C:\Users\Rina_Mekuli>cd C:\Users\Rina_Mekuli\Documents\Python_MD

C:\Users\Rina_Mekuli\Documents\Python_MD>git clone
[Link] metadraft2

Cloning into 'metadraft2'...

remote: Enumerating objects: 675, done.

remote: Counting objects: 100% (75/75), done.

remote: Compressing objects: 100% (55/55), done.

Receiving objects: 99% (669/675), 37.26 MiB | 14.61 MiB/sremote: Total 675 (delta 34), reused 55
(delta 20), pack-reuse

Resolving deltas: 100% (285/285), done.

C:\Users\Rina_Mekuli\Documents\Python_MD>cd metadraft2

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>dir

Volume in drive C is OS

Volume Serial Number is 0C29-A4A3

Directory of C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2

19/09/2022 15:32 <DIR> .

19/09/2022 15:32 <DIR> ..

19/09/2022 15:32 1,428 .gitignore

19/09/2022 15:32 352 .gitmodules

19/09/2022 15:32 <DIR> bin_base

19/09/2022 15:32 719 [Link]

19/09/2022 15:32 <DIR> docs

19/09/2022 15:32 371 [Link]

19/09/2022 15:32 <DIR> images

19/09/2022 15:32 443 [Link]

19/09/2022 15:32 <DIR> libpython

19/09/2022 15:32 35,817 LICENSE

19/09/2022 15:32 2,568 [Link]

19/09/2022 15:32 <DIR> log

19/09/2022 15:32 2,787 [Link]

19/09/2022 15:32 <DIR> modeldb

19/09/2022 15:32 4,830 [Link]

19/09/2022 15:32 716 [Link]

19/09/2022 15:32 36 [Link]

19/09/2022 15:32 266 [Link]

19/09/2022 15:32 6,468 [Link]

19/09/2022 15:32 <DIR> testfiles

19/09/2022 15:32 <DIR> tmp

19/09/2022 15:32 <DIR> tools

19/09/2022 15:32 247 _metadraft.cfg

19/09/2022 15:32 204,862 _metadraft.ico

15 File(s) 261,910 bytes

11 Dir(s) 828,562,960,384 bytes free

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>git pull

Already up to date.

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>conda env create -n metadraft8 -f

[Link]

'conda' is not recognized as an internal or external command,

operable program or batch file.

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>git

usage: git [-v | --version] [-h | --help] [-C <path>] [-c <name>=<value>]

[--exec-path[=<path>]] [--html-path] [--man-path] [--info-path]

[-p | --paginate | -P | --no-pager] [--no-replace-objects] [--bare]

[--git-dir=<path>] [--work-tree=<path>] [--namespace=<name>]

 [--super-prefix=<path>] [--config-env=<name>=<envvar>]

<command> [<args>]

These are common Git commands used in various situations:

start a working area (see also: git help tutorial)

clone Clone a repository into a new directory

init Create an empty Git repository or reinitialize an existing one

work on the current change (see also: git help everyday)

add Add file contents to the index

mv Move or rename a file, a directory, or a symlink

restore Restore working tree files

rm Remove files from the working tree and from the index

examine the history and state (see also: git help revisions)

bisect Use binary search to find the commit that introduced a bug

diff Show changes between commits, commit and working tree, etc

grep Print lines matching a pattern

log Show commit logs

show Show various types of objects

status Show the working tree status

grow, mark and tweak your common history

branch List, create, or delete branches

commit Record changes to the repository

merge Join two or more development histories together

rebase Reapply commits on top of another base tip

reset Reset current HEAD to the specified state

switch Switch branches

tag Create, list, delete or verify a tag object signed with GPG
collaborate (see also: git help workflows)

fetch Download objects and refs from another repository

pull Fetch from and integrate with another repository or a local branch

push Update remote refs along with associated objects

'git help -a' and 'git help -g' list available subcommands and some

concept guides. See 'git help <command>' or 'git help <concept>'

to read about a specific subcommand or concept.

See 'git help git' for an overview of the system.

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>git submodule update --init --remote --

modeldb/2019-1/

Submodule '2019-1' ([Link]

registered for path 'modeldb/2019-1'

Cloning into 'C:/Users/Rina_Mekuli/Documents/Python_MD/metadraft2/modeldb/2019-1'...

Submodule path 'modeldb/2019-1': checked out '4763f838889d4a47e89e966aeb5c8f332a29920c'

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>
__________________________________________________________________________________

(c) Microsoft Corporation. All rights reserved.

