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Hi shujun!
I have some genome mod.EDTA.TEanno.sum files that are empty, so I checked part of the EDTA process. I found that buildSummary.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 the buildSummary.pl script to "next"? I am not sure if this will affect subsequent processes.
This out line is the first instance of the change:
10000 0.001 0.001 0.001 scaffold398 121760 121980 NA + TE_00000280_INT LTR/unknown
missing type for TE_00002102 ... <>
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
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