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Rostlab / SNAP2

SNP effect predictor
https://rostlab.org/services/snap/
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runtime error of snap2 #4

Open seitza opened 8 years ago

seitza commented 8 years ago

After finally having installed the tool, now running it fails. First I edited the config file in ~/.snap2rc:

[snap2]
# snapfun_utildir=path - path to package utilities, default: /usr/share/snap2
snap2dir=/usr/share/snap2
#use snap cache [0|1], default: 0
use_snap_cache=0
#snap cache fetch executable
snapc_fetch=/usr/bin/snapc_fetch
#snap cache store executable
snapc_store=/usr/bin/snapc_store
#snap cache root - overrides snap-cache-mgr configuration
snap_cache_root=
# blastpgp_processors
blastpgp_processors=1
#use predictprotein cache, default: 0
use_pp_cache=0
#predictprotein executable
pp_exe=/usr/bin/predictprotein
#sift executable
sift_exe=/usr/bin/sift_for_submitting_fasta_seq.csh
#reprof executable
reprof_exe=/usr/bin/reprof
#blast executable
blast_exe=/usr/bin/blastpgp

[data]
# swiss_dat=path - location of UniProt/Swiss-Prot dat file
swiss_dat=/home/vagrant/snap_db_mnt/uniprot_sprot.dat
# db_swiss=path - path to ID index of Swiss-Prot dat file (generated by /usr/share/librg-utils-perl/dbSwiss.pl)
db_swiss=/home/vagrant/snap_db_mnt/dbswiss
# PHAT substitution matrix
phat_matrix=/usr/share/snap2/phat.txt

[blast]
# big80=path - path to redundancy reduced database (UniProtKB 80 or equivalent)
big80=/home/vagrant/snap_db_mnt/uniref90.fasta
# swiss=path - path to SwissProt database
swiss=/home/vagrant/snap_db_mnt/uniprot_sprot.fasta

Please note the last lines concerning $big80 and $swiss, which I regard as the cause for the error. The rest of the config is default. I tried to enter only the path, the path to the original fast file, a path containing a wildcard to all files, which were generated by makeblastdb, and all single files, which were created by makeblastdb. All runs failed and result in the following error:

$ snap2 --seq AAAAAAAAAAAAAAAAA --cmdmuts A10S -o ~/test
Working directory: /tmp/8U7BA0jRh9
Job name: test

Running external programs..
*** ERROR blastpgp_to_saf.pl : *** ERROR blastp_to_saf: blast file format not recognized
Died at /usr/share/librg-utils-perl//blastpgp_to_saf.pl line 76.
make: *** [query.safBlastPsi80] Error 255
make --no-builtin-rules INFILE=query.in -C /tmp/DSXzkuyD2k JOBID=query -j 1 BLASTCORES=1 LIBRGUTILS=/usr/share/librg-utils-perl/ PPROOT=/usr/share/predictprotein/ PROFNUMRESMIN=17 PROFROOT=/usr/share/profphd/prof/ BIGBLASTDB=/mnt/project/rost_db/data/blast/big BIG80BLASTDB=/mnt/project/rost_db/data/blast/big_80 PFAM2DB=/mnt/project/rost_db/data/pfam/Pfam_ls PFAM3DB=/mnt/project/rost_db/data/pfam/Pfam-A.hmm PROSITEDAT=/mnt/project/rost_db/data/prosite/prosite.dat PROSITECONVDAT=/mnt/project/rost_db/data/prosite/prosite_convert.dat PSICEXE=/usr/share/rost-runpsic/runNewPSIC.pl SPKEYIDX=/mnt/project/rost_db/data/swissprot/keyindex_loctree.txt SWISSBLASTDB=/mnt/project/rost_db/data/blast/swiss --quiet -f /usr/share/predictprotein/MakefilePP.mk query.mdisorder query.profRdb query.prof1Rdb query.profbval query.blastPsiMat query.isis query.clustalngz query.psic failed: 512 at /usr/bin/predictprotein line 391.
Failed to execute '/usr/bin/predictprotein --seqfile=/tmp/8U7BA0jRh9/test.fasta --target=query.blastPsiMat --target=query.psic --target=query.profRdb --target=query.prof1Rdb --target=query.profbval --target=query.isis --target=query.mdisorder --target=query.clustalngz --blast-processors=1 --output-dir=/tmp/8U7BA0jRh9': 25 at /usr/share/perl5/RG/Snap2/Run.pm line 114
    RG::Snap2::Run::predictprotein('/tmp/8U7BA0jRh9', '/tmp/8U7BA0jRh9/test.fasta', undef, 1, 'test', undef, 0, '/usr/bin/predictprotein', 0, ...) called at /usr/share/perl5/RG/Snap2/Run.pm line 14
    RG::Snap2::Run::all('/tmp/8U7BA0jRh9/test.muts', '/tmp/8U7BA0jRh9', '/usr/bin/sift_for_submitting_fasta_seq.csh', '/home/vagrant/snap_db_mnt/uniref90.fasta.', '/home/vagrant/snap_db_mnt/uniprot_sprot.fasta', '/usr/bin/blastpgp', undef, 1, 'test', ...) called at /usr/share/perl5/RG/Snap2/Snap2.pm line 223
    RG::Snap2::Snap2::run('HASH(0x14ea2a0)', 1.0.10) called at /usr/bin/snap2 line 117