(base) C:\Users\Rina_Mekuli>cd C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2

(base) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>conda env create -n metadraft8 -f

[Link]

Collecting package metadata ([Link]): done

Solving environment: done

Downloading and Extracting Packages

icu-70.1 | 17.0 MB |
############################################################################ | 100%

openssl-1.1.1q | 5.8 MB |
############################################################################ | 100%

python_abi-3.8 | 4 KB |
############################################################################ | 100%

libwebp-base-1.2.4 | 328 KB |
############################################################################ | 100%

sip-6.6.2 | 519 KB |
############################################################################ | 100%

libclang13-14.0.6 | 24.5 MB |
############################################################################ | 100%

vs2015_runtime-14.29 | 1.3 MB |
############################################################################ | 100%

libffi-3.4.2 | 41 KB |
############################################################################ | 100%

xlsxwriter-3.0.3 | 108 KB |
############################################################################ | 100%

prompt-toolkit-3.0.3 | 254 KB |
############################################################################ | 100%

qt-main-5.15.4 | 69.8 MB |
############################################################################ | 100%

sympy-1.10.1 | 11.7 MB |
############################################################################ | 100%
libcblas-3.9.0 | 5.6 MB |
############################################################################ | 100%

vc-14.2 | 14 KB |
############################################################################ | 100%

libclang-14.0.6 | 144 KB |
############################################################################ | 100%

ucrt-10.0.20348.0 | 1.2 MB |
############################################################################ | 100%

toml-0.10.2 | 18 KB |
############################################################################ | 100%

zstd-1.5.2 | 401 KB |
############################################################################ | 100%

pip-22.2.2 | 1.5 MB |
############################################################################ | 100%

ca-certificates-2022 | 189 KB |
############################################################################ | 100%

pyqt5-sip-12.11.0 | 82 KB |
############################################################################ | 100%

jpeg-9e | 366 KB |
############################################################################ | 100%

glib-2.72.1 | 460 KB |
############################################################################ | 100%

wcwidth-0.2.5 | 33 KB |
############################################################################ | 100%

pyqt-5.15.7 | 4.7 MB |
############################################################################ | 100%

pygments-2.13.0 | 821 KB |
############################################################################ | 100%

nose-1.3.7 | 118 KB |
############################################################################ | 100%

gstreamer-1.20.3 | 2.1 MB |
############################################################################ | 100%

libogg-1.3.4 | 34 KB |
############################################################################ | 100%

libiconv-1.16 | 680 KB |
############################################################################ | 100%

libpng-1.6.38 | 773 KB |
############################################################################ | 100%
backports-1.0 | 4 KB |
############################################################################ | 100%

mpmath-1.2.1 | 437 KB |
############################################################################ | 100%

libvorbis-1.3.7 | 267 KB |
############################################################################ | 100%

libwebp-1.2.4 | 76 KB |
############################################################################ | 100%

python-libsbml-5.19. | 4.3 MB |
############################################################################ | 100%

libblas-3.9.0 | 5.6 MB |
############################################################################ | 100%

mkl-2022.1.0 | 182.7 MB |
############################################################################ | 100%

sqlite-3.39.3 | 656 KB |
############################################################################ | 100%

qt-5.15.4 | 14 KB |
############################################################################ | 100%

libsqlite-3.39.3 | 642 KB |
############################################################################ | 100%

setuptools-65.3.0 | 782 KB |
############################################################################ | 100%

packaging-21.3 | 36 KB |
############################################################################ | 100%

tornado-6.2 | 655 KB |
############################################################################ | 100%

qt-webengine-5.15.4 | 60.1 MB |
############################################################################ | 100%

glib-tools-2.72.1 | 167 KB |
############################################################################ | 100%

liblapack-3.9.0 | 5.6 MB |
############################################################################ | 100%

gettext-[Link] | 4.9 MB |
############################################################################ | 100%

prompt_toolkit-3.0.3 | 5 KB |
############################################################################ | 100%

certifi-2022.9.14 | 156 KB |
############################################################################ | 100%
libglib-2.72.1 | 3.1 MB |
############################################################################ | 100%

python-3.8.0 | 18.8 MB |
############################################################################ | 100%

ply-3.11 | 44 KB |
############################################################################ | 100%

krb5-1.19.3 | 847 KB |
############################################################################ | 100%

pyparsing-3.0.9 | 79 KB |
############################################################################ | 100%

intel-openmp-2022.1. | 3.7 MB |
############################################################################ | 100%

libzlib-1.2.12 | 71 KB |
############################################################################ | 100%

gst-plugins-base-1.2 | 2.4 MB |
############################################################################ | 100%

pcre-8.45 | 518 KB |
############################################################################ | 100%

numpy-1.23.3 | 6.3 MB |
############################################################################ | 100%

decorator-5.1.1 | 12 KB |
############################################################################ | 100%

wheel-0.37.1 | 31 KB |
############################################################################ | 100%

biopython-1.79 | 2.6 MB |
############################################################################ | 100%

tbb-2021.5.0 | 164 KB |
############################################################################ | 100%

backports.functools_ | 9 KB |
############################################################################ | 100%

parso-0.8.3 | 69 KB |
############################################################################ | 100%

