Opened 15 years ago

Closed 8 years ago

#190 closed issue (wontfix)

RAxML (DNA) ; RAxML algorithm --> "add new sequences to input tree" bricht mit Fehlermeldung ab

Reported by: meierh Owned by: westram
Priority: normal Milestone:
Component: External_tools Version: SVN
Keywords: RAxML Cc:

Description (last modified by westram) 

+ raxml2arb.pl ThisRun 1 1 import Message: 
can't open 'RAxML_log.ThisRun' (Reason: D
(atei oder Verzeichnis nicht gefunden) at /home/meierh/arb.64.noOPENGL/bin/raxml2arb.pl line 61.)

Please check console for additional error reasons
can't open 'RAxML_log.ThisRun' (Reason: D
(atei oder Verzeichnis nicht gefunden) at /home/meierh/arb.64.noOPENGL/bin/raxml2arb.pl line 61.)
Please check console for additional error reasons at /home/meierh/arb.64.noOPENGL/bin/raxml2arb.pl line 32.
+ arb_wait

Change History (8)

comment:1 Changed 15 years ago by westram

  • Component changed from SourceCode to GDE (external tools)
  • Owner changed from devel to westram

comment:2 follow-up: Changed 15 years ago by westram

  • Resolution set to fixlater
  • Status changed from new to closed
  • Version changed from RC2 to SVN
  • this is a RAxML problem. RAxML can only read trees in which short branches occur first, otherwise it assumes that the tree is rooted/multifurcated.
  • did not try with raxml v 7.2.0 (alpha), but a quick look at the source code revealed that the bug is still there
  • added a workaround to helpfile (see [6064])

TODO (when trac-attachments work again)

  • attach two beautified trees (one ok, one rejected)
  • cc to alexi

comment:3 Changed 10 years ago by westram

  • Description modified (diff)
  • Type changed from defect to issue

comment:4 Changed 10 years ago by westram

  • Resolution fixlater deleted
  • Status changed from closed to reopened

comment:5 in reply to: ↑ 2 Changed 10 years ago by westram

  • Status changed from reopened to infoneeded_new
  • attach two beautified trees (one ok, one rejected)

Test if behavior still occurs.

comment:6 Changed 10 years ago by epruesse

  • Status changed from infoneeded_new to new

raxml8 will probably be integrated w/o the perl script

comment:7 Changed 10 years ago by epruesse

  • Status changed from new to infoneeded_new

comment:8 Changed 8 years ago by westram

  • Resolution set to wontfix
  • Status changed from infoneeded_new to closed

workaround provided by [6064] is good enough. if behavior persists with raxml8 ⇒ open new ticket

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