A very short personal meeting with @hechtm revealed a a potential problem (using the longest common suffix of all makeblastdb-generated files as input path), but didn't help so far. Anyone any ideas?

hechtm commented 8 years ago

Looks like predictprotein is not configured correctly. Can you please show the contents of your predictproteinrc? Default: /usr/share/predictprotein/predictproteinrc.default

Also, to facilitate the process, please use the example from the snap2 man page (you can simply copy and paste it). It would greatly improve my understanding of the problem if you used the additional debugging option (-d), possibly twice to increase verbosity (-d -d). If the problem persists I would also like to ask you to use the --workdir option to store intermediate files so we can find out whether the blast file really has an unrecognized format.

hechtm commented 8 years ago

oh and thanks for pointing out these problems - it shows I need to rework the documentation significantly

juanmirocks commented 8 years ago

@seitza did you find out sth else?

seitza commented 8 years ago

we did not find out something else. we checked the predict protein config, which was wrong per default of course. However, there are some paths, which we could not associate with any of the databases we downloaded and install. furthermore, the documentation of predict protein for standalone tools is short. the man page only states 

Resources
        Database                             Cmd line argument
        --------                             -----------------
        big (Uniprot+PDB) blast database     --bigblastdb
        big_80 (big @ 80% sequence identity  --big80blastdb
          redunancy level) blast database
        swiss blast database                 --swissblastdb
        pfam v2 database                     --pfam2db
        pfam v3 database                     --pfam3db
        prosite_convert.dat                  --prositeconvdat

       Resources for optional targets

        Database                             Cmd line argument
        --------                             -----------------
        big (Uniprot+PDB) blast database     --bigblastdb
        prosite.dat                          --prositedat
        Swiss-Prot keyword-to-accession      --spkeyidx
         'index' for loctree

   Generating Resources
       Courtesy of Wiktor Jurkowski:

        * rostlab-data-prosite_convert prosite.dat prosite_convert.dat
        * perl /usr/share/loctree/perl/keyindex4loctree.pl < keyindex.txt > keyindex_loctree.txt
        * hmmpress Pfam-A.hmm

Until now, we can not handle the generate resources part, because none of the tools comes with the installation process, we came up with by collection infomartion from the readme etc. furthermore, we ignored pram completely, since we are not using it with snap2 (we think at least). the same accounts for prosite.

Running the second example of the snap2 man page, with the following snap2 config file

[snap2]
# snapfun_utildir=path - path to package utilities, default: /usr/share/snap2
snap2dir=/usr/share/snap2
#use snap cache [0|1], default: 0
use_snap_cache=0
#snap cache fetch executable
snapc_fetch=/usr/bin/snapc_fetch
#snap cache store executable
snapc_store=/usr/bin/snapc_store
#snap cache root - overrides snap-cache-mgr configuration
snap_cache_root=
# blastpgp_processors
blastpgp_processors=1
#use predictprotein cache, default: 0
use_pp_cache=0
#predictprotein executable
pp_exe=/usr/bin/predictprotein
#sift executable
sift_exe=/usr/bin/sift_for_submitting_fasta_seq.csh
#reprof executable
reprof_exe=/usr/bin/reprof
#blast executable
blast_exe=/usr/bin/blastpgp

