workbench environment analysis----directly saved analysis after

* Support: https://ubuntu.com/advantage

102 packages can be updated.
53 updates are security updates.

New release '18.04.2 LTS' available.
Run 'do-release-upgrade' to upgrade to it.

Last login: Fri Aug 30 22:35:24 2019 from 10.64.0.191
dangmingai@PROTEIN:~$ cd .mnt
-bash: cd: .mnt: No such file or directory
dangmingai@PROTEIN:~$ cd /mnt/data
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon RaptorXCommon
FALCONCommon SPARKS-X
HHCommon lost+found
I-TASSER original_databases
ImageCommon softwares
dangmingai@PROTEIN:/mnt/data$ cd /home/dangmingai
dangmingai@PROTEIN:~$ ls
1.txt psitmp31089400a0800.mtx
casp13_targets result
data softwares
dangmingai@PROTEIN:~$ cd /home/dangmingai
dangmingai@PROTEIN:~$ ls
1.txt psitmp31089400a0800.mtx
casp13_targets result
data softwares
dangmingai@PROTEIN:~$ cd softwares/
dangmingai@PROTEIN:~/softwares$ ls
softwares
dangmingai@PROTEIN:~/softwares$ cd s
-bash: cd: s: No such file or directory
dangmingai@PROTEIN:~/softwares$ cd softwares/
dangmingai@PROTEIN:~/softwares/softwares$ lsCNFsearch1.66_release
PDB_Tool
TGT_Package
anaconda3
blast-2.2.26
cd-hit-v4.6.8-2017-0621
confold-v2.0
csblast-2.2.3_linux64
dDFIRE1.1-bin
dssp-3.0.0
fasta-36.3.8g
freecontact-1.0.21
gcc-7.1.0
glibc-2.23
hhomp-1.0-x86_64
hhsuite-2.0.16-linux-x86_64
hhsuite-3.0-beta.3-Linux
hhsuite-3.2.0-SSE2-Linux
hmmer-3.2.1
metapsicov-1.0.4
metapsicov-2.0.2
packages
psicov-2.4.0
psipred-4.0.1
rosetta_bin_linux_2017.08.59291_bundle
dangmingai@PROTEIN:~/softwares/softwares$ cd psipred-4.0.1/
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+ VERSION example src
LICENSE bin runpsipred
README data runpsipred_single
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ pwd
/home/dangmingai/softwares/softwares/psipred-4.0.1
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ cp example/example.fasta ./
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+ bin runpsipred
LICENSE data runpsipred_single
README example src
VERSION example.fasta
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred_single example.fast
a
#!/bin/tcsh
Generating mtx file from sequence example.fasta ...
Predicting secondary structure based on single sequence ...
Pass1 ...
Pass2 ...
Cleaning up ...
Final output files: example.ss2 example.horiz
Finished.
#!/bin/tcsh
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+ data example.ss2
LICENSE example runpsipred
README example.fasta runpsipred_single
VERSION example.horiz src
bin example.ss
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim example.ss
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim example.horiz
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+ data example.ss2
LICENSE example runpsipred
README example.fasta runpsipred_single
VERSION example.horiz src
bin example.ss
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim runpsipred
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred example.fasta
set: Variable name must begin with a letter.
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim runpsipred
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred example.fasta
set: Variable name must begin with a letter.
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim runpsipred
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred example.fasta
Running PSI-BLAST with sequence example.fasta ...
Predicting secondary structure...
Pass1 ...
Pass2 ...
Cleaning up ...
Final output files: example.ss2 example.horiz
Finished.
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ks
ks: command not found
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+
LICENSE
README
VERSION
bin
data
example
example.fasta
example.horiz
example.ss
example.ss2
runpsipred
runpsipred_single
src
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ cd /mnt/data
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon
FALCONCommon
HHCommon
I-TASSER
ImageCommon
RaptorXCommon
SPARKS-X
lost+found
original_databases
softwares
dangmingai@PROTEIN:/mnt/data$ cd softwares/
dangmingai@PROTEIN:/mnt/data/softwares$ ls
CCMpred-0.3.2
CNFsearch1.66_release
I-TASSER5.1
MRFsearch0.90_release
PDB_Tool
Predict_Property
SPARKS-X
TGT_Package
anaconda2
anaconda3
bin
blast-2.2.26
cd-hit-v4.6.8-2017-0621
confold-v2.0
csblast-2.2.3_linux64
dDFIRE1.1-bin
dssp-2.2.1
dssp-3.0.0
fasta-36.3.8g
freecontact-1.0.21
gcc-7.1.0
glibc-2.23
hhomp-1.0-x86_64
hhsuite-2.0.16-linux-x86_64
hhsuite-3.0-beta.3-Linux
hhsuite-3.2.0-SSE2-Linux
hmmer-3.1b2-linux-intel-x86_64
hmmer-3.2.1
metapsicov-1.0.4
metapsicov-2.0.2
ncbi-blast-2.6.0+
ncbi-blast-2.9.0+
packages
psicov-2.1.0
psicov-2.4.0
psipred-4.0.1
psipred-4.0.2
rosetta3.8
rosetta3.9
rosetta_bin_linux_2017.08.59291_bundle
rosetta_bin_linux_2018.09.60072_bundle
dangmingai@PROTEIN:/mnt/data/softwares$ cd psipred
-4.0.2
dangmingai@PROTEIN:/mnt/data/softwares/psipred-4.0.2$ ls
BLAST+
LICENSE
README
VERSION
bin
data
example
runpsipred
runpsipred_single
src
dangmingai@PROTEIN:/mnt/data/softwares/psipred-4.0.2$ pwd
dangmingai@PROTEIN:/mnt/data/softwares/psipred-4.0.2$ cd OTEIN:/mnt/data/softwares/psiprdangmingai@PROTEIN:~$ ls
1.txt psitmp31089400a0800.mtx
casp13_targets result
data softwares
dangmingai@PROTEIN:~$ cd /mnt/data
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon RaptorXCommon
FALCONCommon SPARKS-X
HHCommon lost+found
I-TASSER original_databases
ImageCommon softwares
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon RaptorXCommon
FALCONCommon SPARKS-X
HHCommon lost+found
I-TASSER original_databases
ImageCommon softwares
dangmingai@PROTEIN:/mnt/data$ cd FALCONCommon/
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP SCOP_series