Preparing transaction: done

Verifying transaction: done

Executing transaction: done

Installing pip dependencies: | Ran pip subprocess with arguments:

['C:\\Users\\Rina_Mekuli\\anaconda3\\envs\\metadraft8\\[Link]', '-m', 'pip', 'install', '-U', '-r',
'C:\\Users\\Rina_Mekuli\\Documents\\Python_MD\\metadraft2\\
[Link]']

Pip subprocess output:

Collecting cbmpy

Using cached [Link] (607 kB)

Collecting xlwt

Using cached [Link] (99 kB)

Collecting xlrd

Downloading [Link] (96 kB)

---------------------------------------- 96.5/96.5 kB 5.4 MB/s eta 0:00:00

Requirement already satisfied: numpy in c:\users\rina_mekuli\anaconda3\envs\metadraft8\lib\site-

packages (from cbmpy->-r C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\
[Link] (line 1)) (1.23.3)

Requirement already satisfied: packaging in c:\users\rina_mekuli\anaconda3\envs\metadraft8\lib\

site-packages (from cbmpy->-r C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\
[Link] (line 1)) (21.3)

Requirement already satisfied: nose in c:\users\rina_mekuli\anaconda3\envs\metadraft8\lib\site-

packages (from cbmpy->-r C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\
[Link] (line 1)) (1.3.7)

Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in c:\users\rina_mekuli\anaconda3\envs\

metadraft8\lib\site-packages (from packaging->cbmpy->-r C:\Users\Rina_Mekuli\Documents\
Python_MD\metadraft2\[Link] (line 1)) (3.0.9)

Installing collected packages: xlwt, xlrd, cbmpy

Successfully installed cbmpy-0.8.2 xlrd-2.0.1 xlwt-1.3.0

done

# To activate this environment, use

# $ conda activate metadraft8

# To deactivate an active environment, use

# $ conda deactivate
Retrieving notices: ...working... done

(base) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>conda env create -n metadraft8 -f

[Link]

CondaValueError: prefix already exists: C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8

(base) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>conda activate metadraft8

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>conda remove cbmpy

Collecting package metadata ([Link]): done

Solving environment: failed

PackagesNotFoundError: The following packages are missing from the target environment:

- cbmpy

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>pip install cbmpy

Requirement already satisfied: cbmpy in c:\users\rina_mekuli\anaconda3\envs\metadraft8\lib\site-

packages (0.8.2)

Requirement already satisfied: nose in c:\users\rina_mekuli\anaconda3\envs\metadraft8\lib\site-

packages (from cbmpy) (1.3.7)

Requirement already satisfied: packaging in c:\users\rina_mekuli\anaconda3\envs\metadraft8\lib\

site-packages (from cbmpy) (21.3)

Requirement already satisfied: numpy in c:\users\rina_mekuli\anaconda3\envs\metadraft8\lib\site-

packages (from cbmpy) (1.23.3)

Requirement already satisfied: pyparsing!=3.0.5,>=2.0.2 in c:\users\rina_mekuli\anaconda3\envs\

metadraft8\lib\site-packages (from packaging->cbmpy) (3.0.9)

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>python [Link]

Traceback (most recent call last):

File "[Link]", line 62, in <module>

import [Link]

File "C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\libpython\[Link]", line

40, in <module>

import sip

ModuleNotFoundError: No module named 'sip'

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>python [Link]

Using Qt5 - the next generation

You are using BioPython 1.79

GLPK not available

No module named 'cplex'

CPLEX not available

*****

WARNING: No linear solver present, please install IBM CPLEX with Python bindings or PyGLPK, please
see [Link] for Windows binary or [Link] for
source.

*****

No solver present, unable to create shortcuts

No Matplotlib available

***********************************************************************
* Welcome to CBMPy (0.8.2) - PySCeS Constraint Based Modelling *

* [Link] *

* Copyright(C) Brett G. Olivier 2014 - 2020 *

* Systems Biology Lab, Vrije Universiteit Amsterdam *

* Amsterdam, The Netherlands *

* CBMPy is developed as part of the BeBasic MetaToolKit Project *

* Distributed under the GNU GPL v 3.0 licence, see *

* LICENCE (supplied with this release) for details *

***********************************************************************

MSG: Could not load template database. Please ensure the template library submodule has been
initialised (see [Link]) and correctly set in the _metadraft.cfg, for example:
'metadraft_db_version: 2019-1'.

