gjospin/PhyloSift

Issues

• Use of uninitialized value $timestamp in scalar chomp at /data/software//PhyloSift/bin/../lib/Phylosift/Utilities.pm line 365, <$FH> line 1

  #507 opened 3 years ago by xieyg5
  0

• rm: cannot remove blastDir/*.aa.1*

  #466 opened 10 years ago by xapple
  5

• PhyloSift error running (Can't locate App/Cmd/Setup.pm in @INC)

  #487 opened 7 years ago
  4

• Failed to open covariance model save file

  #502 opened 5 years ago by Oakley-Lab
  1

• Link broken for download

  #504 opened 5 years ago by jolespin
  2

• broken link to download?

  #506 opened 5 years ago by ltom6
  1

• hmmalign error

  #505 opened 5 years ago by kyselad
  1

• [Feature Request] Please make this available via conda

  #503 opened 5 years ago by jolespin
  0

• Error running Phylosift

  #490 opened 7 years ago by nhudag
  6

• error with phylosift search

  #501 opened 5 years ago by ucassee
  13

• The download URL may be disabled

  #492 opened 7 years ago by bioinformaticspcj
  8

• Use of uninitialized value $timestamp in scalar chomp at..

  #500 opened 6 years ago by ganiatgithub
  1

• running aborted

  #499 opened 6 years ago by bonniethesheng
  1

• markers.rep not found

  #498 opened 6 years ago by Ians14
  0

• NCBI taxonomy data not found and unable to connect to update server

  #497 opened 6 years ago by bonniethesheng
  4

• problem indexing, process running without any progress

  #496 opened 6 years ago by novitch
  1

• Problem indexing , can't find repository for most of markers

  #495 opened 6 years ago by novitch
  2

• error using phylosift... rm: cannot remove ... No such file or directory

  #488 opened 6 years ago by itiago
  0

• Error: requested HMM banded DP mx of 3903.86 Mb > 2500.00 Mb limit.

  #494 opened 6 years ago by itiago
  0

• pplacer not found

  #493 opened 6 years ago by AvdReis
  3

• Dead Download Link

  #491 opened 7 years ago by jesipr
  1

• Running phylosift

  #489 opened 7 years ago by nhudag
  0

• Grinder.pm missing...

  #485 opened 7 years ago by jamesabbott
  1

• Marker gene webpage down?

  #486 opened 7 years ago by evensannesriiser
  1

• Problems understanding summary results

  #484 opened 8 years ago by itiago
  0

• Gor this Error: requested HMM banded DP mx of 5030.12 Mb > 2500.00 Mb limit. Increase limit with --mxsize or tau with --tau.

  #483 opened 8 years ago by itiago
  0

• --extended db

  #482 opened 8 years ago by rjsorr
  2

• Marker files not readable

  #481 opened 8 years ago by gjospin
  0

• --coverage option formatting

  #480 opened 8 years ago by ursky
  0

• Can't locate loadable object for module Digest::MD5

  #479 opened 9 years ago by matiasirazoqui
  0

• phylosift infinite run with tutorial files?

  #478 opened 9 years ago by Sanrrone
  1

• cmalign seg fault

  #477 opened 9 years ago by gjospin
  0

• unzipping markers.gz

  #476 opened 9 years ago by ryanjw
  0

• Trouble to run phylosift on server

  #475 opened 9 years ago by dong5600
  7

• How to obtain confidence values concatenated tree?

  #473 opened 9 years ago by driscolc
  0

• error when running tutorial files

  #472 opened 9 years ago by harrysunny998
  0

• Misclassifications

  #471 opened 9 years ago by rohansachdeva
  0

• Analysis

  #470 opened 10 years ago by dee31n
  1

• Alignment file parse error

  #469 opened 10 years ago
  1

• build_marker taxids invalid

  #468 opened 10 years ago by KevinAMeyer
  2

• Error: requested HMM banded DP mx > limit. But nowhere to add --mxsize according to mannual

  #467 opened 10 years ago by yoyohashao
  0

• Sequence IDs with tab characters not handled

  #465 opened 10 years ago by koadman
  1

• Input Sequence IDs lost in all mode

  #464 opened 10 years ago by augustlongino
  10

• Increase limit with --mxsize or tau with --tau

  #463 opened 10 years ago by javiercnav
  1

• Incorrect grammar in error message

  #462 opened 10 years ago by gjospin
  0

• db_update --config uses default phylosiftrc

  #461 opened 11 years ago by gjospin
  0

• Broken concatenation when multiple hits to dngngnwu markers

  #460 opened 11 years ago by gjospin
  0

• With multithreading, only one process is using CPU

  #457 opened 11 years ago by jmeppley
  8

• improve configurability for pplacer mmap usage

  #459 opened 11 years ago by koadman
  0

• print version to screen & run_info.txt

  #458 opened 11 years ago by koadman
  0