Closed fan040 closed 1 month ago
pauline-ng
commented
2 months ago Install switch for perl
Can't locate Switch.pm in @inc (you may need to install the Switch module
Is your fasta file in the typical format with 60 DNA bases per line? If it's one long string, please break it up.
fan040
commented
2 months ago Thank you for your reply. I have installed switch.pm for many times, but it sometimes reports such errors, I would like to ask why? My fasta file, shown here, is 60 bases.
pauline-ng
commented
2 months ago Is Switch in any of your @inc paths ( /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0 /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/5.22.0/x86_64-linux-thread-multi /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/5.22.0 )?
Did the test files work for you? I'm seeing Chinese characters in the error messages -- SIFT has not been tested for other languages, so that may be throwing it off.
fan040
commented
2 months ago Thank you for your reply.
1.I found that there was no switch in these folders. I used the conda method to install the switch before, and the installation was successful. May I ask whether this installation is invalid? How do I install it?
2.For the test file, I don't know how to solve this problem
pauline-ng
commented
2 months ago You need to change the config file to your paths. I see my name in the path /home/pauline which means the config file hasn't been changed to reflect your system.
fan040
commented
2 months ago Thank you for your reply. I said to listen to your suggestions to modify, see the running result is what.
fan040
commented
2 months ago I tried to run the test file and it is OK to create, the following is a picture of it.
But I can't build my own database and I'd like to ask why.
pauline-ng
commented
2 months ago It still says Switch isn't installed.Maybe you should try the Dockerfile
fan040
commented
2 months ago Thank you very much for your reply. There is only apptainer in my system, so docker cannot be run. Is my test file successfully run? It doesn't seem to have this module installed either.
pauline-ng
commented
2 months ago Read this to see if your database is made correctly.
fan040
commented
2 months ago Thank you for your reply. I would like you to have a look at my configuration process. I did not find anything wrong. I hope to get your help.
pauline-ng
commented
2 months ago It's not working. You have to install Switch.pm correctly
fan040
commented
2 months ago Thanks for your reply, I will try to install it again.
fan040
commented
2 months ago I installed the module, but still reported an error, I want to ask the reason, I am not familiar with programming, hope you can help me.
fan040
commented
2 months ago
I have a question, how did the file in this error report get generated and what went wrong with my configuration?
(sift4G) perl make-SIFT-db-all.pl --config test_files/AK58V4MP.txt converting gene format to use-able input Can't locate Switch.pm in @INC (you may need to install the Switch module) (@INC contains: /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/x86_64-linux-thread-multi /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0 /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/5.22.0/x86_64-linux-thread-multi /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/5.22.0 .) at gff_gene_format_to_ucsc.pl line 4. BEGIN failed--compilation aborted at gff_gene_format_to_ucsc.pl line 4. done converting gene format making single records file Possible precedence issue with control flow operator at /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm line 791.
------------- EXCEPTION ------------- MSG: Each line of the qual file must be less than 65,536 characters. Line 3 is 300037501 chars. STACK Bio::DB::IndexedBase::_check_linelength /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:744 STACK Bio::DB::Fasta::_calculate_offsets /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/Fasta.pm:175 STACK Bio::DB::IndexedBase::_index_files /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:648 STACK Bio::DB::IndexedBase::index_dir /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:446 STACK Bio::DB::IndexedBase::new /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:361 STACK main::generateOutput make-single-records-BIOPERL.pl:147 STACK toplevel make-single-records-BIOPERL.pl:105
done making single records template making noncoding records file Possible precedence issue with control flow operator at /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm line 791.
------------- EXCEPTION ------------- MSG: Each line of the qual file must be less than 65,536 characters. Line 3 is 300037501 chars. STACK Bio::DB::IndexedBase::_check_linelength /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:744 STACK Bio::DB::Fasta::_calculate_offsets /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/Fasta.pm:175 STACK Bio::DB::IndexedBase::_index_files /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:648 STACK Bio::DB::IndexedBase::index_dir /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:446 STACK Bio::DB::IndexedBase::new /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:361 STACK main::generateOutput make-single-records-noncoding.pl:62 STACK toplevel make-single-records-noncoding.pl:51
done making noncoding records make the fasta sequences Possible precedence issue with control flow operator at /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm line 791.
------------- EXCEPTION ------------- MSG: Each line of the qual file must be less than 65,536 characters. Line 3 is 300037501 chars. STACK Bio::DB::IndexedBase::_check_linelength /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:744 STACK Bio::DB::Fasta::_calculate_offsets /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/Fasta.pm:175 STACK Bio::DB::IndexedBase::_index_files /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:648 STACK Bio::DB::IndexedBase::index_dir /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:446 STACK Bio::DB::IndexedBase::new /cluster/home/fanrong/.conda/envs/sift4G/lib/perl5/site_perl/5.22.0/Bio/DB/IndexedBase.pm:361 STACK main::generateOutput generate-fasta-subst-files-BIOPERL.pl:374 STACK toplevel generate-fasta-subst-files-BIOPERL.pl:178
done making the fasta sequences start siftsharp, getting the alignments cat: '/cluster/home/fanrong/perl5/scripts_to_build_SIFT_db/test_files/AK58V4MP/fasta/*.fasta': 没有那个文件或目录 /cluster/home/fanrong/.conda/envs/sift4G/bin/sift4g -d /cluster/home/fanrong/perl5/scripts_to_build_SIFT_db/test_files/uniref90.fasta -q /cluster/home/fanrong/perl5/scripts_to_build_SIFT_db/test_files/AK58V4MP/all_prot.fasta --subst /cluster/home/fanrong/perl5/scripts_to_build_SIFT_db/test_files/AK58V4MP/subst --out /cluster/home/fanrong/perl5/scripts_to_build_SIFT_db/test_files/AK58V4MP/SIFT_predictions --sub-results Checking query data and substitutions files