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\blast_results\default

INITDB: connecting geneDB

INITDB: connecting notesDB

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>git submodule update --init

--remote -- modeldb/2019-1/

'git' is not recognized as an internal or external command,

operable program or batch file.

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>git

'git' is not recognized as an internal or external command,

operable program or batch file.

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>python [Link]

Using Qt5 - the next generation

You are using BioPython 1.79

GLPK not available

No module named 'cplex'

CPLEX not available

*****

WARNING: No linear solver present, please install IBM CPLEX with Python bindings or PyGLPK, please
see [Link] for Windows binary or [Link] for
source.

*****

No solver present, unable to create shortcuts

No Matplotlib available

***********************************************************************

* Welcome to CBMPy (0.8.2) - PySCeS Constraint Based Modelling *

* [Link] *

* Copyright(C) Brett G. Olivier 2014 - 2020 *

* Systems Biology Lab, Vrije Universiteit Amsterdam *

* Amsterdam, The Netherlands *

* CBMPy is developed as part of the BeBasic MetaToolKit Project *

* Distributed under the GNU GPL v 3.0 licence, see *

* LICENCE (supplied with this release) for details *

***********************************************************************

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\blast_results\default

INITDB: extracting geneDB archive: C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\

modeldb\2019-1\dbx\_metadraft_genedb.[Link]

INITDB: connecting notesDB

Pseudo genes: 0

FASTA sequence file created: C:\Users\Rina_Mekuli\Desktop\Metadraft\Ba_converted.[Link]

Pseudogenes: 0

Proteins: 4337

Optimization: True

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\modeldb\2019-1\lib_model

720 720

createMetaProteome [bigg1-mtub] is using filtered ids

FBC version: 2

[Link]: 1025

[Link]: 912

[Link]: 1

[Link]: 5

[Link]: 661

FluxBounds process1: 0.045

INFO: Active objective: obj

Adding objective: obj

FluxBounds process2: 0.06

SBML3 load time: 1.945

655 genseqs added

MegaGenome file created as: C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\modeldb\

2019-1\lib_metaproteome\(bigg1-mtub)_metaproteome.fasta

Optimization: True

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\modeldb\2019-1\lib_model

1944 1944

createMetaProteome [bigg2-eco1] is using filtered ids

FBC version: 2
[Link]: 2382

[Link]: 1668

[Link]: 1

[Link]: 7

[Link]: 1261

FluxBounds process1: 0.082

INFO: Active objective: obj

Adding objective: obj

FluxBounds process2: 0.169

Groups support: <GroupsModelPlugin>

[Link]: 39

SBML3 load time: 5.392

1259 genseqs added

MegaGenome file created as: C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\modeldb\

2019-1\lib_metaproteome\(bigg2-eco1)_metaproteome.fasta

Work directory: C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\data_blast\1663595775

OS call: perl [Link] IN DB

4337 sequences in file IN

1259 sequences in file DB

Trying to run BLAST now - this may take several hours ... or longer!

Formatting BLAST databases

'[Link]' is not recognized as an internal or external command,

operable program or batch file.

'[Link]' is not recognized as an internal or external command,

operable program or batch file.

Done formatting

Starting BLAST searches...

Starting first BLAST pass for IN - IN on 09/19/2022'[Link]' is not recognized as an internal or
external command,

operable program or batch file.

Starting second BLAST pass for IN - IN on

Starting first BLAST pass for IN - DB on 09/19/202209/19/2022'[Link]' is not recognized as an

internal or external command,

operable program or batch file.

Starting second BLAST pass for IN - DB on

Starting first BLAST pass for DB - IN on 09/19/202209/19/2022'[Link]' is not recognized as an

internal or external command,

operable program or batch file.

Starting second BLAST pass for DB - IN on

Starting first BLAST pass for DB - DB on 09/19/202209/19/2022'[Link]' is not recognized as an

internal or external command,

operable program or batch file.

Starting second BLAST pass for DB - DB on Done BLAST searches. Starting ortholog detection...

Blast output file A->B is missing

09/19/2022

PERL/BLAST ERROR: possible no homology between source and target proteomes!

