ProABC2 - error. log file

HADDOCK
1

The HADDOCK category is meant to discuss any HADDOCK-related issue. For general information about HADDOCK refer to HADDOCK – Bonvin Lab

Dear Dr. Alexandre Bonvin
When I use PROABC2 to identify the paratope following the HADDOCK2.4 Antibody - Antigen tutorial using PDB-tools webserver, I have submitted the fasta sequence for both heavy and light chains. But I got the following error：

An error occurred. Check error.log file.

(No sequence present in heavy.fasta file. Please check your input file) during

Below I just summarize what I have done

~$ docker pull Package proabc-2 · GitHub
latest: Pulling from haddocking/proabc-2
Digest: sha256:a59563ab99c27becdbd8ceebf40c42a93cec7d9fcdb873e2441f3c1f520d4ab7
Status: Image is up to date for Package proabc-2 · GitHub

~$ mkdir proabc2-prediction
~$ echo “>APDB_H\nEVQLVESGGGLVQPGGSLRLSCAASGYTFTNYGMNWVRQAPGKGLEWVGWINTYTGEPTYAADFKRRFTFSLDTSKSTAYLQMNSLRAEDTAVYYCAKYPHYYGSSHWYFDVWGQGTLVTVSS” > proabc2-prediction/heavy.fasta
~$ echo “>APDB_L\nDIQMTQSPSSLSASVGDRVTITCSASQDISNYLNWYQQKPGKAPKVLIYFTSSLHSGVPSRFSGSGSGTDFTLTISSLQPEDFATYYCQQYSTVPWTFGQGTKVEIKRTV” > proabc2-prediction/light.fasta
~$ docker run
–rm
–user $(id -u):$(id -g)
-v pwd:/data

proabc2-prediction/ heavy.fasta light.fasta
An error occurred. Check error.log file

~$ cd proabc2-prediction
~/proabc2-prediction$ ls
error.log heavy.fasta light.fasta session.log
~/proabc2-prediction$ cat error.log
No sequence present in heavy.fasta file. Please check your input file

Please can you help me to fix this issue?

Thank you

Sura

2

Are your sequence files correct and not empty (which is the error message)?

Aren’t you missing part of the docker command?

3

My sequence files correct and not empty and for docker command, sorry you mean the docker execution

I run the command below

docker run
–rm
–user $(id -u):$(id -g)
-v pwd:/data


proabc2-prediction/ heavy.fasta light.fasta