No such file or directory: '/home/***/proabc2-work/session.log

[AbDiscover]

I used docker as " docker run ghcr.io/haddocking/proabc-2:latest /home//proabc2-work h.fasta l.fasta", however, the error cames"[Errno 2] No such file or directory: '/home//proabc2-work/session.log". May I have your advice on this？

[rvhonorato]

From your command it seems that you are missing the -v flag;

docker run \
    ghcr.io/haddocking/proabc-2:latest \
    -v `pwd`:/data \ ## This line
    /home/user/proabc2-work h.fasta l.fasta

you might need to adjust the paths to your case

[AbDiscover]

“yilu@localhost:~/proabc2-work$ docker run ghcr.io/haddocking/proabc-2:latest -v /home/yilu/proabc2-work h.fasta l.fasta
usage: proabc2 [-h] folder heavy light
proabc2: error: unrecognized arguments: -v” It seems that “-v” can be recognized

[rvhonorato]

The -v goes inside the docker arguments, try this:

Go into your home directory

cd /home/yilu

Run the command:

docker run \
  -v `pwd`:/data
  ghcr.io/haddocking/proabc-2:latest \
  proabc2-work h.fasta l.fasta

[AbDiscover]

***@***.***:~$ docker run ghcr.io/haddocking/proabc-2:latest -v 'pwd':/data /home/yilu/proabc2-work h.fasta l.fasta usage: proabc2 [-h] folder heavy light proabc2: error: unrecognized arguments: -v l.fasta” At the same time，I tried “pip install” method，however, it was stopped as "ERROR: Could not find a version that satisfies the requirement tensorflow==1.14.0 (from proabc-2) (from versions: 2.2.0 ..." The environement is based on Windows 11+WSL2+Docker-Desktop(win)+ubuntu20.04.

…

________________________________ 发件人: Rodrigo Vargas Honorato ***@***.***> 发送时间: 2024年6月6日 17:51 收件人: haddocking/proABC-2 ***@***.***> 抄送: AbDiscover ***@***.***>; Author ***@***.***> 主题: Re: [haddocking/proABC-2] [Errno 2] No such file or directory: '/home/***/proabc2-work/session.log". (Issue #14) The -v goes inside the docker arguments, try this: Go into your home directory cd /home/yilu Run the command: docker run \ -v `pwd`:/data ghcr.io/haddocking/proabc-2:latest \ proabc2-work h.fasta l.fasta ― Reply to this email directly, view it on GitHub<#14 (comment)>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/BI6TRHIRYOFMXJE5X3XR5Z3ZGAWJ7AVCNFSM6AAAAABI2GECC2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDCNJRHA3TCNJVGA>. You are receiving this because you authored the thread.Message ID: ***@***.***>

[rvhonorato]

It's ` not '

docker run \
  -v `pwd`:/data
  ghcr.io/haddocking/proabc-2:latest \
  proabc2-work h.fasta l.fasta

[rvhonorato]

Could you please share what command you tried to input?

[rvhonorato]

Thanks @Iqrarshad, indeed with powershell/cmd i'm also getting this error. Could you instead try via WSL and check if that works for you?

[Iqrarshad]

My issue has been resolved. The folder we created earlier, "proabc2-prediction," required permission to write a log file. I updated the permissions of the folder, and it worked for me.

[rvhonorato]

Thanks for the update on the workaround 👍🏽

[PCRandChill]

Hey - I'm running the following command

docker run \
  -v `pwd`:/data \
  ghcr.io/haddocking/proabc-2:latest \
  proabc2-prediction/ heavy.fasta light.fasta

and I still have the following error:
[Errno 2] No such file or directory: 'proabc2-prediction/session.log'

The tried the permission fix and I have all permissions for "proabc2-prediction" directory. However the error persists.
ls -l drwxrwxrwx 2 root root 4096 Feb 5 10:35 proabc2-prediction

[rvhonorato]

@PCRandChill could you please post here the full error and try running this command instead?

docker run \
  --rm \
  --user $(id -u):$(id -g) \
  -v `pwd`:/data \
  ghcr.io/haddocking/proabc-2:latest \
  proabc2-prediction/ heavy.fasta light.fasta

[PCRandChill]

@rvhonorato Thanks for the reply. I figured out my problem was in the directory creation. My top level directory is proabc2-prediction and I have the two .fasta files in there. So, when I mount this directory to the /data directory of the container only the files inside we mounted essentially making the next call proabc2-prediction/ heavy.fasta light.fastainvalid. I modified it as below and it works.
docker run \ -v /home/user/proabc2-prediction:/data \ ghcr.io/haddocking/proabc-2:latest \ /data heavy.fasta light.fasta

[rvhonorato]

Thanks for the update - we will think of a execution script to facilitate execution and avoid these issues.