Sequence search took 0 minutes to complete with return code: 2

MSG: There has been an error in the BLAST search subsystems

please see data_blast directory for debug information

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\blast_results\default
(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>path

PATH=C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8;C:\Users\Rina_Mekuli\anaconda3\envs\
metadraft8\Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\usr\
bin;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\bin;C:\Users\Rina_Mekuli\
anaconda3\envs\metadraft8\Scripts;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\bin;C:\
Users\Rina_Mekuli\anaconda3\condabin;C:\Users\Rina_Mekuli\anaconda3;C:\Users\Rina_Mekuli\
anaconda3\Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\Library\usr\bin;C:\Users\
Rina_Mekuli\anaconda3\Library\bin;C:\Users\Rina_Mekuli\anaconda3\Scripts;C:\Program Files
(x86)\Common Files\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\
System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\
OpenSSH;C:\Program Files\PuTTY;C:\Program Files\dotnet;C:\Strawberry\c\bin;C:\Strawberry\perl\
site\bin;C:\Strawberry\perl\bin;C:\Users\Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\
Users\Rina_Mekuli\anaconda3b;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310\Scripts;C:\Users\
Rina_Mekuli\Documents\Python_MD\cbmpy-metadraft\blast-BLAST_VERSION+\bin;C:\Program
Files\NCBI\blast-BLAST_VERSION+\bin;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310\Scripts;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310;C:\Users\
Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\Users\Rina_Mekuli\AppData\Local\
Programs\Microsoft VS Code\bin

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>path=%path%;C:\Users\
Rina_Mekuli\Documents\Python_MD\metadraft2\tools\ncbi-blast-2.2.26

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>path

PATH=C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8;C:\Users\Rina_Mekuli\anaconda3\envs\
metadraft8\Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\usr\
bin;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\bin;C:\Users\Rina_Mekuli\
anaconda3\envs\metadraft8\Scripts;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\bin;C:\
Users\Rina_Mekuli\anaconda3\condabin;C:\Users\Rina_Mekuli\anaconda3;C:\Users\Rina_Mekuli\
anaconda3\Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\Library\usr\bin;C:\Users\
Rina_Mekuli\anaconda3\Library\bin;C:\Users\Rina_Mekuli\anaconda3\Scripts;C:\Program Files
(x86)\Common Files\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\
System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\
OpenSSH;C:\Program Files\PuTTY;C:\Program Files\dotnet;C:\Strawberry\c\bin;C:\Strawberry\perl\
site\bin;C:\Strawberry\perl\bin;C:\Users\Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\
Users\Rina_Mekuli\anaconda3b;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310\Scripts;C:\Users\
Rina_Mekuli\Documents\Python_MD\cbmpy-metadraft\blast-BLAST_VERSION+\bin;C:\Program
Files\NCBI\blast-BLAST_VERSION+\bin;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310\Scripts;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310;C:\Users\
Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\Users\Rina_Mekuli\AppData\Local\
Programs\Microsoft VS Code\bin;C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\tools\
ncbi-blast-2.2.26
(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>blastall

blastall 2.2.26 arguments:

-p Program Name [String]

-d Database [String]

default = nr

-i Query File [File In]

default = stdin

-e Expectation value (E) [Real]

default = 10.0

-m alignment view options:

0 = pairwise,

1 = query-anchored showing identities,

2 = query-anchored no identities,

3 = flat query-anchored, show identities,

4 = flat query-anchored, no identities,

5 = query-anchored no identities and blunt ends,

6 = flat query-anchored, no identities and blunt ends,

7 = XML Blast output,

8 = tabular,

9 tabular with comment lines

10 ASN, text

11 ASN, binary [Integer]

default = 0

range from 0 to 11

-o BLAST report Output File [File Out] Optional

default = stdout

-F Filter query sequence (DUST with blastn, SEG with others) [String]

default = T

-G Cost to open a gap (-1 invokes default behavior) [Integer]

 default = -1

-E Cost to extend a gap (-1 invokes default behavior) [Integer]

default = -1

-X X dropoff value for gapped alignment (in bits) (zero invokes default behavior)

blastn 30, megablast 20, tblastx 0, all others 15 [Integer]

default = 0

-I Show GI's in deflines [T/F]

default = F

-q Penalty for a nucleotide mismatch (blastn only) [Integer]

default = -3

-r Reward for a nucleotide match (blastn only) [Integer]

default = 1

-v Number of database sequences to show one-line descriptions for (V) [Integer]

default = 500

-b Number of database sequence to show alignments for (B) [Integer]

default = 250

-f Threshold for extending hits, default if zero

blastp 11, blastn 0, blastx 12, tblastn 13

tblastx 13, megablast 0 [Real]

default = 0

-g Perform gapped alignment (not available with tblastx) [T/F]

default = T

-Q Query Genetic code to use [Integer]

default = 1

-D DB Genetic code (for tblast[nx] only) [Integer]

default = 1

-a Number of processors to use [Integer]

default = 1

-O SeqAlign file [File Out] Optional

-J Believe the query defline [T/F]

default = F
 -M Matrix [String]

default = BLOSUM62

-W Word size, default if zero (blastn 11, megablast 28, all others 3) [Integer]

default = 0

-z Effective length of the database (use zero for the real size) [Real]

default = 0

-K Number of best hits from a region to keep. Off by default.

