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DaehwanKimLab / centrifuge

Classifier for metagenomic sequences
GNU General Public License v3.0
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centrifuge-inspect throws SyntaxError error #238

Closed phlatphish closed 2 years ago

phlatphish commented 2 years ago

Both bioconda package and the downloaded binary centrifuge-1.0.3-beta for linux are doing this, with any kind of invocation:

e.g. 

centrifuge-inspect -h

  File "/home/xxx/xxx/centrifuge-1.0.3-beta/centrifuge-inspect", line 45
    inspect_bin_spec += '-debug'
                       ^
SyntaxError: invalid syntax                     ^

  File "/home/xxx/miniconda3/envs/centrifuge/bin/centrifuge-inspect", line 45
    inspect_bin_spec += '-debug'
                      ^
SyntaxError: invalid syntax                      ^

System:

uname -a Linux inbre01.ncgr.org 3.10.0-1062.1.2.el7.x86_64 #1 SMP Mon Sep 30 14:19:46 UTC 2019 x86_64 x86_64 x86_64 GNU/Linux

more /etc/os-release NAME="CentOS Linux" VERSION="7 (Core)" ID="centos" ID_LIKE="rhel fedora" VERSION_ID="7" PRETTY_NAME="CentOS Linux 7 (Core)" ANSI_COLOR="0;31" CPE_NAME="cpe:/o:centos:centos:7" HOME_URL="https://www.centos.org/" BUG_REPORT_URL="https://bugs.centos.org/"

CENTOS_MANTISBT_PROJECT="CentOS-7" CENTOS_MANTISBT_PROJECT_VERSION="7" REDHAT_SUPPORT_PRODUCT="centos" REDHAT_SUPPORT_PRODUCT_VERSION="7"

phlatphish commented 2 years ago

I just cloned from github and built from source. centrifuge-kreport is breaking now with:

Loading names file ...
  File "/home/xxx/xxx/centrifuge/bin/centrifuge-inspect", line 45
    inspect_bin_spec += '-debug'
                      ^
SyntaxError: invalid syntax
Loading nodes file ...
  File "/home/xxx/xxx/centrifuge/bin/centrifuge-inspect", line 45
    inspect_bin_spec += '-debug'
                      ^
SyntaxError: invalid syntax
Couldn't find parent of taxID 1642299 - directly assigned to root.
Couldn't find parent of taxID 1642299 - directly assigned to root.
Couldn't find parent of taxID 1906 - directly assigned to root.
Couldn't find parent of taxID 1967 - directly assigned to root.
Couldn't find parent of taxID 1642299 - directly assigned to root.
Couldn't find parent of taxID 102891 - directly assigned to root.
etc.
phlatphish commented 2 years ago

I rebuilt everything from source and used a freshly prepared set of inputs. The error has gone away.