Opened 4 years ago

Last modified 3 years ago

#621 new defect

arb_export_rates crashes

Reported by: westram Owned by: devel
Priority: major Milestone: arb6.1
Component: External_tools Version: SVN
Keywords: Cc:

Description

reproduce:

  • run arb_ntree with $ARBHOME/UNIT_TESTER/run/TEST_nuc.arb
  • run attached macro

console says:

[Action: '(mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; arb_export_rates --arb-notify -r "POS_VAR_BY_PARSIMONY" > weights && arb_convert_aln --arb-notify -GenBank /home/ralf/.arb_tmp/tmp/gde20599_0 -phylip infile && ${ARB_XCMD} bash -x -c 'LD_LIBRARY_PATH="${ARB_LIBRARY_PATH:-/usr/arb/lib}";export LD_LIBRARY_PATH; arb_raxml DNA infile weights "" 0 0 0 d "" "" "3" "3" import "PRG=RAxML FILTER=none RATE=POS_VAR_BY_PARSIMONY ALGO=new rapid hill climbing" GTRGAMMA 25  ;arb_wait'; mkdir -p ~/.arb_tmp/$$; cd ~/.arb_tmp/$$ ; cd .. ; rm -rf $$ )&']
[Terminating with signal 11]
arbdb.cxx:429: Assertion 'openedDBs == closedDBs' failed
ARB_DB_SERVER: a client died abnormally

running arb_export_rates as above segfaults at

(gdb) whe
#0  0x00007ffff6947512 in ?? () from /lib/libc.so.6
#1  0x00007ffff692cb5e in fputs () from /lib/libc.so.6
#2  0x00000000004028ca in ARB_main (argc=0, argv=0x7fffffffe2c8) at arb_export_rates.cxx:227
#3  0x0000000000401f70 in main (argc=4, argv=0x7fffffffe2a8) at arb_main.cxx:10

Attachments (1)

_logged.amc (668 bytes) - added by westram 3 years ago.
macro IDs changed

Download all attachments as: .zip

Change History (2)

Changed 3 years ago by westram

macro IDs changed

comment:1 Changed 3 years ago by westram

  • Milestone set to arb6.1
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