DSSP_series TrainingTestData
FALCON_databases hmmer
FALCON_softwares uniprot
PDB_series
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd ..
dangmingai@PROTEIN:/mnt/data$ cd original_databases/
dangmingai@PROTEIN:/mnt/data/original_databases$ ls
CASP SPARKS_series scripts
CATH_series blast sifts
PDB_series cmbi_series uniprot
Pfam hhsuite_series
SCOP_series image_series
dangmingai@PROTEIN:/mnt/data/original_databases$ cd CATH_series/
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series$ ls
README
backup
cath-download.README
known-version-differences.README
releases
supplementary-materials
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series$ cd backup
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series/backup$ ls
v3_5_0 v4_0_0
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series/backup$ cd v_3_5
-bash: cd: v_3_5: No such file or directory
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series/backup$ cd v_3_5_0
-bash: cd: v_3_5_0: No such file or directory
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series/backup$ ls
v3_5_0 v4_0_0
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series/backup$ cd v3_5_0
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series/backup/v3_5_0$ ls
CathChainList.v3.5.0
CathDomainDescriptionFile.v3.5.0
CathDomainList.S100.v3.5.0
CathDomainList.S35.v3.5.0
CathDomainList.S60.v3.5.0
CathDomainList.S95.v3.5.0
CathDomainList.v3.5.0
CathDomainPdb.S35.v3.5.0.tgz
CathDomainPdb.v3.5.0.tgz
CathDomainSeqs.ATOM.v3.5.0
CathDomainSeqs.COMBS.v3.5.0
CathDomainSeqs.S100.ATOM.v3.5.0
CathDomainSeqs.S100.COMBS.v3.5.0
CathDomainSeqs.S35.ATOM.v3.5.0
CathDomainSeqs.S35.COMBS.v3.5.0
CathDomainSeqs.S60.ATOM.v3.5.0
CathDomainSeqs.S60.COMBS.v3.5.0
CathDomainSeqs.S95.ATOM.v3.5.0
CathDomainSeqs.S95.COMBS.v3.5.0
CathDomall.seqreschopping.v3.5.0
CathDomall.v3.5.0
CathNames.v3.5.0
CathSuperfamilyList.v3.5.0
CathUnclassifiedList.v3.5.0
Class1-4_v3_5_0.s35.cathedral.library
Class1-4_v3_5_0.s60.cathedral.library
Class1-4_v3_5_0.s95.cathedral.library
README.CDDF_FORMAT_2.0
README.CDF_FORMAT_2.0
README.CLF_FORMAT_2.0
README.CNF_FORMAT_2.0
README.file_formats
SequenceBySuperfamily
blast_index_files
hmmer2.lib
hmmer3
hmmer3.lib
supplementary
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series/backup/v3_5_0$ cd ..
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series/backup$ ls
v3_5_0 v4_0_0
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series/backup$ cd ..
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series$ ls
README
backup
cath-download.README
known-version-differences.README
releases
supplementary-materials
dangmingai@PROTEIN:/mnt/data/original_databases/CATH_series$ cd ..
dangmingai@PROTEIN:/mnt/data/original_databases$ ls
CASP SPARKS_series scripts
CATH_series blast sifts
PDB_series cmbi_series uniprot
Pfam hhsuite_series
SCOP_series image_series
dangmingai@PROTEIN:/mnt/data/original_databases$ cd ..
dangmingai@PROTEIN:/mnt/data$ ;s
-bash: syntax error near unexpected token `;'
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon RaptorXCommon
FALCONCommon SPARKS-X
HHCommon lost+found
I-TASSER original_databases
ImageCommon softwares
dangmingai@PROTEIN:/mnt/data$ cd lost+found/dangmingai@PROTEIN:/mnt/data/lost+found$ ls
ls: reading directory '.': Permission denied
dangmingai@PROTEIN:/mnt/data/lost+found$ ls
ls: reading directory '.': Permission denied
dangmingai@PROTEIN:/mnt/data/lost+found$ cd softwares
-bash: cd: softwares: Permission denied
dangmingai@PROTEIN:/mnt/data/lost+found$ cd ..
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon RaptorXCommon
FALCONCommon SPARKS-X
HHCommon lost+found
I-TASSER original_databases
ImageCommon softwares
dangmingai@PROTEIN:/mnt/data$ cd softwares/
dangmingai@PROTEIN:/mnt/data/softwares$ ls
CCMpred-0.3.2
CNFsearch1.66_release
I-TASSER5.1
MRFsearch0.90_release
PDB_Tool
Predict_Property
SPARKS-X
TGT_Package
anaconda2
anaconda3
bin
blast-2.2.26
cd-hit-v4.6.8-2017-0621
confold-v2.0
csblast-2.2.3_linux64
dDFIRE1.1-bin
dssp-2.2.1
dssp-3.0.0
fasta-36.3.8g
freecontact-1.0.21
gcc-7.1.0
glibc-2.23
hhomp-1.0-x86_64
hhsuite-2.0.16-linux-x86_64
hhsuite-3.0-beta.3-Linux
hhsuite-3.2.0-SSE2-Linux
hmmer-3.1b2-linux-intel-x86_64
hmmer-3.2.1
metapsicov-1.0.4
metapsicov-2.0.2
ncbi-blast-2.6.0+
ncbi-blast-2.9.0+
packages
psicov-2.1.0
psicov-2.4.0
psipred-4.0.1
psipred-4.0.2
rosetta3.8
rosetta3.9
>1ctfA
rosetta_bin_linux_2017.08.59291_bundle
rosetta_bin_linux_2018.09.60072_bundle
dangmingai@PROTEIN:/mnt/data/softwares$ cd
dangmingai@PROTEIN:~$ pwd
/home/dangmingai
dangmingai@PROTEIN:~$ ls
1.txt psitmp31089400a0800.mtx
casp13_targets result
data softwares
dangmingai@PROTEIN:~$ mkdir result
mkdir: cannot create directory 'result': File exists
dangmingai@PROTEIN:~$ mkdir results
dangmingai@PROTEIN:~$ cd results
dangmingai@PROTEIN:~/results$ ls
dangmingai@PROTEIN:~/results$ cp /mnt/data/RaptorXCommon/
CAL_EPAD/ README
CAL_TGT/ relnotes.txt
CAL_TPL/ TemplateLists/
Download/ TGT_BC100/
NR_new/ TPL_BC100/
pdb_BC100/
dangmingai@PROTEIN:~/results$ cp /mnt/data/RaptorXCommon/TGT_BC100/1ctfA.tgt .
dangmingai@PROTEIN:~/results$ ls
1ctfA.tgt
dangmingai@PROTEIN:~/results$ vim 1ctfA.tgt dangmingai@PROTEIN:~/results$ vim 1ctfA.fasta
dangmingai@PROTEIN:~/results$ rm 1ctfA.tgt
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hh
hhomp-1.0-x86_64/ hhsuite-3.0-beta.3-Linux/
hhsuite-2.0.16-linux-x86_64/ hhsuite-3.2.0-SSE2-Linux/
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/
cstranslate ffindex_modify hhfilter
ffindex_apply ffindex_unpack hhmake
ffindex_build hhalign hhsearch
ffindex_from_fasta hhblits
ffindex_get hhconsensus
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits

