.bed