[data]
# swiss_dat=path - location of UniProt/Swiss-Prot dat file
swiss_dat=/home/snap_db/uniprot_sprot.dat
# db_swiss=path - path to ID index of Swiss-Prot dat file (generated by /usr/share/librg-utils-perl/dbSwiss.pl)
db_swiss=/home/snap_db/dbswiss
# PHAT substitution matrix
phat_matrix=/usr/share/snap2/phat.txt

[blast]
# big80=path - path to redundancy reduced database (UniProtKB 80 or equivalent)
big80=/home/snap_db/uniref90.fasta
# swiss=path - path to SwissProt database
swiss=/home/snap_db/uniprot_sprot.fasta

leads to

snap2 -i /usr/share/doc/snap2/examples/MT4_HUMAN.fasta -m all -o MT4_HUMAN.snap2 -d -d --workdir /home/workdir
Working directory: /home/workdir
Job name: MT4_HUMAN

Running external programs..
/usr/bin/predictprotein--seqfile=/home/workdir/MT4_HUMAN.fasta--target=query.blastPsiMat--target=query.psic--target=query.profRdb--target=query.prof1Rdb--target=query.profbval--target=query.isis--target=query.mdisorder--target=query.clustalngz--blast-processors=1--output-dir=/home/workdir at /usr/share/perl5/RG/Snap2/Run.pm line 113
    RG::Snap2::Run::predictprotein('/home/workdir', '/home/workdir/MT4_HUMAN.fasta', undef, 1, 'MT4_HUMAN', undef, 0, '/usr/bin/predictprotein', 1, ...) called at /usr/share/perl5/RG/Snap2/Run.pm line 14
    RG::Snap2::Run::all('/home/workdir/MT4_HUMAN.allmuts', '/home/workdir', '/usr/bin/sift_for_submitting_fasta_seq.csh', '/home/snap_db/uniref90.fasta', '/home/snap_db/uniprot_sprot.fasta', '/usr/bin/blastpgp', undef, 1, 'MT4_HUMAN', ...) called at /usr/share/perl5/RG/Snap2/Snap2.pm line 223
    RG::Snap2::Snap2::run('HASH(0x17bbed8)', 1.0.10) called at /usr/bin/snap2 line 117
Killed
*** ERROR blastpgp_to_saf.pl : *** ERROR blastp_to_saf: blast file format not recognized
Died at /usr/share/librg-utils-perl//blastpgp_to_saf.pl line 76.
make: *** [query.safBlastPsi80] Error 255
make --no-builtin-rules INFILE=query.in -C /tmp/MuvvjepQq6 JOBID=query -j 1 BLASTCORES=1 LIBRGUTILS=/usr/share/librg-utils-perl/ PPROOT=/usr/share/predictprotein/ PROFNUMRESMIN=17 PROFROOT=/usr/share/profphd/prof/ BIGBLASTDB=/home/snap_db/uniref100.fasta BIG80BLASTDB=/home/snap_db/uniref90.fasta PFAM2DB=/mnt/project/rost_db/data/pfam/Pfam_ls PFAM3DB=/mnt/project/rost_db/data/pfam/Pfam-A.hmm PROSITEDAT=/home/snap_db/uniprot_sprot.dat PSICEXE=/usr/share/rost-runpsic/runNewPSIC.pl SPKEYIDX=/mnt/project/rost_db/data/swissprot/keyindex_loctree.txt SWISSBLASTDB=/mnt/project/rost_db/data/blast/swiss --quiet -f /usr/share/predictprotein/MakefilePP.mk query.mdisorder query.profRdb query.prof1Rdb query.profbval query.blastPsiMat query.isis query.clustalngz query.psic failed: 512 at /usr/bin/predictprotein line 391.
Failed to execute '/usr/bin/predictprotein --seqfile=/home/workdir/MT4_HUMAN.fasta --target=query.blastPsiMat --target=query.psic --target=query.profRdb --target=query.prof1Rdb --target=query.profbval --target=query.isis --target=query.mdisorder --target=query.clustalngz --blast-processors=1 --output-dir=/home/workdir': 25 at /usr/share/perl5/RG/Snap2/Run.pm line 114
    RG::Snap2::Run::predictprotein('/home/workdir', '/home/workdir/MT4_HUMAN.fasta', undef, 1, 'MT4_HUMAN', undef, 0, '/usr/bin/predictprotein', 1, ...) called at /usr/share/perl5/RG/Snap2/Run.pm line 14
    RG::Snap2::Run::all('/home/workdir/MT4_HUMAN.allmuts', '/home/workdir', '/usr/bin/sift_for_submitting_fasta_seq.csh', '/home/snap_db/uniref90.fasta', '/home/snap_db/uniprot_sprot.fasta', '/usr/bin/blastpgp', undef, 1, 'MT4_HUMAN', ...) called at /usr/share/perl5/RG/Snap2/Snap2.pm line 223
    RG::Snap2::Snap2::run('HASH(0x17bbed8)', 1.0.10) called at /usr/bin/snap2 line 117

