jotech
windows installation problems
Can the model be used on windows and what is the recommended minimum configuration
problem: Collecting package metadata (repodata.json): done Solving environment: failed
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/)
Thank you very much for your answer. Another question I have is what is the recommended computer configuration for gapseq to run？
hi, Fake-star. It should run without problems on desktop computers or notebooks, even older ones.
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`
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
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 -> <Anonymous> 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
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!