If used a value of 100 is recommended. Very high values of -v or -b is also suggested [Integer]

default = 0

-P 0 for multiple hit, 1 for single hit (does not apply to blastn) [Integer]

default = 0

-Y Effective length of the search space (use zero for the real size) [Real]

default = 0

-S Query strands to search against database (for blast[nx], and tblastx)

3 is both, 1 is top, 2 is bottom [Integer]

default = 3

-T Produce HTML output [T/F]

default = F

-l Restrict search of database to list of GI's [String] Optional

-U Use lower case filtering of FASTA sequence [T/F] Optional

-y X dropoff value for ungapped extensions in bits (0.0 invokes default behavior)

blastn 20, megablast 10, all others 7 [Real]

default = 0.0

-Z X dropoff value for final gapped alignment in bits (0.0 invokes default behavior)

blastn/megablast 100, tblastx 0, all others 25 [Integer]

default = 0

-R PSI-TBLASTN checkpoint file [File In] Optional

-n MegaBlast search [T/F]

default = F

-L Location on query sequence [String] Optional

-A Multiple Hits window size, default if zero (blastn/megablast 0, all others 40 [Integer]
 default = 0

-w Frame shift penalty (OOF algorithm for blastx) [Integer]

default = 0

-t Length of the largest intron allowed in a translated nucleotide sequence when linking multiple
distinct alignments. (0 invokes default behavior; a negative value disables linking.) [Integer]

default = 0

-B Number of concatenated queries, for blastn and tblastn [Integer] Optional

default = 0

-V Force use of the legacy BLAST engine [T/F] Optional

default = F

-C Use composition-based score adjustments for blastp or tblastn:

As first character:

D or d: default (equivalent to T)

0 or F or f: no composition-based statistics

2 or T or t: Composition-based score adjustments as in Bioinformatics 21:902-911,

1: Composition-based statistics as in NAR 29:2994-3005, 2001

2005, conditioned on sequence properties

3: Composition-based score adjustment as in Bioinformatics 21:902-911,

2005, unconditionally

For programs other than tblastn, must either be absent or be D, F or 0.

As second character, if first character is equivalent to 1, 2, or 3:

U or u: unified p-value combining alignment p-value and compositional p-value in round 1 only

[String]

default = D

-s Compute locally optimal Smith-Waterman alignments (This option is only

available for gapped tblastn.) [T/F]

default = F

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>path

PATH=C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8;C:\Users\Rina_Mekuli\anaconda3\envs\
metadraft8\Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\usr\
bin;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\bin;C:\Users\Rina_Mekuli\
anaconda3\envs\metadraft8\Scripts;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\bin;C:\
Users\Rina_Mekuli\anaconda3\condabin;C:\Users\Rina_Mekuli\anaconda3;C:\Users\Rina_Mekuli\
anaconda3\Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\Library\usr\bin;C:\Users\
Rina_Mekuli\anaconda3\Library\bin;C:\Users\Rina_Mekuli\anaconda3\Scripts;C:\Program Files
(x86)\Common Files\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\
System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\
OpenSSH;C:\Program Files\PuTTY;C:\Program Files\dotnet;C:\Strawberry\c\bin;C:\Strawberry\perl\
site\bin;C:\Strawberry\perl\bin;C:\Users\Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\
Users\Rina_Mekuli\anaconda3b;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310\Scripts;C:\Users\
Rina_Mekuli\Documents\Python_MD\cbmpy-metadraft\blast-BLAST_VERSION+\bin;C:\Program
Files\NCBI\blast-BLAST_VERSION+\bin;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310\Scripts;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310;C:\Users\
Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\Users\Rina_Mekuli\AppData\Local\
Programs\Microsoft VS Code\bin;C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\tools\
ncbi-blast-2.2.26