where the predict protein config contains

......
# bigblastdb: Path to comprehensive blast database
# bigblastdb=/mnt/project/rost_db/data/blast/big
bigblastdb=/home/snap_db/uniref100.fasta

# big80blastdb: Path to comprehensive blast database at 80% sequence identity redundancy level
# big80blastdb=/mnt/project/rost_db/data/blast/big_80
big80blastdb=/home/snap_db/uniref90.fasta

# path to profphd
prof=/usr/share/profphd/prof/

# prof numresMin, default: 17
profnumresmin=17

# maximum length of input AA sequence, default: 6000
numresmax=6000

# prositedat: Path to `prosite.dat' file, see L<https://rostlab.org/owiki/index.php/Packages#Resource_definitions>
# prositedat=/mnt/project/rost_db/data/prosite/prosite.dat
prositedat=/home/snap_db/uniprot_sprot.dat

# prositeconvdat: Path to `prosite_convert.dat' file, see L<https://rostlab.org/owiki/index.php/Packages#Resource_definitions>
# prositeconvdat=/mnt/project/rost_db/data/prosite/prosite_convert.dat
prositeconvdat=

# swissblastdb: Path to SwissProt blast database
swissblastdb=/mnt/project/rost_db/data/blast/swiss

# psicexe: psic wrapper executable
psicexe=/usr/share/rost-runpsic/runNewPSIC.pl

# pfam2 db
pfam2db=/mnt/project/rost_db/data/pfam/Pfam_ls

# pfam3 db
pfam3db=/mnt/project/rost_db/data/pfam/Pfam-A.hmm

# Swiss-Prot key 'index' (e.g.) for loctree
spkeyidx=/mnt/project/rost_db/data/swissprot/keyindex_loctree.txt

# default_targets: targets to make if none is given on the command line (separate targets with space)
default_targets=all

EDIT 20.1.16 @hechtm can you have a short look an the files above and propose a method how to get the stuff running on my local machine? There is not tutorial how to install predictportein locally. I guess because it is too labor intensive to do it manually. Of course I found the VMs with preinstalled predictprotein, but in my case I don't really consider them as a solution to my problem. Any ideas

juanmirocks commented 8 years ago

Thanks @seitza

Will look deeper into this this week.

juanmirocks commented 8 years ago

@seitza Hey, just checking all the documentation now. Big sorry for my delay.

Do you have any updates on the tool status? Does it run under normal conditions/parameters?

I've been cleaning a bit the README. Overall you guys have made a GREAT job in documenting everything; it's very clear. Some long detailed information I've moved it to the wiki.

I'm trying now to reproduce everything myself. I've added a few small TODOs in the README. Could you please check? The biggest thing that I'm missing is a clear example of how to run the cli tool. Please write an example and commit possibly necessary sample files in the repo.

I'm fully reachable these days to help resolving these things together.

juanmirocks commented 8 years ago

@seitza @leidigl should we merge branch feature/vagrant into develop ?

On the same topic, it would be required to add the Vagrantfile to the develop branch itself.

leidigl commented 8 years ago

@jmcejuela It is not necessary to to merge feature/vagrant into develop as feature/vagrant does not include any new data. At the beginning we planned to share the Vagrant file and the .vagrant folder. However this is not possible as different settings for different machines are necessary e.g. the path to the local databases in the Vagrant file. We will delete the branch at the end of this project.

juanmirocks commented 8 years ago

Thanks for the info.

Nonetheless please send me ur file so that I can take a look. Typically vagrantfiles are indeed committable.

