windows installation problems about gapseq HOT 7 OPEN

hi, Fake-star. It should run without problems on desktop computers or notebooks, even older ones.

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hi @Fake-star

The conda package is currently in development and unavailable under Windows (see #217).
In general, installing gapseq in a Windows environment is not supported yet. However, it should be possible, for example, by using the WSL (https://learn.microsoft.com/en-us/windows/wsl/)

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Thank you very much for your answer.
Another question I have is what is the recommended computer configuration for gapseq to run？

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My software has been installed successfully.
I'm having a new problem running . /gapseq doall toy/myb71.fna.gz it shows an error, here is the exact error message：
Nucleotide fasta detected.
index file myb71.fna.tmp.fai not found, generating...
Predicted taxonomy: Bacteria
ATTENTION: gapseq sequence archives are missing! Sequences will be needed to be downloaded from uniprot directly which is rather slow.
3541
** FATAL ERROR **: Duplicate fasta identifier []
exiting ...
** FATAL ERROR **: Could not find identifier [sp|O85692|ETFA_MEGEL] (missing -F ?)
exiting ...
ls: cannot access 'query_subunit.part-.fasta': No such file or directory
rm: cannot remove 'query_subunit.part-.fasta*': No such file or directory
** FATAL ERROR **: Duplicate fasta identifier []
exiting ...
** FATAL ERROR **: Could not find identifier [sp|O85691|ETFB_MEGEL] (missing -F ?)
exiting ...
ls: cannot access 'query_subunit.part-.fasta': No such file or directory
rm: cannot remove 'query_subunit.part-.fasta*': No such file or directory
** FATAL ERROR **: Duplicate fasta identifier []
exiting ...
** FATAL ERROR **: Could not find identifier [sp|P52042|ACDS_CLOAB] (missing -F ?)
exiting ...
ls: cannot access 'query_subunit.part-.fasta': No such file or directory
rm: cannot remove 'query_subunit.part-.fasta*': No such file or directory
FASTA-Reader: Ignoring invalid residues at position(s): On line 7: 23-24, 37-38, 43, 46, 51, 56
FASTA-Reader: Ignoring invalid residues at position(s): On line 8: 2-5, 27-28, 34, 37-38, 43, 46, 51, 56, 58-59
FASTA-Reader: Ignoring invalid residues at position(s): On line 9: 6-8, 30-31, 33-34, 39, 41
FASTA-Reader: Ignoring invalid residues at position(s): On line 10: 2-3, 5, 10, 12-13, 29-31, 33-34, 39, 41, 45, 47-57, 59
FASTA-Reader: Ignoring invalid residues at position(s): On line 11: 1, 4, 9, 11, 32-33, 35, 38-39, 44-46, 51
Warning: [tblastn] Query_1 UniRef90_Q59987 L.. : One or more O characters replaced by X for alignment score calculations at positions 323, 374, 381, 435, 466
** FATAL ERROR **: Duplicate fasta identifier []
exiting ...
** FATAL ERROR **: Could not find identifier [sp|Q31L05|NDHN_SYNE7] (missing -F ?)
exiting ...
ls:

Here's what I get when I run the . /gapseq test：
`gapseq version: 1.2 2d739a5
linux-gnu
#1 SMP Thu Jan 11 04:09:03 UTC 2024

#######################
#Checking dependencies#
#######################
ldconfig (Ubuntu GLIBC 2.35-0ubuntu3.4) 2.35
libsbml.so.5 -> libsbml.so.5.19.0
libglpk.so.40 -> libglpk.so.40.3.1
GNU Awk 5.1.0, API: 3.0 (GNU MPFR 4.1.0, GNU MP 6.2.1)
sed (GNU sed) 4.8
grep (GNU grep) 3.7
This is perl 5, version 34, subversion 0 (v5.34.0) built for x86_64-linux-gnu-thread-multi
tblastn: 2.12.0+
exonerate from exonerate version 2.4.0
bedtools v2.30.0
barrnap 0.9 - rapid ribosomal RNA prediction
R version 4.1.2 (2021-11-01) -- "Bird Hippie"
R scripting front-end version 4.1.2 (2021-11-01)
Rscript NOT FOUND
git version 2.34.1
GNU parallel 20210822
HMMER 3.3.2 (Nov 2020); http://hmmer.org/
bc 1.07.1

