Skani external command error

[magicprotoss]

Issue: the command that runs skani subprocess not working properly

The command that runs skani subprocess sends the output to /dev/stdout, however on morden linux distributions this is not allowed.

I checked on both Ubuntu 22 and RockyOS 9, and go the same result:

$echo "ASDF" > /dev/stdout
bash: /dev/stdout: Permission denied

###OS Info

• Ubuntu:
  $cat /etc/os-release
  PRETTY_NAME="Ubuntu 22.04.5 LTS"
  NAME="Ubuntu"
  VERSION_ID="22.04"
  VERSION="22.04.5 LTS (Jammy Jellyfish)"
  VERSION_CODENAME=jammy
  ID=ubuntu
  ID_LIKE=debian
  HOME_URL="https://www.ubuntu.com/"
  SUPPORT_URL="https://help.ubuntu.com/"
  BUG_REPORT_URL="https://bugs.launchpad.net/ubuntu/"
  PRIVACY_POLICY_URL="https://www.ubuntu.com/legal/terms-and-policies/privacy-policy"
  UBUNTU_CODENAME=jammy

• RockyOS 9:
  $cat /etc/os-release
  NAME="Rocky Linux"
  VERSION="9.1 (Blue Onyx)"
  ID="rocky"
  ID_LIKE="rhel centos fedora"
  VERSION_ID="9.1"
  PLATFORM_ID="platform:el9"
  PRETTY_NAME="Rocky Linux 9.1 (Blue Onyx)"
  ANSI_COLOR="0;32"
  LOGO="fedora-logo-icon"
  CPE_NAME="cpe:/o:rocky:rocky:9::baseos"
  HOME_URL="https://rockylinux.org/"
  BUG_REPORT_URL="https://bugs.rockylinux.org/"
  ROCKY_SUPPORT_PRODUCT="Rocky-Linux-9"
  ROCKY_SUPPORT_PRODUCT_VERSION="9.1"
  REDHAT_SUPPORT_PRODUCT="Rocky Linux"
  REDHAT_SUPPORT_PRODUCT_VERSION="9.1"

Debugging information

[2024-10-14 15:40:58] TASK: Calculating average nucleotide identity using skani (v0.2.2).
==> Processed 0/34 comparisons (0%) | | [?comparison/s, ETA ?][2024-10-14 15:40:58] ERROR: STDOUT:

[2024-10-14 15:40:58] ERROR: STDERR:
[00:00:00.000] (73ee5ec73800) INFO skani dist --medium -q query_genome/M23.fna -r /mnt/gtdbtk-db/skani/database/GCF/004/123/795/GCF_004123795.1_genomic.fna.gz -o /dev/stdout
[00:00:00.134] (73ee5ec73800) INFO Learned ANI mode detected. ANI may be adjusted according to a regression model trained on MAGs.
[00:00:00.134] (73ee5ec73800) INFO Generating sketch time: 0.13419788
thread 'main' panicked at src/file_io.rs:661:60:
/dev/stdout: Os { code: 13, kind: PermissionDenied, message: "Permission denied" }
note: run with RUST_BACKTRACE=1 environment variable to display a backtrace

Process Process-115:
Traceback (most recent call last):
File "/home/navi/miniconda3/envs/gtdbtk-2.4.0/lib/python3.8/multiprocessing/process.py", line 315, in _bootstrap
self.run()
File "/home/navi/miniconda3/envs/gtdbtk-2.4.0/lib/python3.8/multiprocessing/process.py", line 108, in run
self._target(*self._args, **self._kwargs)
File "/home/navi/miniconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/external/skani.py", line 157, in _worker
result = self.run_proc(q, r, q_path, r_path, preset)
File "/home/navi/miniconda3/envs/gtdbtk-2.4.0/lib/python3.8/site-packages/gtdbtk/external/skani.py", line 211, in run_proc
raise GTDBTkExit('skani returned a non-zero exit code.')
gtdbtk.exceptions.GTDBTkExit: skani returned a non-zero exit code.
[2024-10-14 15:40:58] ERROR: skani returned a non-zero exit code.
[2024-10-14 15:40:58] ERROR: Controlled exit resulting from an unrecoverable error or warning.

[pchaumeil]

Hi,
How are you running GTDB-Tk? are you using docker? if so , Are you starting the docker as root? Docker can block /dev/stdout to unprivileged user is the docker image was started as su

[magicprotoss]

Hi, How are you running GTDB-Tk? are you using docker? if so , Are you starting the docker as root? Docker can block /dev/stdout to unprivileged user is the docker image was started as su

Hi, we are running gtdb-tk natively installed in linux enviroment via conda, we think the issue was that the system had some security hardening feautures enbaled by default that blocks outputing to /dev/stdout. (both ubuntu22LTS and RockyOS9 exibit the same behavior)

I think changing that line of code to output to a temp file then read from it would be a better :)