Open magicprotoss opened 1 month ago
pchaumeil
commented
1 month ago 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
commented
1 month ago Hi, How are you running GTDB-Tk? are you using docker? if so , Are you starting the docker as root? Docker can block
/dev/stdoutto unprivileged user is the docker image was started assu
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 :)
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_004123795.1genomic.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/fileio.rs:661:60: /dev/stdout: Os { code: 13, kind: PermissionDenied, message: "Permission denied" }_ note: run with
RUST_BACKTRACE=1environment variable to display a backtraceProcess 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.