U can just drag ur local file to this issue comment and it will get uploaded On Fri, 15 Jan 2016 at 18:43, Linda Leidig notifications@github.com wrote:

@jmcejuela https://github.com/jmcejuela It is not necessary to to merge feature/vagrant into develop as feature/vagrant does not include any new data. At the beginning we planned to share the Vagrant file and the .vagrant folder. However this is not possible as different settings for different machines are necessary e.g. the path to the local databases in the Vagrant file. We will delete the branch at the end of this project.

— Reply to this email directly or view it on GitHub https://github.com/Rostlab/SNAP2/issues/4#issuecomment-172029420.

seitza commented 8 years ago

Hi @jmcejuela here's the Vagrantfile, I use. Please note, that there are some absolute paths, which require to be changed, before it can be used on another machine. Vagrantfile.txt

juanmirocks commented 8 years ago

@seitza thanks André. Concerning this specific runtime issue, does it still happen?

seitza commented 8 years ago

@jmcejuela the runtime issue is not solved yet. I guess, that I just can not configure the databases correctly, because they either are not provided anymore or the updated versions of tools to prepare certain databases return another output than few years ago. I tried it several times, but gave up around christmas.

juanmirocks commented 8 years ago

@seitza thanks for the info.

@GrimSmiler could help on this? They may need the same databases (formats) you use in ConSurf.

seitza commented 8 years ago

I checked the docu of ConSurf and only found references to swissprot and uniprot.

In the config file of SNAP2 there is the following section:

[data]
# swiss_dat=path - location of UniProt/Swiss-Prot dat file
swiss_dat=
# db_swiss=path - path to ID index of Swiss-Prot dat file (generated by /usr/share/librg-utils-perl/dbSwiss.pl)
db_swiss=
# PHAT substitution matrix
phat_matrix=/usr/share/snap2/phat.txt

[blast]
# big80=path - path to redundancy reduced database (UniProtKB 80 or equivalent)
big80=
# swiss=path - path to SwissProt database
swiss=

My problem is, that I cannot find the respective databases or am not sure, which is which, and how to generate the swiss_dat and db_swiss files.

juanmirocks commented 8 years ago

@GrimSmiler successfully installed the DBs, but he still needs to write the documentation for how to get those.

Cross link: https://github.com/Rostlab/ConSurf/issues/9

juanmirocks commented 8 years ago

Status: unresolved

mbelmadani commented 8 years ago

I'm getting a very similar (same?) runtime error as the one reported above. This happens either when I follow the wiki's instructions, and I've even tried to copy the databases from a VM to a local repository, repointing to them, but I'm still getting failures on the blast database format.


mbelmadani@pavdesk-27:~/development/snap2$ snap2 --seq AAAAAAAAAAAAAAAAA --cmdmuts A10S -o ~/test
Working directory: /tmp/lBzgEa74ee
Job name: test