HHblits version 2.0.15 (June 2012):
HMM-HMM-based lightning-fast iterative sequence search
HHblits is a sensitive, general-purpose, iterative sequence search tool that represents
both query and database sequences by HMMs. You can search HHblits databases starting
with a single query sequence, a multiple sequence alignment (MSA), or an HMM. HHblits
prints out a ranked list of database HMMs/MSAs and can also generate an MSA by merging
the significant database HMMs/MSAs onto the query MSA.

Remmert M., Biegert A., Hauser A., and Soding J.
HHblits: Lightning-fast iterative protein sequence searching by HMM-HMM alignment.
Nat. Methods 9:173-175 (2011)
(C) Johannes Soeding, Michael Remmert, Andreas Biegert, Andreas Hauser

Usage: hhblits -i query [options]
-i <file> input/query: single sequence or multiple sequence alignment (MSA)
in a3m, a2m, or FASTA format, or HMM in hhm format

Options:
-d <name> database name (e.g. uniprot20_29Feb2012) (default=)
-n [1,8] number of iterations (default=2)
-e [0,1] E-value cutoff for inclusion in result alignment (def=0.001)

Input alignment format:
-M a2m use A2M/A3M (default): upper case = Match; lower case = Insert;
' -' = Delete; '.' = gaps aligned to inserts (may be omitted)
-M first use FASTA: columns with residue in 1st sequence are match states
-M [0,100] use FASTA: columns with fewer than X% gaps are match states

Output options:
-o <file> write results in standard format to file (default=<infile.hhr>)
-oa3m <file> write result MSA with significant matches in a3m format
Analogous for -opsi and -ohhm
-oalis <name> write MSAs in A3M format after each iteration
Filter options applied to query MSA, database MSAs, and result MSA
-all show all sequences in result MSA; do not filter result MSA
-id [0,100] maximum pairwise sequence identity (def=90)
-diff [0,inf[ filter MSAs by selecting most diverse set of sequences, keeping
at least this many seqs in each MSA block of length 50 (def=1000)
-cov [0,100] minimum coverage with master sequence (%) (def=0)
-qid [0,100] minimum sequence identity with master sequence (%) (def=0)
-qsc [0,100] minimum score per column with master sequence (default=-20.0)
-neff [1,inf] target diversity of multiple sequence alignment (default=off)

HMM-HMM alignment options:
-norealign do NOT realign displayed hits with MAC algorithm (def=realign)
-mact [0,1[ posterior probability threshold for MAC re-alignment (def=0.350)
Parameter controls alignment greediness: 0:global >0.1:local
-glob/-loc use global/local alignment mode for searching/ranking (def=local)
Other options:
-v <int> verbose mode: 0:no screen output 1:only warings 2: verbose (def=2)
-neffmax ]1,20] skip further search iterations when diversity Neff of query MSA
becomes larger than neffmax (default=10.0)
-cpu <int> number of CPUs to use (for shared memory SMPs) (default=2)

An extended list of options can be obtained by calling 'hhblits -help'

Example: hhblits -i query.fas -oa3m query.a3m -n 1

Error in hhblits: input file missing!
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m query.a3m -n 1

Usage: hhblits -i query [options]
-i <file> input/query: single sequence or multiple sequence alignment (MSA)
in a3m, a2m, or FASTA format, or HMM in hhm format

Options:
-d <name> database name (e.g. uniprot20_29Feb2012) (default=)
-n [1,8] number of iterations (default=1)
-e [0,1] E-value cutoff for inclusion in result alignment (def=0.001)

An extended list of options can be obtained by calling 'hhblits -help'

Example: hhblits -i query.fas -oa3m query.a3m -n 1

Error in hhblits: database missing (see -d)
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1

Usage: hhblits -i query [options]
-i <file> input/query: single sequence or multiple sequence alignment (MSA)
in a3m, a2m, or FASTA format, or HMM in hhm format

Options:
-d <name> database name (e.g. uniprot20_29Feb2012) (default=)
-n [1,8] number of iterations (default=1)
-e [0,1] E-value cutoff for inclusion in result alignment (def=0.001)

