all.manifest"

#

If you are having trouble with your genome, please ensure that you can run the pipeline with one of our test genomes first. If your installation works fine with the sample input, please tell us if you are willing and able to share your genome with us, if asked.

Software versions (please complete the following information):

OS [e.g. CentOS 7, macOS , etc.]. CentOS7
Python version if using FCS-GX [python --version]. Python 3.6.8

Log Files Please rerun with the --debug flag and attach an archive (e.g. zip or tarball) of the logs in the directory [debug/tmp-outdir*.log] for FCS-adaptor or the saved log file [run_gx.py ... > GX.log 2>&1] for FCS-GX.

balintb@node7:/node7_data/balintb/fcs$ python3 fcs.py db get --mft "$SOURCE_DB_MANIFEST" --dir "$LOCAL_DB/gxdb" Traceback (most recent call last): File "fcs.py", line 480, in sys.exit(main()) File "fcs.py", line 469, in main gx.run() File "fcs.py", line 386, in run self.args.func(self) File "fcs.py", line 376, in run_db_mode self.run_sync_files() File "fcs.py", line 189, in run_sync_files self.safe_exec(sync_files_args) File "fcs.py", line 150, in safe_exec subprocess.run(args, shell=False, check=True, text=True, stdout=sys.stdout, stderr=sys.stderr) File "/usr/lib64/python3.6/subprocess.py", line 423, in run with Popen(*popenargs, **kwargs) as process: TypeError: init() got an unexpected keyword argument 'text'

Additional context Add any other context about the problem here.

pstrope commented 10 months ago

Hi, Could you try with python3.7, and see if it works?

thanks, Pooja

h836472 commented 10 months ago

Dear Pooja,

Thank you for your prompt answer. Yes, the error occurred because of python version conflict. Then, I tried installing pyenv and then python v3.10.12 on the centOS 7 compute server but python compilation keeps failing with some openssl issue. That way, I am now pulling the "all" database with the python script using my more recent desktop, while sending the files on the big central storage. Duct-tape with wd40 kind of solution but works...

Thanks again!

Balazs

On Wed, 30 Aug 2023, 18:23 Pooja Strope, @.***> wrote:

Hi, Could you try with python3.7, and see if it works?

thanks, Pooja

— Reply to this email directly, view it on GitHub https://github.com/ncbi/fcs/issues/51#issuecomment-1699489002, or unsubscribe https://github.com/notifications/unsubscribe-auth/AL2BSTHTW3W33WSTS72QGJTXX5SJ5ANCNFSM6AAAAAA4EQH7MQ . You are receiving this because you authored the thread.Message ID: @.***>

pstrope commented 10 months ago

We'll that's a solution for now. I wonder if you're going to come across problems during the run due to version conflict.

h836472 commented 10 months ago

Dear Pooja,

Plan is to start the fcs-gx docker image on the compute node with an interactive console and manually command the analysis engine from the inside. I can manage mounting host directories for docker and the command line options of the embedded app also seems to be straightforward. I might not need the wrapper .py script any longer. Too bad that python interpreter changes so much between sub-versions and such version conflicts can occur.

Balazs

On Wed, 30 Aug 2023 at 19:24, Pooja Strope @.***> wrote:

We'll that's a solution for now. I wonder if you're going to come across problems during the run due to version conflict.

— Reply to this email directly, view it on GitHub https://github.com/ncbi/fcs/issues/51#issuecomment-1699570303, or unsubscribe https://github.com/notifications/unsubscribe-auth/AL2BSTHKQCI2QXRNSWVQP5TXX5ZLBANCNFSM6AAAAAA4EQH7MQ . You are receiving this because you authored the thread.Message ID: @.***>

pstrope commented 9 months ago

Closing the ticket. Hope it's working for you.

ncbi / fcs

[BUG]: fcs.py fails to download database #51

SOURCE_DB_MANIFEST="https://ftp.ncbi.nlm.nih.gov/genomes/TOOLS/FCS/database/latest/all.manifest"