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Read Assembly and Annotation Pipeline Tool
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Failure for RAPT testing mode #8

Open mglgc opened 3 years ago

mglgc commented 3 years ago

The ./run_rapt.py --test command outputs some error messages below as contained in the verbose.log file. My institutional firewall has the https:443 port open for next servers: www.ncbi.nlm.nih.gov locate.ncbi.nlm.nih.gov sra-download.ncbi.nlm.nih.gov Please, could the developers contribute with additional info to fix it? Thank you in advance.

[2021-02-10 23:11:19] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2020-09-24.build4894&uuid=47b31f2e-6bf5-11eb-82ab-901b0e950242&evt=rapt_start& [2021-02-10 23:11:59] rapt-29571188

[2021-02-10 23:11:59] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2020-09-24.build4894&uuid=47b31f2e-6bf5-11eb-82ab-901b0e950242&evt=test_start [2021-02-10 23:12:40] Running functional tests... [2021-02-10 23:12:41] problem with tcp access to ncbi.gov sdl host

[2021-02-10 23:12:41] port closed

[2021-02-10 23:12:41] SRA connection check failed with code 1, abort.. [2021-02-10 23:12:41] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2020-09-24.build4894&uuid=47b31f2e-6bf5-11eb-82ab-901b0e950242&evt=test_end [2021-02-10 23:13:21] status=1 [2021-02-10 23:13:21] Sending PINGER url https://www.ncbi.nlm.nih.gov/stat?ncbi_app=raptdocker&version=2020-09-24.build4894&uuid=47b31f2e-6bf5-11eb-82ab-901b0e950242&evt=rapt_exit

lwagnerdc commented 3 years ago

Thanks for contacting us with your error log, sorry you've again encountered a problem with this.

I see in NCBI's web logs that your first step (whose logging output you've given above) succeeded in reaching our web host.

So the network access verification we have in place as part of RAPT is the next place to check and for us to fix.

We tested on linux hosts running docker; it looks like there are some differences in how networking is handled by MacOS running docker. To help us understand what's happening, could you share the version of Docker and the OS version that you are running?

mglgc commented 3 years ago

Thanks for contacting us with your error log, sorry you've again encountered a problem with this.

I see in NCBI's web logs that your first step (whose logging output you've given above) succeeded in reaching our web host.

So the network access verification we have in place as part of RAPT is the next place to check and for us to fix.

We tested on linux hosts running docker; it looks like there are some differences in how networking is handled by MacOS running docker. To help us understand what's happening, could you share the version of Docker and the OS version that you are running?

Thank you for your reply. I'm running Docker 18.09.6 under Ubuntu 16.04. Anyway, you say I'm successufully reaching your web host but the error log's stated the message "problem with tcp access to ncbi.gov sdl host".