An extended list of options can be obtained by calling 'hhblits -help'

Example: hhblits -i query.fas -oa3m query.a3m -n 1

Error in hhblits: database missing (see -d)
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1 -d /mnt/data/
BLASTCommon/ I-TASSER/ softwares/
FALCONCommon/ lost+found/ SPARKS-X/
HHCommon/ original_databases/
ImageCommon/ RaptorXCommon/
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1 -d /mnt/data/HHCommon/
Search results will be written to 1ctfA.hhr

Error in hhblits: Could not open A3M database /mnt/data/HHCommon/_a3m_db, No such file or directory (needed to construct result MSA)
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1 -d /mnt/data/HHCommon/
hhomp/ HHsearch/ hhsuite_dbs/ uniclust/
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1 -d /mnt/data/HHCommon/hhsuite_dbs/
Search results will be written to 1ctfA.hhr

Error in hhblits: Could not open A3M database /mnt/data/HHCommon/hhsuite_dbs/_a3m_db, No such file or directory (needed to construct result MSA)
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1 -d /mnt/data/HHCommon/hhsuite_dbs/
pdb70_02Apr16/ pdb70_from_mmcif_190522/
pdb70_06Sep14/ uniprot20_2013_03/
pdb70_14Sep16/ uniprot20_2015_06/
pdb70_from_mmcif_180411/ uniprot20_2016_02/
pdb70_from_mmcif_180808/
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1 -d /mnt/data/HHCommon/hhsuite_dbs/uniprot20_2016_02/
md5sum uniprot20_a3m_db
uniprot20_2016_02_a3m_db uniprot20_a3m_db.index
uniprot20_2016_02_a3m_db.index uniprot20_a3m.ffdata
uniprot20_2016_02_a3m.ffdata uniprot20_a3m.ffindex
uniprot20_2016_02_a3m.ffindex uniprot20.cs219
uniprot20_2016_02.cs219 uniprot20_cs219.ffdata
uniprot20_2016_02_cs219.ffdata uniprot20_cs219.ffindex
uniprot20_2016_02_cs219.ffindex uniprot20.cs219.sizes
uniprot20_2016_02.cs219.sizes uniprot20_hhm_db
uniprot20_2016_02_hhm_db uniprot20_hhm_db.index
uniprot20_2016_02_hhm_db.index uniprot20_hhm.ffdata
uniprot20_2016_02_hhm.ffdata uniprot20_hhm.ffindex
uniprot20_2016_02_hhm.ffindex
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1 -d /mnt/data/HHCommon/hhsuite_dbs/uniprot20_2016_02/uniprot20
Search results will be written to 1ctfA.hhr
Reading in 8290068 column state sequences with a total of 1874100330 residues
^C
dangmingai@PROTEIN:~/results$ /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1 -d /mnt/data/HHCommon/hhsuite_dbs/uniprot20_2016_02/uniprot20 -cpu 16
Search results will be written to 1ctfA.hhr
Reading in 8290068 column state sequences with a total of 1874100330 residues

Iteration 1
Prefiltering database
...................................................................................
HMMs passed 1st prefilter (gapless profile-profile alignment) : 104506
HMMs passed 2nd prefilter (gapped profile-profile alignment) : 364
HMMs passed 2nd prefilter and not found in previous iterations : 364
Scoring 364 HMMs using HMM-HMM Viterbi alignment
..................
Realigning 348 HMMs using HMM-HMM Maximum Accuracy algorithm
...................................
Merging hits to query profile
164 sequences belonging to 164 database HMMs found with an E-value < 0.001
Number of effective sequences of resulting query HMM: Neff = 5.38

Query 1ctfA
Match_columns 74
No_of_seqs 1 out of 1
Neff 1.0
Searched_HMMs 364
Date Sat Aug 31 11:59:39 2019
Command /mnt/data/softwares/hhsuite-2.0.16-linux-x86_64/bin/hhblits -i 1ctfA.fasta -oa3m 1ctfA.a3m -n 1 -d /mnt/data/HHCommon/hhsuite_dbs/uniprot20_2016_02/uniprot20 -cpu 16