Running external programs..
*** ERROR blastpgp_to_saf.pl : *** ERROR blastp_to_saf: blast file format not recognized
Died at /usr/share/librg-utils-perl//blastpgp_to_saf.pl line 76.
make: *** [query.safBlastPsi80] Error 255
make --no-builtin-rules INFILE=query.in -C /tmp/gqmAMdwEjg JOBID=query -j 1 BLASTCORES=1 LIBRGUTILS=/usr/share/librg-utils-perl/ PPROOT=/usr/share/predictprotein/ PROFNUMRESMIN=17 PROFROOT=/usr/share/profphd/prof/ BIGBLASTDB=/mnt/project/rost_db/data/blast/big BIG80BLASTDB=/mnt/project/rost_db/data/blast/big_80 PFAM2DB=/mnt/project/rost_db/data/pfam/Pfam_ls PFAM3DB=/mnt/project/rost_db/data/pfam/Pfam-A.hmm PROSITEDAT=/mnt/project/rost_db/data/prosite/prosite.dat PROSITECONVDAT=/mnt/project/rost_db/data/prosite/prosite_convert.dat PSICEXE=/usr/share/rost-runpsic/runNewPSIC.pl SPKEYIDX=/mnt/project/rost_db/data/swissprot/keyindex_loctree.txt SWISSBLASTDB=/mnt/project/rost_db/data/blast/swiss --quiet -f /usr/share/predictprotein/MakefilePP.mk query.mdisorder query.clustalngz query.prof1Rdb query.isis query.psic query.profbval query.profRdb query.blastPsiMat failed: 512 at /usr/bin/predictprotein line 391.
Failed to execute '/usr/bin/predictprotein --seqfile=/tmp/lBzgEa74ee/test.fasta --target=query.blastPsiMat --target=query.psic --target=query.profRdb --target=query.prof1Rdb --target=query.profbval --target=query.isis --target=query.mdisorder --target=query.clustalngz --blast-processors=1 --output-dir=/tmp/lBzgEa74ee': 25 at /usr/share/perl5/RG/Snap2/Run.pm line 114.
    RG::Snap2::Run::predictprotein('/tmp/lBzgEa74ee', '/tmp/lBzgEa74ee/test.fasta', undef, 1, 'test', undef, 0, '/usr/bin/predictprotein', 0, ...) called at /usr/share/perl5/RG/Snap2/Run.pm line 14
    RG::Snap2::Run::all('/tmp/lBzgEa74ee/test.muts', '/tmp/lBzgEa74ee', '/usr/bin/sift_for_submitting_fasta_seq.csh', '/mnt/rostlab-data/big/big_80', '/mnt/rostlab-data/swissprot/uniprot_sprot', '/usr/bin/blastpgp', undef, 1, 'test', ...) called at /usr/share/perl5/RG/Snap2/Snap2.pm line 223
    RG::Snap2::Snap2::run('HASH(0x2303f60)', 1.0.10) called at /usr/bin/snap2 line 117

Curiously, I reran the same command immediately and got a different error.

mbelmadani@pavdesk-27:~/development/snap2$ snap2 --seq AAAAAAAAAAAAAAAAA --cmdmuts A10S -o ~/test
Working directory: /tmp/i4lDZ5vM5x
Job name: test

Running external programs..
Incorrect blast file: /tmp/yrCqMGio9J/query.blast at /usr/share/rost-runpsic/runNewPSIC.pl line 384.
    main::checkBlast('', 0, '/mnt/project/rost_db/data/blast/big', 'query.fasta', '/tmp/yrCqMGio9J', 'query.blast', 'F', 1) called at /usr/share/rost-runpsic/runNewPSIC.pl line 171
make: *** [query.clustalngz] Error 255
make --no-builtin-rules INFILE=query.in -C /tmp/9ecL7f3R1X JOBID=query -j 1 BLASTCORES=1 LIBRGUTILS=/usr/share/librg-utils-perl/ PPROOT=/usr/share/predictprotein/ PROFNUMRESMIN=17 PROFROOT=/usr/share/profphd/prof/ BIGBLASTDB=/mnt/project/rost_db/data/blast/big BIG80BLASTDB=/mnt/project/rost_db/data/blast/big_80 PFAM2DB=/mnt/project/rost_db/data/pfam/Pfam_ls PFAM3DB=/mnt/project/rost_db/data/pfam/Pfam-A.hmm PROSITEDAT=/mnt/project/rost_db/data/prosite/prosite.dat PROSITECONVDAT=/mnt/project/rost_db/data/prosite/prosite_convert.dat PSICEXE=/usr/share/rost-runpsic/runNewPSIC.pl SPKEYIDX=/mnt/project/rost_db/data/swissprot/keyindex_loctree.txt SWISSBLASTDB=/mnt/project/rost_db/data/blast/swiss --quiet -f /usr/share/predictprotein/MakefilePP.mk query.clustalngz query.isis query.profRdb query.psic query.mdisorder query.profbval query.prof1Rdb query.blastPsiMat failed: 512 at /usr/bin/predictprotein line 391.
Failed to execute '/usr/bin/predictprotein --seqfile=/tmp/i4lDZ5vM5x/test.fasta --target=query.blastPsiMat --target=query.psic --target=query.profRdb --target=query.prof1Rdb --target=query.profbval --target=query.isis --target=query.mdisorder --target=query.clustalngz --blast-processors=1 --output-dir=/tmp/i4lDZ5vM5x': 25 at /usr/share/perl5/RG/Snap2/Run.pm line 114.
    RG::Snap2::Run::predictprotein('/tmp/i4lDZ5vM5x', '/tmp/i4lDZ5vM5x/test.fasta', undef, 1, 'test', undef, 0, '/usr/bin/predictprotein', 0, ...) called at /usr/share/perl5/RG/Snap2/Run.pm line 14
    RG::Snap2::Run::all('/tmp/i4lDZ5vM5x/test.muts', '/tmp/i4lDZ5vM5x', '/usr/bin/sift_for_submitting_fasta_seq.csh', '/mnt/rostlab-data/big/big_80', '/mnt/rostlab-data/swissprot/uniprot_sprot', '/usr/bin/blastpgp', undef, 1, 'test', ...) called at /usr/share/perl5/RG/Snap2/Snap2.pm line 223
    RG::Snap2::Snap2::run('HASH(0x26dfd40)', 1.0.10) called at /usr/bin/snap2 line 117

