IOError: [Errno 2] No such file or directory: /haddock2.4/tools/results_processing.tgz'

HADDOCK
1

##############################################################################

Starting HADDOCK2.4

N-components version of HADDOCK (current maximum is 20)

Copyright 2003-2020 Alexandre Bonvin, Utrecht University.

Originally adapted from Aria 1.2 from Nilges and Linge, EMBL.

All rights reserved.

This code is part of the HADDOCK software and governed by its

license. Please see the LICENSE file that should have been included

as part of this package.

##############################################################################

Starting HADDOCK on: 2020-06-05 12:03:06

HADDOCK version: 2.4
Python version: 2.7.17 (default, Apr 15 2020, 17:20:14)
[GCC 7.5.0]
PYTHONPATH system variable contains:
[’/home/sandeep/haddock2.4/Haddock’, ‘/Bioinfo/haddock2.4’, ‘/home/sandeep/haddock2.4’, ‘/usr/lib/python2.7’, ‘/usr/lib/python2.7/plat-x86_64-linux-gnu’, ‘/usr/lib/python2.7/lib-tk’, ‘/usr/lib/python2.7/lib-old’, ‘/usr/lib/python2.7/lib-dynload’, ‘/home/sandeep/.local/lib/python2.7/site-packages’, ‘/usr/local/lib/python2.7/dist-packages’, ‘/usr/lib/python2.7/dist-packages’]
reading parameters from the file ./run.param
setting some variables:
N_COMP set to: 2
RUN_NUMBER set to: 1
HADDOCK_DIR set to: /home/sandeep/haddock2.4
UNAMBIG_TBL set to: antibody-antigen-unambig.tbl
PROT_SEGID_2 set to: B
PROT_SEGID_1 set to: A
PDB_FILE1 set to: 4G6K-clean.pdb
AMBIG_TBL set to: antibody-antigen-ambig.tbl
PROJECT_DIR set to: .
PDB_FILE2 set to: 4I1B.pdb
runDir= ./run1
project . exists, run 1 does not exist
create the new run 1
Traceback (most recent call last):
File “/home/sandeep/haddock2.4/Haddock/RunHaddock.py”, line 156, in
new[‘CRYO-EM_FILE’],
File “/Bioinfo/haddock2.4/Haddock/Main/Setup.py”, line 210, in SetupNewProject
shutil.copy(filetocopy, runDir + ‘/tools’)
File “/usr/lib/python2.7/shutil.py”, line 139, in copy
copyfile(src, dst)
File “/usr/lib/python2.7/shutil.py”, line 96, in copyfile
with open(src, ‘rb’) as fsrc:
IOError: [Errno 2] No such file or directory: ‘/home/sandeep/haddock2.4/tools/results_processing.tgz’

2

Please refer to: HADDOCK 2.4 local installation

3

Hi

i used your suggestion and removed the results_processing.tgz and POSTPROCESS entry in the config.local file. When i was running haddock it creates run1 and after that it gives error

There is a problem with the CNS executable defined in run.cns:
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL

it checked with cns its give following error
server1:/Bioinfo/cns_solve_1.3> source cns_solve_env **
server1:/Bioinfo/cns_solve_1.3> cns
** %SETFPEPS Machine epsilon determined to be 0.494-323
** %SETFPEPS error encountered: Machine epsilon value is too small**
** (CNS is in mode: SET ABORT=NORMal END)**
** WARNING: program encountered a fatal error.**
** However, in interactive mode, program execution**
** will continue. Proceed at your own risk.**
** Program will stop immediately.**
** ============================================================**
** Maximum dynamic memory allocation: 0 bytes**
** Maximum dynamic memory overhead: 0 bytes**
** Program started at: on **
** Program stopped at: 13:10:54 on 06-Jul-2020**
** CPU time used: 0.0047 seconds**
** ============================================================**
Note: The following floating-point exceptions are signalling: IEEE_UNDERFLOW_FLAG IEEE_DENORMAL

I checked with forum and performed all kind of recommendation such as

set MXFPEPS2 value to 8192 in machvar.inc
removed flag -fastm in make file
MXRTP to 4000 in rtf.inc in the source directory

I am using 64 bit maching and ubuntu-16.
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
Model: 85
Model name: Intel® Xeon® Platinum 8168 CPU @ 2.70GHz
Stepping: 4
CPU MHz: 1200.025
BogoMIPS: 5400.00

Before removing haddock2.4/tools/results_processing.tgz, cns was not giving any error.
Thank you in advance

best

4

Do you mean you are able to call CNS manually and it works?

You might want to update anyway your haddock distribution. We are about to have a July release.

5

Thank you
I checked it manually and got mention error . Used version is 2.4.
When we will have it

6

It’s then a CNS problem…

Check the forum for compilation issues.
Possibly compile it with static option (should be the default) on a different Linux system and use that executable in your system