No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 tr|A0A077ZM27|A0A077ZM27_TRITR 99.9 1.6E-31 8.4E-37 241.1 0.0 73 1-73 34-106 (2867)
2 tr|A0A0G1BNT8|A0A0G1BNT8_9BACT 99.9 4E-28 2.3E-33 157.4 0.0 66 9-74 1-66 (66)
3 tr|M8A0K4|M8A0K4_TRIUA 50S rib 99.9 1.3E-27 9E-33 160.9 0.0 73 2-74 21-94 (94)
4 tr|M1VB33|M1VB33_CYAME Mitocho 99.9 1.5E-27 1E-32 178.3 0.0 73 2-74 144-217 (217)
5 tr|D3T4S6|D3T4S6_THEIA 50S rib 99.9 5.2E-27 4.3E-32 161.1 0.0 73 2-74 53-125 (125)
6 tr|A0A0F9J1B3|A0A0F9J1B3_9ZZZZ 99.8 4.7E-24 2.7E-29 156.8 0.0 73 2-74 99-171 (171)
7 tr|A6CUA4|A6CUA4_9BACI 50S rib 99.8 1.2E-23 5.4E-29 144.4 0.0 71 4-74 22-92 (92)
8 tr|A0A0D6R0N2|A0A0D6R0N2_ARACU 99.7 5.7E-22 3.6E-27 146.4 0.0 74 1-74 108-182 (182)
9 tr|B9WC05|B9WC05_CANDC Mitocho 99.7 4.7E-22 3.6E-27 143.9 0.0 73 2-74 102-175 (175)
10 tr|C2F9U6|C2F9U6_LACPA Ribosom 99.7 9.6E-22 4.6E-27 132.6 0.0 54 1-54 26-79 (80)
11 tr|F6RGQ1|F6RGQ1_CIOIN Unchara 99.7 3.4E-21 2.5E-26 140.8 0.0 73 2-74 110-184 (184)
12 tr|A0A0F7V782|A0A0F7V782_TOXGO 99.7 1E-20 5.7E-26 144.4 0.0 72 2-73 156-229 (230)
13 tr|A0A0D6ESC6|A0A0D6ESC6_SPOSA 99.6 1.4E-19 1E-24 133.1 0.0 73 2-74 117-191 (191)
14 tr|A0A0G4FBR6|A0A0G4FBR6_9ALVE 99.6 5.9E-19 3E-24 131.8 0.0 73 2-74 105-179 (179)
15 tr|K4BC31|K4BC31_SOLLC Unchara 99.6 5.2E-19 3.7E-24 132.6 0.0 73 2-74 133-207 (219)
16 tr|A7SMP9|A7SMP9_NEMVE Predict 99.6 6.8E-19 4.8E-24 126.2 0.0 73 2-74 75-149 (150)
17 tr|A0A0Q0XGV6|A0A0Q0XGV6_NEIME 99.6 1.1E-18 6.3E-24 106.9 0.0 43 32-74 1-43 (43)
18 tr|A0A0A9S1E5|A0A0A9S1E5_ARUDO 99.6 2.1E-18 1.2E-23 113.4 0.0 69 6-74 1-70 (70)
19 tr|A0A0G1VDB1|A0A0G1VDB1_9BACT 99.6 3.8E-18 1.7E-23 126.1 0.0 63 2-64 46-108 (160)
20 tr|D8TQZ8|D8TQZ8_VOLCA Plastid 99.5 3.8E-18 2.4E-23 124.8 0.0 73 2-74 89-162 (162)
21 sp|P58138|RK12_EUGLO 50S ribos 99.5 3.2E-17 1.6E-22 119.2 0.0 73 2-74 61-134 (138)
22 tr|J9FFI8|J9FFI8_9ZZZZ Ribosom 99.4 1.3E-16 7E-22 111.1 0.0 46 1-46 55-100 (100)
23 tr|X1B2T7|X1B2T7_9ZZZZ Unchara 99.4 1.5E-16 9.3E-22 108.2 0.0 38 1-38 52-89 (89)
24 tr|I7JDH7|I7JDH7_BABMI Unchara 99.4 4.8E-16 3.1E-21 118.9 0.0 71 4-74 165-236 (236)
25 tr|A0A0G1V4K5|A0A0G1V4K5_9BACT 99.3 4.5E-15 2E-20 104.2 0.0 67 8-74 34-100 (100)
26 tr|Q1NYW2|Q1NYW2_9FLAO Ribosom 99.3 5.4E-15 3E-20 117.0 0.0 72 3-74 228-299 (299)
27 tr|A0A0D2IK34|A0A0D2IK34_9EURO 99.3 4.9E-15 3.1E-20 111.7 0.0 73 2-74 130-203 (203)
28 tr|A0A0C1VJR8|A0A0C1VJR8_9ENTR 99.2 2E-14 8.9E-20 100.9 0.0 71 3-74 29-99 (99)
29 tr|Q96Q74|Q96Q74_HUMAN Mitocho 99.2 1.8E-14 9.6E-20 93.5 0.0 57 18-74 2-59 (59)
30 tr|M2WWU5|M2WWU5_GALSU [pt] 50 99.1 1.1E-13 5.1E-19 114.3 0.0 71 3-73 398-469 (470)
31 tr|C1E7K2|C1E7K2_MICSR Unchara 99.1 1.2E-13 6E-19 107.0 0.0 73 2-74 158-231 (231)
32 tr|Q2IA21|Q2IA21_DIALT Chlorop 99.1 1.5E-13 6.6E-19 105.4 0.0 58 2-59 89-147 (208)
33 tr|A0A0F9DXB6|A0A0F9DXB6_9ZZZZ 99.1 2.5E-13 1.1E-18 101.2 0.0 72 3-74 88-159 (159)
34 tr|X0ZAN1|X0ZAN1_9ZZZZ Unchara 99.0 6.6E-13 2.9E-18 103.6 0.0 73 2-74 170-242 (242)
35 tr|G6ELX9|G6ELX9_STRTR LSU rib 99.0 7.2E-13 3.3E-18 89.1 0.0 64 11-74 8-71 (71)
36 tr|A0A0E0C5M1|A0A0E0C5M1_9ORYZ 99.0 9.2E-13 4.1E-18 104.3 0.0 73 1-73 207-280 (281)
37 tr|A0A0F9V372|A0A0F9V372_9ZZZZ 99.0 1.6E-12 7.2E-18 97.0 0.0 68 6-73 91-158 (159)
38 tr|K3Z941|K3Z941_SETIT Unchara 98.9 2.8E-12 1.3E-17 100.4 0.0 72 2-73 175-247 (248)
39 tr|A0A068VD77|A0A068VD77_COFCA 98.9 2.4E-12 1.3E-17 100.0 0.0 72 2-73 162-234 (235)
40 tr|A0A0P6HYL4|A0A0P6HYL4_9CRUS 98.9 2.5E-12 1.4E-17 95.5 0.0 49 2-50 109-158 (158)
41 tr|A0A068U376|A0A068U376_COFCA 98.9 3.8E-12 1.8E-17 101.8 0.0 73 2-74 231-304 (304)
42 tr|A0A0N0VD94|A0A0N0VD94_9TRYP 98.9 2.9E-12 2E-17 96.8 0.0 72 2-73 136-208 (209)
43 tr|X7ZNA2|X7ZNA2_MYCXE 50S rib 98.8 1.2E-11 5.2E-17 91.2 0.0 46 2-47 58-104 (139)
44 tr|R7QPT0|R7QPT0_CHOCR Unchara 98.7 4.5E-11 2E-16 93.2 0.0 72 3-74 156-228 (228)
45 tr|K2FAF6|K2FAF6_9BACT Unchara 98.7 5.8E-11 2.7E-16 77.4 0.0 55 20-74 1-56 (56)
46 tr|A0A0G1T1V5|A0A0G1T1V5_9BACT 98.7 6.4E-11 2.8E-16 90.6 0.0 48 1-48 65-113 (190)
47 tr|U6JY92|U6JY92_9EIME 50S rib 98.7 7E-11 3.5E-16 93.2 0.0 72 2-73 182-255 (256)
48 tr|A0A0B2QZB0|A0A0B2QZB0_GLYSO 98.6 1.5E-10 6.8E-16 97.0 0.0 69 2-70 121-190 (504)
49 tr|M0ZM47|M0ZM47_SOLTU Unchara 98.6 1.9E-10 8.4E-16 94.6 0.0 73 2-74 321-395 (395)
50 tr|G8NQQ0|G8NQQ0_GRAMM Ribosom 98.6 2E-10 9.1E-16 86.8 0.0 69 1-69 96-164 (168)