It seems that if I repeat the command, I randomly get the two different errors. Any suggestions to resolve this?

juanmirocks commented 8 years ago

Thank you @mbelmadani -- May I ask what you use SNAP2 for?

At the moment the tool is not actively maintained (I'm not the author). Your code improvements are very much welcome.

The user @dmitry-n may contribute some fixes in the future

mbelmadani commented 8 years ago

I was interested in looking up the effect of specific point mutations and comparing them with other variant effect prediction scores. I'm aware of snap2web which is nice for a few mutations, but I wanted to do it programmatically.

I ended up using the Biolinux VMWare image. This worked out fine for the time being.

If I have some code improvements, I'll fork and submit a pull requests!

juanmirocks commented 8 years ago

Thanks @mbelmadani - all the best with your project!

ghost commented 7 years ago

Hey everyone,

I was wondering if there was a solution to the blast file format not recognized error. I have followed the steps that are listed here up to "HOWTO workaround the "runtime" error due to probable configuration errors". I can't seem to get that step to work and was wondering if someone could help me. Here is the error that comes up when I try to run the MT4_Human example: *** ERROR blastpgp_to_saf.pl : *** ERROR blastp_to_saf: blast file format not recognized Died at /usr/share/librg-utils-perl//blastpgp_to_saf.pl line 76. make: *** [query.safBlastPsi80] Error 255 make --no-builtin-rules INFILE=query.in -C /tmp/Wis7N3AEN4 JOBID=query -j 1 BLASTCORES=1 LIBRGUTILS=/usr/share/librg-utils-perl/ PPROOT=/usr/share/predictprotein/ PROFNUMRESMIN=8 PROFROOT=/usr/share/profphd/prof/ BIGBLASTDB=/mnt/project/rost_db/data/blast/big BIG80BLASTDB=/mnt/project/rost_db/data/blast/big_80 PFAM2DB=/mnt/project/rost_db/data/pfam/Pfam_ls PFAM3DB=/mnt/project/rost_db/data/pfam/Pfam-A.hmm PROSITEDAT=/mnt/project/rost_db/data/prosite/prosite.dat PROSITECONVDAT=/mnt/project/rost_db/data/prosite/prosite_convert.dat PSICEXE=/usr/share/rost-runpsic/runNewPSIC.pl SPKEYIDX=/mnt/project/rost_db/data/swissprot/keyindex_loctree.txt SWISSBLASTDB=/mnt/project/rost_db/data/blast/swiss --quiet -f /usr/share/predictprotein/MakefilePP.mk query.mdisorder query.profRdb query.prof1Rdb query.profbval query.blastPsiMat query.isis query.clustalngz query.psic failed: 512 at /usr/bin/predictprotein line 391. Failed to execute '/usr/bin/predictprotein --seqfile=/tmp/K7l6mLm_TT/MT4_HUMAN.fasta --target=query.blastPsiMat --target=query.psic --target=query.profRdb --target=query.prof1Rdb --target=query.profbval --target=query.isis --target=query.mdisorder --target=query.clustalngz --profnumresmin=8 --blast-processors=1 --output-dir=/tmp/K7l6mLm_TT': 25 at /usr/share/perl5/RG/Snap2/Run.pm line 115 RG::Snap2::Run::predictprotein('/tmp/K7l6mLm_TT', '/tmp/K7l6mLm_TT/MT4_HUMAN.fasta', undef, 1, 'MT4_HUMAN', undef, 0, '/usr/bin/predictprotein', 0, ...) called at /usr/share/perl5/RG/Snap2/Run.pm line 14 RG::Snap2::Run::all('/tmp/K7l6mLm_TT/MT4_HUMAN.allmuts', '/tmp/K7l6mLm_TT', '/usr/bin/sift_for_submitting_fasta_seq.csh', '/root/uniref90.fasta', '/root/uniprot_sprot.fasta', '/usr/bin/blastpgp', undef, 1, 'MT4_HUMAN', ...) called at /usr/share/perl5/RG/Snap2/Snap2.pm line 223 RG::Snap2::Snap2::run('HASH(0x2280768)', 1.0.10) called at /usr/bin/snap2 line 117

