search

JBerthelier / PiRATE

PiRATE (Pipeline to Retrieve and Annotate Transposable Elements)
http://doi.org/10.17882/51795
18 stars 5 forks source link

Error with Helsearch #31

Closed pwkooij closed 4 years ago

pwkooij commented 4 years ago

I have changed the input file with 60bp per line, but I still get an error for Helsearch

Fatal error: Exit code 1 () 

[formatdb] ERROR: ./working/GCAGGT_CGA_ACCTGC_5/GCAGGT_CGA_ACCTGC_5.nhrOutput Blast-def-line-set.E.<title> 

Invalid value(s) [9] in VisibleString [genome_P#12826044#12826244 ...] 

[formatdb] ERROR: ./working/GCAGGT_CGA_ACCTGC_5/
JBerthelier commented 4 years ago

Dear pwkooij,

Sevreral users reported me errors with helsearch.

Because this tool seems to be very capricious and generate numerous false positifs, it will be removed in the new Pirate version.

I advise you to not use it in your analyses.

If there is Helitron in the genome you are studying, they should be found by repeatitiveness-based approach tools such as TEdenovo or Repeatscout.

Best

Jeremy

pwkooij commented 4 years ago

Hi Jeremy

Thanks for your response! I will skip the analysis.

Cheers Pepijn