51 tr|W4UAC4|W4UAC4_PROAA 50S rib 98.6 1.6E-10 9.1E-16 93.3 0.0 62 1-69 266-329 (329)
52 tr|R1IQH8|R1IQH8_9GAMM Cyclohe 98.6 2.1E-10 9.5E-16 92.7 0.0 69 6-74 256-324 (327)
53 tr|A0A0R0FQ88|A0A0R0FQ88_SOYBN 98.6 2.2E-10 9.8E-16 88.3 0.0 73 2-74 104-201 (201)
54 tr|M7ZDT3|M7ZDT3_TRIUA 50S rib 98.6 2E-10 9.9E-16 89.7 0.0 73 2-74 155-228 (228)
55 tr|A0A0Q4Y3N1|A0A0Q4Y3N1_9BURK 98.6 2.2E-10 9.9E-16 93.5 0.0 70 5-74 181-250 (365)
56 tr|K8F238|K8F238_9CHLO Unchara 98.6 2.3E-10 1E-15 91.5 0.0 72 3-74 216-288 (288)
57 tr|I2CQV4|I2CQV4_9STRA Unchara 98.6 2.4E-10 1.1E-15 92.0 0.0 71 3-73 241-312 (313)
58 tr|J3MN62|J3MN62_ORYBR Unchara 98.6 2.4E-10 1.1E-15 85.1 0.0 72 3-74 76-148 (148)
59 tr|F0WYB6|F0WYB6_9STRA Mitocho 98.5 5.5E-10 2.5E-15 91.9 0.0 70 3-72 104-174 (393)
60 tr|H3GMR9|H3GMR9_PHYRM Unchara 98.5 6E-10 2.7E-15 95.7 0.0 66 1-66 105-171 (673)
61 tr|B7KN08|B7KN08_CYAP7 Ribosom 98.5 5.9E-10 2.8E-15 84.5 0.0 72 3-74 95-167 (171)
62 tr|D7FPT9|D7FPT9_ECTSI 50S rib 98.5 7.9E-10 3.5E-15 87.1 0.0 74 1-74 170-244 (244)
63 tr|J3M9J4|J3M9J4_ORYBR Unchara 98.5 8.4E-10 3.8E-15 91.1 0.0 73 1-73 328-401 (402)
64 tr|A0BSI2|A0BSI2_PARTE Unchara 98.4 1.1E-09 5.4E-15 87.2 0.0 71 3-73 197-268 (269)
65 tr|R7W4R0|R7W4R0_AEGTA 50S rib 98.4 1.3E-09 5.7E-15 86.8 0.0 73 1-73 194-267 (268)
66 tr|J9IU41|J9IU41_9SPIT Ribosom 98.4 1.3E-09 6.5E-15 86.9 0.0 71 3-73 203-274 (275)
67 tr|B9T5A3|B9T5A3_RICCO 50S rib 98.4 1.8E-09 8.2E-15 86.9 0.0 73 2-74 228-301 (301)
68 tr|K0S2E6|K0S2E6_THAOC Unchara 98.4 2.2E-09 9.9E-15 93.0 0.0 72 2-73 102-174 (734)
69 tr|Q0KIV9|Q0KIV9_SOLDE Ribosom 98.4 2.2E-09 1E-14 85.3 0.0 70 2-71 115-185 (262)
70 tr|A5C502|A5C502_VITVI Putativ 98.3 3E-09 1.3E-14 91.1 0.0 73 2-74 542-615 (615)
71 tr|E7NHN4|E7NHN4_YEASO Mnp1p O 98.3 2.7E-09 1.3E-14 76.4 0.0 73 2-74 33-106 (106)
72 tr|A0A0G4B2R2|A0A0G4B2R2_9BACT 98.3 2.9E-09 1.3E-14 82.6 0.0 73 2-74 133-206 (206)
73 tr|A0A022R403|A0A022R403_ERYGU 98.3 5E-09 2.2E-14 84.0 0.0 72 2-73 209-281 (282)
74 tr|F0VRC6|F0VRC6_NEOCL 50S rib 98.3 5E-09 2.3E-14 86.5 0.0 71 4-74 311-382 (382)
75 tr|A0A078EDI1|A0A078EDI1_BRANA 98.3 5.6E-09 2.5E-14 72.5 0.0 46 28-73 36-81 (82)
76 tr|A0A0D3B9X5|A0A0D3B9X5_BRAOL 98.2 6.8E-09 3.3E-14 75.3 0.0 57 17-73 58-114 (115)
77 tr|G0QQH8|G0QQH8_ICHMG Ribosom 98.2 7.6E-09 3.8E-14 80.3 0.0 73 2-74 131-204 (204)
78 tr|A0A0L9UXN4|A0A0L9UXN4_PHAAN 98.2 8.9E-09 4E-14 88.9 0.0 71 1-71 83-154 (671)
79 tr|A0A0P5NF26|A0A0P5NF26_9CRUS 98.2 9.3E-09 4.2E-14 77.7 0.0 43 2-44 117-160 (160)
80 tr|V7PC69|V7PC69_9APIC Ribosom 98.2 7.7E-09 4.2E-14 82.2 0.0 72 3-74 191-263 (263)
81 tr|R4X7J3|R4X7J3_TAPDE 54S rib 98.1 2E-08 9.3E-14 80.5 0.0 74 1-74 199-273 (273)
82 tr|O81061|O81061_ARATH 50S rib 98.1 2.1E-08 9.5E-14 72.5 0.0 73 1-73 17-90 (110)
83 tr|J9I3J3|J9I3J3_9SPIT Ribosom 98.1 2.1E-08 1E-13 89.5 0.0 72 2-73 938-1010(1011)
84 tr|A0A0F2TN70|A0A0F2TN70_9ACTN 98.0 2.5E-08 1.5E-13 68.6 0.0 66 8-73 15-80 (83)
85 tr|A0A0G4GB80|A0A0G4GB80_9ALVE 98.0 4.6E-08 2.1E-13 79.1 0.0 73 2-74 224-298 (298)
86 tr|A0A0G4H615|A0A0G4H615_9ALVE 98.0 6E-08 2.7E-13 79.0 0.0 71 3-73 244-316 (317)
87 tr|A0A074TEM3|A0A074TEM3_HAMHA 97.9 8.4E-08 3.8E-13 81.7 0.0 73 2-74 445-519 (519)
88 tr|A0A0F6W9I2|A0A0F6W9I2_9DELT 97.9 9.3E-08 4.2E-13 77.9 0.0 65 8-72 244-308 (315)
89 tr|V5BGN2|V5BGN2_TRYCR Ribosom 97.9 1.2E-07 5.3E-13 76.7 0.0 72 2-73 220-292 (293)
90 tr|F0VBV0|F0VBV0_NEOCL 50S rib 97.8 2E-07 8.9E-13 74.8 0.0 74 1-74 190-265 (265)
91 tr|A0A077KTD1|A0A077KTD1_9CAUD 97.8 1.9E-07 9.5E-13 66.1 0.0 33 12-44 8-40 (92)
92 tr|G0QMB9|G0QMB9_ICHMG Ribosom 97.8 2.4E-07 1.1E-12 76.8 0.0 70 4-73 306-376 (377)
93 tr|J9GLN4|J9GLN4_9ZZZZ Protein 97.8 2.7E-07 1.2E-12 53.3 0.0 25 50-74 1-25 (25)
94 tr|W1PK54|W1PK54_AMBTC Unchara 97.7 3.2E-07 1.4E-12 66.9 0.0 72 2-73 40-112 (113)
95 tr|H9MCZ1|H9MCZ1_PINRA Unchara 97.7 4E-07 1.8E-12 63.9 0.0 48 2-49 36-84 (84)
96 tr|A0A0F9JCY0|A0A0F9JCY0_9ZZZZ 97.7 4.3E-07 1.9E-12 72.4 0.0 43 32-74 203-245 (245)
97 tr|Q4Y140|Q4Y140_PLACH Ribosom 97.7 5.1E-07 2.3E-12 65.5 0.0 71 4-74 36-107 (107)
98 tr|A0A0C2GIX0|A0A0C2GIX0_9BILA 97.6 6.1E-07 2.8E-12 60.7 0.0 63 6-68 1-65 (65)
99 tr|R7LSE9|R7LSE9_9FUSO 50S rib 97.6 7.3E-07 3.3E-12 66.8 0.0 66 9-74 73-138 (138)
100 tr|X7ZHL5|X7ZHL5_MYCXE Ribosom 97.5 1.2E-06 5.3E-12 59.0 0.0 47 22-68 1-48 (62)