Any help would be appreciated. Thank you.

juanmirocks commented 7 years ago

I'm very sorry but cannot help with this. Please if you find a solution even if partial that would be really helpful. On Fri 1. Sep 2017 at 18:50, philcharron17 notifications@github.com wrote:

Hey everyone,

I was wondering if there was a solution to the blast file format not recognized error. I have followed the steps that are listed here https://github.com/Rostlab/SNAP2 up to "HOWTO workaround the "runtime" error due to probable configuration errors". I can't seem to get that step to work and was wondering if someone could help me. Here is the error that comes up when I try to run the MT4_Human example:

ERROR blastpgp_to_saf.pl : ERROR blastp_to_saf: blast file format not recognized Died at /usr/share/librg-utils-perl//blastpgp_to_saf.pl line 76. make: *** [query.safBlastPsi80] Error 255

make --no-builtin-rules INFILE=query.in -C /tmp/Wis7N3AEN4 JOBID=query -j 1 BLASTCORES=1 LIBRGUTILS=/usr/share/librg-utils-perl/ PPROOT=/usr/share/predictprotein/ PROFNUMRESMIN=8 PROFROOT=/usr/share/profphd/prof/ BIGBLASTDB=/mnt/project/rost_db/data/blast/big BIG80BLASTDB=/mnt/project/rost_db/data/blast/big_80 PFAM2DB=/mnt/project/rost_db/data/pfam/Pfam_ls PFAM3DB=/mnt/project/rost_db/data/pfam/Pfam-A.hmm PROSITEDAT=/mnt/project/rost_db/data/prosite/prosite.dat PROSITECONVDAT=/mnt/project/rost_db/data/prosite/prosite_convert.dat PSICEXE=/usr/share/rost-runpsic/runNewPSIC.pl SPKEYIDX=/mnt/project/rost_db/data/swissprot/keyindex_loctree.txt SWISSBLASTDB=/mnt/project/rost_db/data/blast/swiss --quiet -f /usr/share/predictprotein/MakefilePP.mk query.mdisorder query.profRdb query.prof1Rdb query.profbval query.blastPsiMat query.isis query.clustalngz query.psic failed: 512 at /usr/bin/predictprotein line 391. Failed to execute '/usr/bin/predictprotein --seqfile=/tmp/K7l6mLm_TT/MT4_HUMAN.fasta --target=query.blastPsiMat --target=query.psic --target=query.profRdb --target=query.prof1Rdb --target=query.profbval --target=query.isis --target=query.mdisorder --target=query.clustalngz --profnumresmin=8 --blast-processors=1 --output-dir=/tmp/K7l6mLm_TT': 25 at /usr/share/perl5/RG/Snap2/Run.pm line 115 RG::Snap2::Run::predictprotein('/tmp/K7l6mLm_TT', '/tmp/K7l6mLm_TT/MT4_HUMAN.fasta', undef, 1, 'MT4_HUMAN', undef, 0, '/usr/bin/predictprotein', 0, ...) called at /usr/share/perl5/RG/Snap2/Run.pm line 14 RG::Snap2::Run::all('/tmp/K7l6mLm_TT/MT4_HUMAN.allmuts', '/tmp/K7l6mLm_TT', '/usr/bin/sift_for_submitting_fasta_seq.csh', '/root/uniref90.fasta', '/root/uniprot_sprot.fasta', '/usr/bin/blastpgp', undef, 1, 'MT4_HUMAN', ...) called at /usr/share/perl5/RG/Snap2/Snap2.pm line 223 RG::Snap2::Snap2::run('HASH(0x2280768)', 1.0.10) called at /usr/bin/snap2 line 117

Any help would be appreciated. Thank you.

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