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>path

PATH=C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8;C:\Users\Rina_Mekuli\anaconda3\envs\
metadraft8\Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\usr\
bin;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\bin;C:\Users\Rina_Mekuli\
anaconda3\envs\metadraft8\Scripts;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\bin;C:\
Users\Rina_Mekuli\anaconda3\condabin;C:\Users\Rina_Mekuli\anaconda3;C:\Users\Rina_Mekuli\
anaconda3\Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\Library\usr\bin;C:\Users\
Rina_Mekuli\anaconda3\Library\bin;C:\Users\Rina_Mekuli\anaconda3\Scripts;C:\Program Files
(x86)\Common Files\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\
System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\
OpenSSH;C:\Program Files\PuTTY;C:\Program Files\dotnet;C:\Strawberry\c\bin;C:\Strawberry\perl\
site\bin;C:\Strawberry\perl\bin;C:\Users\Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\
Users\Rina_Mekuli\anaconda3b;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310\Scripts;C:\Users\
Rina_Mekuli\Documents\Python_MD\cbmpy-metadraft\blast-BLAST_VERSION+\bin;C:\Program
Files\NCBI\blast-BLAST_VERSION+\bin;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310\Scripts;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310;C:\Users\
Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\Users\Rina_Mekuli\AppData\Local\
Programs\Microsoft VS Code\bin;C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\tools\
ncbi-blast-2.2.26

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>path=C:\Users\
Rina_Mekuli\Documents\Python_MD\metadraft2\tools\ncbi-blast-2.2.26;%path%

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>path
PATH=C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\tools\ncbi-blast-2.2.26;C:\Users\
Rina_Mekuli\anaconda3\envs\metadraft8;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\
Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\usr\bin;C:\
Users\Rina_Mekuli\anaconda3\envs\metadraft8\Library\bin;C:\Users\Rina_Mekuli\anaconda3\
envs\metadraft8\Scripts;C:\Users\Rina_Mekuli\anaconda3\envs\metadraft8\bin;C:\Users\
Rina_Mekuli\anaconda3\condabin;C:\Users\Rina_Mekuli\anaconda3;C:\Users\Rina_Mekuli\
anaconda3\Library\mingw-w64\bin;C:\Users\Rina_Mekuli\anaconda3\Library\usr\bin;C:\Users\
Rina_Mekuli\anaconda3\Library\bin;C:\Users\Rina_Mekuli\anaconda3\Scripts;C:\Program Files
(x86)\Common Files\Oracle\Java\javapath;C:\WINDOWS\system32;C:\WINDOWS;C:\WINDOWS\
System32\Wbem;C:\WINDOWS\System32\WindowsPowerShell\v1.0;C:\WINDOWS\System32\
OpenSSH;C:\Program Files\PuTTY;C:\Program Files\dotnet;C:\Strawberry\c\bin;C:\Strawberry\perl\
site\bin;C:\Strawberry\perl\bin;C:\Users\Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\
Users\Rina_Mekuli\anaconda3b;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310\Scripts;C:\Users\
Rina_Mekuli\Documents\Python_MD\cbmpy-metadraft\blast-BLAST_VERSION+\bin;C:\Program
Files\NCBI\blast-BLAST_VERSION+\bin;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\
Python310\Scripts;C:\Users\Rina_Mekuli\AppData\Local\Programs\Python\Python310;C:\Users\
Rina_Mekuli\AppData\Local\Microsoft\WindowsApps;C:\Users\Rina_Mekuli\AppData\Local\
Programs\Microsoft VS Code\bin;C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\tools\
ncbi-blast-2.2.26

(metadraft8) C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2>python [Link]

Using Qt5 - the next generation

You are using BioPython 1.79

GLPK not available

No module named 'cplex'

CPLEX not available

*****

WARNING: No linear solver present, please install IBM CPLEX with Python bindings or PyGLPK, please
see [Link] for Windows binary or [Link] for
source.
*****

No solver present, unable to create shortcuts

No Matplotlib available

***********************************************************************

* Welcome to CBMPy (0.8.2) - PySCeS Constraint Based Modelling *

* [Link] *

* Copyright(C) Brett G. Olivier 2014 - 2020 *

* Systems Biology Lab, Vrije Universiteit Amsterdam *

* Amsterdam, The Netherlands *

* CBMPy is developed as part of the BeBasic MetaToolKit Project *

* Distributed under the GNU GPL v 3.0 licence, see *

* LICENCE (supplied with this release) for details *

***********************************************************************

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\blast_results\default

INITDB: connecting geneDB

INITDB: connecting notesDB

Pseudo genes: 0

FASTA sequence file created: C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\testfiles\

default\[Link]

Pseudogenes: 0

Proteins: 48

Optimization: True

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\modeldb\2019-1\lib_model

1944 1944

createMetaProteome [bigg2-eco1] is using filtered ids

FBC version: 2

[Link]: 2382

[Link]: 1668

[Link]: 1

[Link]: 7

[Link]: 1261

FluxBounds process1: 0.07

INFO: Active objective: obj

Adding objective: obj

FluxBounds process2: 0.172

Groups support: <GroupsModelPlugin>

[Link]: 39

SBML3 load time: 5.199

1259 genseqs added

MegaGenome file created as: C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\modeldb\

2019-1\lib_metaproteome\(bigg2-eco1)_metaproteome.fasta

Work directory: C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\data_blast\1663597854

OS call: perl [Link] IN DB

48 sequences in file IN

1259 sequences in file DB

Trying to run BLAST now - this may take several hours ... or longer!