Writing A3M alignment to 1ctfA.a3m
Done
dangmingai@PROTEIN:~/results$ ls
1ctfA.a3m 1ctfA.fasta 1ctfA.hhr
dangmingai@PROTEIN:~/results$ vim 1ctfA.hhr
dangmingai@PROTEIN:~/results$ vim 1ctfA.a3m
dangmingai@PROTEIN:~/results$

***************************************************************************************

The above is example to run

Below is example to Catalog

***************************************************************************************

set basename = $1:r
set rootname = $basename:t
-- INSERT -- 14,36 11%
.0.1$ ls
BLAST+ bin runpsipred_single
LICENSE data src
README example
VERSION runpsipred
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim runpsipred
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim runpsipred
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+ bin runpsipred_single
LICENSE data src
README example
VERSION runpsipred
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim runpsipred
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred example/example.fas
ta
set: Variable name must begin with a letter.
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+ VERSION example src
LICENSE bin runpsipred
README data runpsipred_single
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred example/example.fas
ta
set: Variable name must begin with a letter.
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred /example/example.fasta
set: Variable name must begin with a letter.
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ cd example/
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/example$ ls
example.fasta example.horiz example.ss2
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/example$ pwd
/home/dangmingai/softwares/softwares/psipred-4.0.1/example
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/example$ cd ..
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+ VERSION example src
LICENSE bin runpsipred
README data runpsipred_single
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred /example/example.fa
sta
set: Variable name must begin with a letter.
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred example.fasta
set: Variable name must begin with a letter.
#!/bin/tcsh

# This is a simple script which will carry out all of the basic steps
# required to make a PSIPRED prediction. Note that it assumes that the
# following programs are in the appropriate directories:
# blastpgp - PSIBLAST executable (from NCBI toolkit)
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V4 program
# psipass2 - PSIPRED V4 program

