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SPADA
1–27 of 27
Welcome to SPADA User Discussion Group, you can post any questions related with SPADA. Before posting, you might want to have a look at
SPADA_Readme
and also
SPADA_FAQ
.
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Liangliang Gao
, …
Karthika
6
1/10/24
configure error Install clustalo
Same error facing as @shivam gupta. Did the installation of clustalo. But throws error while checking
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configure error Install clustalo
Same error facing as @shivam gupta. Did the installation of clustalo. But throws error while checking
1/10/24
Diya Prabhuram
9/15/22
malformat location string error
Hello! I've been trying to run SPADA but I keep getting this error. What exactly does this mean
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malformat location string error
Hello! I've been trying to run SPADA but I keep getting this error. What exactly does this mean
9/15/22
Diya P
4/5/22
System Requirements
Hello, Will SPADA run on a system with 16 GB RAM? Or is it too memory intensive? What is the minimum
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System Requirements
Hello, Will SPADA run on a system with 16 GB RAM? Or is it too memory intensive? What is the minimum
4/5/22
zhang iris
2
7/17/19
Q&A
cannot execute hmmsearch when running spada.pl
I have fixed the error, just revised the hmm variable setting in Hmm.pm and it works well.
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Q&A
cannot execute hmmsearch when running spada.pl
I have fixed the error, just revised the hmm variable setting in Hmm.pm and it works well.
7/17/19
gillianl...@gmail.com
1/4/19
Permission Error
Hello, I'm trying to run SPADA and I keep encountering this error: ===== setting up environment
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Permission Error
Hello, I'm trying to run SPADA and I keep encountering this error: ===== setting up environment
1/4/19
Anita Tripathi
, …
Clarissa B.
3
5/18/18
Problem in running spada
I am having the same issue: Possible precedence issue with control flow operator at /usr/local/lib/
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Problem in running spada
I am having the same issue: Possible precedence issue with control flow operator at /usr/local/lib/
5/18/18
Alexey Afonin
8/19/16
Persistent error Can't use string "HASH"
Hi group! When using the latest release from git-hub i got the following message, much like a couple
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Persistent error Can't use string "HASH"
Hi group! When using the latest release from git-hub i got the following message, much like a couple
8/19/16
Clarissa B.
8/3/16
error running Spada
Dear all, I installed all the tools and perl modules. When I tried the command: perl spada.pl --cfg
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error running Spada
Dear all, I installed all the tools and perl modules. When I tried the command: perl spada.pl --cfg
8/3/16
Michael Seidl
7/15/16
error (perl use hash as string) running SPADA
Hi google group, I yesterday fetched the recent version of SPADA from github. When I run the perl
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error (perl use hash as string) running SPADA
Hi google group, I yesterday fetched the recent version of SPADA from github. When I run the perl
7/15/16
boyas...@gmail.com
,
Peng Zhou
5
7/12/14
How to Build our own profile alignments, and then our own HMM profile for each alignment file
Hi, Sorry for the late response - I was busy the entire last week and didn't got a chance to look
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How to Build our own profile alignments, and then our own HMM profile for each alignment file
Hi, Sorry for the late response - I was busy the entire last week and didn't got a chance to look
7/12/14
Hiroyo Nishide
,
Peng Zhou
4
3/13/14
Q&A
error "Can't use string ("HASH(0x20e9f78)") as a HASH ref while "strict refs"
Hi, Peng Thank you for your quick response! We could have result. Best, Hiroyo
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Q&A
error "Can't use string ("HASH(0x20e9f78)") as a HASH ref while "strict refs"
Hi, Peng Thank you for your quick response! We could have result. Best, Hiroyo
3/13/14
Liangliang Gao
7/13/12
met an error seems related with log file read/write, (solved)
gaoll@lab050: ~/spada_soft/spada$ perl spada.pl --cfg conf.txt --org test --fas ./test/01_refseq.fa -
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met an error seems related with log file read/write, (solved)
gaoll@lab050: ~/spada_soft/spada$ perl spada.pl --cfg conf.txt --org test --fas ./test/01_refseq.fa -
7/13/12
Peng Zhou
,
Joseph Guhlin
3
7/13/12
SPADA updated to generate a GFF comparison table
Sure, attahced is an output of Athaliana. On Friday, July 13, 2012 11:22:54 AM UTC-5, Joseph wrote:
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SPADA updated to generate a GFF comparison table
Sure, attahced is an output of Athaliana. On Friday, July 13, 2012 11:22:54 AM UTC-5, Joseph wrote:
7/13/12
Joseph Guhlin
, …
Peng Zhou
3
7/6/12
Meeting tomorrow
I think maybe it's best we meet every other week since we don't have many updates to report.
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Meeting tomorrow
I think maybe it's best we meet every other week since we don't have many updates to report.