Formatting BLAST databases

Done formatting

Starting BLAST searches...

Starting first BLAST pass for IN - IN on 09/19/2022[blastall 2.2.26] WARNING: the -C 3 argument is
currently experimental
Starting second BLAST pass for IN - IN on 09/19/2022

Starting first BLAST pass for IN - DB on 09/19/2022[blastall 2.2.26] WARNING: the -C 3 argument is
currently experimental

Starting second BLAST pass for IN - DB on 09/19/2022

Starting first BLAST pass for DB - IN on 09/19/2022[blastall 2.2.26] WARNING: the -C 3 argument is
currently experimental

Starting second BLAST pass for DB - IN on 09/19/2022

Starting first BLAST pass for DB - DB on 09/19/2022[blastall 2.2.26] WARNING: the -C 3 argument is
currently experimental

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 140 replaced by X

Selenocysteine (U) at position 196 replaced by X

Selenocysteine (U) at position 196 replaced by X

Starting second BLAST pass for DB - DB on 09/19/2022Done BLAST searches. Starting ortholog
detection...

Output saved to file [Link]-DB

HTML output saved to [Link]

Table output saved to [Link]-DB

mysql output saved to [Link]-DB

Sequence search took 5 minutes to complete with return code: 0

INFO: match not found: in_stu0262

INFO: match not found: in_stu0246

INFO: match not found: in_stu1886

INFO: match not found: in_stu0762

INFO: match not found: in_stu0763

INFO: match not found: in_stu1589

INFO: match not found: in_stu0117

INFO: match not found: in_stu0596

INFO: match not found: in_stu0987

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\testfiles\default\[Link]

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\blast_results\default

Pseudo genes: 0

FASTA sequence file created: C:\Users\Rina_Mekuli\Desktop\Metadraft\Ba_converted.[Link]

Pseudogenes: 0

Proteins: 4337

Optimization: True

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\modeldb\2019-1\lib_model

C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\modeldb\2019-1\lib_model

720 720,904

1336 720,616

createMetaProteome [bigg1-mtub] is using filtered ids

FBC version: 2

[Link]: 1025

[Link]: 912
[Link]: 1

[Link]: 5

[Link]: 661

FluxBounds process1: 0.025

INFO: Active objective: obj

Adding objective: obj

FluxBounds process2: 0.026

SBML3 load time: 0.934

655 genseqs added

createMetaProteome [bigg2v1-bsu] is using filtered ids

FBC version: 2

[Link]: 1250

[Link]: 990

[Link]: 1

[Link]: 6

[Link]: 844

FluxBounds process1: 0.027

INFO: Active objective: obj

Adding objective: obj

FluxBounds process2: 0.036

Groups support: <GroupsModelPlugin>

[Link]: 11

SBML3 load time: 1.919

562 genseqs added

MegaGenome file created as: C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\modeldb\

2019-1\lib_metaproteome\(bigg1-mtub-bigg2v1-bsu)_metaproteome.fasta
Work directory: C:\Users\Rina_Mekuli\Documents\Python_MD\metadraft2\data_blast\1663598293

OS call: perl [Link] IN DB

4337 sequences in file IN

1217 sequences in file DB

Trying to run BLAST now - this may take several hours ... or longer!

Formatting BLAST databases

Done formatting

Starting BLAST searches...

Starting first BLAST pass for IN - IN on 09/19/2022[blastall 2.2.26] WARNING: the -C 3 argument is
currently experimental

Starting second BLAST pass for IN - IN on 09/19/2022

Starting first BLAST pass for IN - DB on 09/19/2022[blastall 2.2.26] WARNING: the -C 3 argument is
currently experimental

Starting second BLAST pass for IN - DB on 09/19/2022

Starting first BLAST pass for DB - IN on 09/19/2022[blastall 2.2.26] WARNING: the -C 3 argument is
currently experimental

Starting second BLAST pass for DB - IN on 09/19/2022

Starting first BLAST pass for DB - DB on 09/19/2022[blastall 2.2.26] WARNING: the -C 3 argument is
currently experimental

Starting second BLAST pass for DB - DB on 09/19/2022Done BLAST searches. Starting ortholog
detection...

Output saved to file [Link]-DB

HTML output saved to [Link]

Table output saved to [Link]-DB

mysql output saved to [Link]-DB