Missing dependencies: 1

#####################
#Checking R packages#
#####################
data.table 1.15.4
stringr 1.5.1
sybil 2.2.0
getopt 1.20.4
doParallel 1.0.17
foreach 1.5.2
R.utils 2.12.3
stringi 1.8.4
glpkAPI 1.3.4
BiocManager 1.30.23
Biostrings NOT FOUND
jsonlite 1.8.8
CHNOSZ 2.1.0
httr 1.4.7

Missing R packages: 1

##############################
#Checking basic functionality#
##############################
Optimization test: OK
Building full model: OK
Blast test: OK

Passed tests: 3/3`

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Your installation still was not successful: Rscript and Biostrings are missing, see the output of gapseq test

Maybe this can help with Rscript on windows: https://info201.github.io/r-intro.html#running-r-cmd

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Hi, jotech
I'm very sorry I'm having a new problem.here is the error message：
./gapseq doall toy/myb71.fna.gz
/tmp/tmp.qB0BtUHKUz
Nucleotide fasta detected.
index file myb71.fna.tmp.fai not found, generating...
Predicted taxonomy: Bacteria
ATTENTION: gapseq sequence archives are missing! Sequences will be needed to be downloaded from uniprot directly which is rather slow.
3541
错误于curl::curl_fetch_memory(url, handle = handle):
Timeout was reached: [rest.uniprot.org] Resolving timed out after 10001 milliseconds
Calls: GET_retries ... request_fetch -> request_fetch.write_memory ->
停止执行
md5sum: 1.14.14.9.fasta: 没有那个文件或目录
cat: 1.14.14.9.fasta: 没有那个文件或目录

Here's what I get when I run the . /gapseq test：
gapseq version: 1.2 2d739a5
linux-gnu
#123~20.04.1-Ubuntu SMP Wed Jun 12 17:33:13 UTC 2024

#######################
#Checking dependencies#
#######################
ldconfig (Ubuntu GLIBC 2.31-0ubuntu9.9) 2.31
libsbml.so.5 -> libsbml.so.5.18.0
libglpk.so.40 -> libglpk.so.40.3.0
GNU Awk 5.0.1, API: 2.0 (GNU MPFR 4.0.2, GNU MP 6.2.0)
sed (GNU sed) 4.7
grep (GNU grep) 3.4
This is perl 5, version 30, subversion 0 (v5.30.0) built for x86_64-linux-gnu-thread-multi
tblastn: 2.9.0+
exonerate from exonerate version 2.4.0
bedtools v2.27.1
barrnap 0.9 - rapid ribosomal RNA prediction
R version 4.4.1 (2024-06-14) -- "Race for Your Life"
git version 2.25.1
GNU parallel 20161222
HMMER 3.3 (Nov 2019); http://hmmer.org/
bc 1.07.1

Missing dependencies: 0

#####################
#Checking R packages#
#####################
data.table 1.15.4
stringr 1.5.1
sybil 2.2.0
getopt 1.20.4
doParallel 1.0.17
foreach 1.5.2
R.utils 2.12.3
stringi 1.8.4
glpkAPI 1.3.4
BiocManager 1.30.23
Biostrings 2.72.1
jsonlite 1.8.8
CHNOSZ 2.1.0
httr 1.4.7

Missing R packages: 0

##############################
#Checking basic functionality#
##############################
Optimization test: OK
Building full model: OK
Blast test: OK

Passed tests: 3/3

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Greetings, author.
gapseq has been successfully installed! Could you please answer whether gapseq can be used to predict the growth of a strain under different conditions. Like FBA. Or do I need to use other software like cobra toolbox to analyze it?
I am very much looking forward to your answer, I would appreciate it!

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