7/6/12
Liangliang Gao
,
Joseph Guhlin
13
7/5/12
Figured out how to get BioPerl work at MSI machines
Thank you Joseph! use lib "/home/msi/gaoll/perl5/lib/perl5" worked! I tried to add export
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Figured out how to get BioPerl work at MSI machines
Thank you Joseph! use lib "/home/msi/gaoll/perl5/lib/perl5" worked! I tried to add export
7/5/12
Liangliang Gao
,
Peng Zhou
3
7/3/12
any one knows how to convert fastq illumina quality encoding 1.3-1.7 to 1.8+?
I figured it out (see below). Thanks for your suggestions! my $seqio_in=Bio::SeqIO->new(-file =
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any one knows how to convert fastq illumina quality encoding 1.3-1.7 to 1.8+?
I figured it out (see below). Thanks for your suggestions! my $seqio_in=Bio::SeqIO->new(-file =
7/3/12
Liangliang Gao
,
Peng Zhou
4
6/28/12
Does this mean 508 genes predicted? With 141 subfamilis?
Good idea - will probably add that to the software TODO list. On Thursday, June 28, 2012 10:57:16 AM
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Does this mean 508 genes predicted? With 141 subfamilis?
Good idea - will probably add that to the software TODO list. On Thursday, June 28, 2012 10:57:16 AM
6/28/12
Liangliang Gao
, …
Peng Zhou
4
6/28/12
Is it realistic to run SPADA on desktop computer?
potato. (Solanum tuberosum) It finished anyway. I checked the files, it seems like the last
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Is it realistic to run SPADA on desktop computer?
potato. (Solanum tuberosum) It finished anyway. I checked the files, it seems like the last
6/28/12
Liangliang Gao
,
Joseph Guhlin
3
6/27/12
cannot locate fasta.pm
Thanks! I miss typed "spada" to "spdada". Now worked, ,? gaoll@VM:~/spada_soft/
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cannot locate fasta.pm
Thanks! I miss typed "spada" to "spdada". Now worked, ,? gaoll@VM:~/spada_soft/
6/27/12
Liangliang Gao
,
Peng Zhou
5
6/26/12
finally worked?
Could these be problems You chose to install Clone and it installed fine Checking prerequisites...
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finally worked?
Could these be problems You chose to install Clone and it installed fine Checking prerequisites...
6/26/12
Liangliang Gao
6/26/12
will that affect usage of perl if modules not installed to local/bin?
llgao@llgao-Studio-1458:~/spada_soft/BioPerl-1.6.1$ cpanm Graph ! ! Can't write to /usr/local/
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will that affect usage of perl if modules not installed to local/bin?
llgao@llgao-Studio-1458:~/spada_soft/BioPerl-1.6.1$ cpanm Graph ! ! Can't write to /usr/local/
6/26/12
Liangliang Gao
6/26/12
missing modules necessary or not?
*** (back in BioPerl Build.PL) *** * You chose to install Clone and it installed fine Checking
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missing modules necessary or not?
*** (back in BioPerl Build.PL) *** * You chose to install Clone and it installed fine Checking
6/26/12
Liangliang Gao
6/26/12
installing aceperl errors... (seem required for BioPerl)
ake[1]: Entering directory `/home/llgao/.cpan/build/AcePerl-1.92-Q43JI3/Freesubs' make[1]:
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installing aceperl errors... (seem required for BioPerl)
ake[1]: Entering directory `/home/llgao/.cpan/build/AcePerl-1.92-Q43JI3/Freesubs' make[1]:
6/26/12
Liangliang Gao
,
Joseph Guhlin
3
6/26/12
error config. clustalo (under ubuntu 11.10 64bit), no c++ compiler
Thanks. Worked On Tuesday, June 26, 2012 12:48:54 PM UTC-4, Joseph wrote: Do this: sudo apt-get build
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error config. clustalo (under ubuntu 11.10 64bit), no c++ compiler
Thanks. Worked On Tuesday, June 26, 2012 12:48:54 PM UTC-4, Joseph wrote: Do this: sudo apt-get build
6/26/12
Liangliang Gao
,
Peng Zhou
2
6/15/12
signalP not working, where is the problem?
I suppose this issue has been resolved. On Friday, June 15, 2012 3:49:38 PM UTC-5, Liangliang Gao
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signalP not working, where is the problem?
I suppose this issue has been resolved. On Friday, June 15, 2012 3:49:38 PM UTC-5, Liangliang Gao
6/15/12
Liangliang Gao
,
Peng Zhou
3
6/15/12
I think we should specify the version numbers for suppporting software packages
Software versions have been added to the SPADA_Readme, please check. On Wednesday, June 13, 2012 2:54
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I think we should specify the version numbers for suppporting software packages
Software versions have been added to the SPADA_Readme, please check. On Wednesday, June 13, 2012 2:54
6/15/12
Peng Zhou
6/12/12
Announcement
Pre-processed plant genome files
SPADA requires the genome fasta file and gene annotation file (GFF) to run, some processed FASTA and
unread,
Announcement
Pre-processed plant genome files
SPADA requires the genome fasta file and gene annotation file (GFF) to run, some processed FASTA and
6/12/12