# NOTE: Script modified to be more cluster friendly (DTJ April 2008)

# The name of the BLAST data bank
set dbname =/mnt/data/BLASTCommon/db/nr.20160521/nr

# Where the NCBI programs have been installed
set ncbidir = /home/dangmingai/bin

# Where the PSIPRED V4 programs have been installed
set execdir = ./bin

# Where the PSIPRED V4 data files have been installed
set datadir = ./data

set basename = $1:r
set rootname = $basename:t

"runpsipred" 80L, 2111C 17,1 Top
#!/bin/tcsh

# This is a simple script which will carry out all of the basic stee
ps
# required to make a PSIPRED prediction. Note that it assumes that
the
# following programs are in the appropriate directories:
# blastpgp - PSIBLAST executable (from NCBI toolkit)
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V4 program
# psipass2 - PSIPRED V4 program

# NOTE: Script modified to be more cluster friendly (DTJ April 20088
)

# The name of the BLAST data bank
set dbname =/mnt/data/BLASTCommon/db/nr.20160521/nr

# Where the NCBI programs have been installed
set ncbidir = /home/dangmingai/bin

# Where the PSIPRED V4 programs have been installed
set execdir = ./bin

# Where the PSIPRED V4 data files have been installed
set datadir = ./data

set basename = $1:r
set rootname = $basename:t

# Generate a "unique" temporary filename root
17,1 Top
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ./runpsipred
set: Variable name must begin with a letter.
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
# following programs are in the appropriate directories:
# blastpgp - PSIBLAST executable (from NCBI toolkit)
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V4 program
# psipass2 - PSIPRED V4 program

# NOTE: Script modified to be more cluster friendly (DTJ April 2008)

# The name of the BLAST data bank
set dbname =/mnt/data/BLASTCommon/db/nr.20160521/nr

# Where the NCBI programs have been installed
set ncbidir = /home/dangmingai/bin

# Where the PSIPRED V4 programs have been installed
set execdir = ./bin

# Where the PSIPRED V4 data files have been installed
set datadir = ./data

set basename = $1:r
set rootname = $basename:t

# Generate a "unique" temporary filename root
set hostid = `hostid`
set tmproot = psitmp$$$hostid

17,1 Top
#!/bin/tcsh

# NOTE: Script modified to be more cluster friendly (DTJ April 2008)

# The name of the BLAST data bank
set dbname =/mnt/data/BLASTCommon/db/nr.20160521/nr

# Where the NCBI programs have been installed
set ncbidir = /home/dangmingai/bin

# Where the PSIPRED V4 programs have been installed
set execdir = ./bin

# Where the PSIPRED V4 data files have been installed
set datadir = ./data

set basename = $1:r
set rootname = $basename:t

# Generate a "unique" temporary filename root 17,1 Top
BLAST+ VERSION example src
LICENSE bin runpsipred
README data runpsipred_single
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ cd bin
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/bin$ ls
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/bin$ ls
chkparse psipass2 psipred seq2mtx
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/bin$ cd ..
dangmingai@PROTEIN:~/softwares/softwares/psipirectories:
# blastpgp - PSIBLAST executable (from NCBI toolkit)
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V4 program
# psipass2 - PSIPRED V4 program

# NOTE: Script modified to be more cluster friendly (DTJ April 2008)

# The name of the BLAST data bank
set dbname =/mnt/data/BLASTCommon/db/nr.20160521/nr

# Where the NCBI programs have been installed
set ncbidir = /home/dangmingai/bin

# Where the PSIPRED V4 programs have been installed
set execdir = ./bin

# Where the PSIPRED V4 data files have been installed
set datadir = ./data

set basename = $1:r
set rootname = $basename:t

17,1 Top
red-4.0.1$ ls
BLAST+ README bin example runpsipred_single
LICENSE VERSION data runpsipred src
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ cd example/dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/example$ ls
example.fasta example.horiz example.ss2
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/example$ cd ..
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+ README bin example runpsipred_single
LICENSE VERSION data runpsipred src
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0ogram

# NOTE: Script modified to be more cluster friendly (DTJ April 2008)

# The name of the BLAST data bank
set dbname =/mnt/data/BLASTCommon/db/nr.20160521/nr

# Where the NCBI programs have been installed
set ncbidir = /home/dangmingai/bin

# Where the PSIPRED V4 programs have been installed
set execdir = ./bin

@
17,1 Top
t)
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V4 program
# psipass2 - PSIPRED V4 program

# NOTE: Script modified to be more cluster friendly (DTJ April 2008)

# The name of the BLAST data bank
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V4 program
# psipass2 - PSIPRED V4 program

# NOTE: Script modified to be more cluster friendly (DTJ April 2008)

# The name of the BLAST data bank
set dbname =/mnt/data/BLASTCommon/db/nr.20160521/nr

# Where the NCBI programs have been installed
set ncbidir = /home/dangmingai/bin

@
17,1 8%
# makemat - IMPALA utilitt
y (from NCBI toolkit)
# psipred - PSIPRED V4 prr
ogram
# psipass2 - PSIPRED V4 pp
rogram

# NOTE: Script modified tt
o be more cluster friendll
y (DTJ April 2008)

# The name of the BLAST dd
ata bank
set dbname =/mnt/data/BLAA
STCommon/db/nr.20160521/nn
r

# Where the NCBI programss
have been installed
set ncbidir = /home/dangmm
ingai/bin

@ r
# following programs are in the appropriate directories:
# blastpgp - PSIBLAST executable (from NCBI toolkit)
# makemat - IMPALA utility (from NCBI toolkit)
# psipred - PSIPRED V4 program
# psipass2 - PSIPRED V4 program

# NOTE: Script modified to be more cluster friendly (DTJ April 2008)

# The name of the BLAST data bank
set dbname =/mnt/data/BLASTCommon/db/nr.20160521/nr

# Where the NCBI programs have been installed
set ncbidir = /home/dangmingai/bin

# Where the PSIPRED V4 programs have been installed
set execdir = ./bin

# Where the PSIPRED V4 data files have been installed
set datadir = ./data

set basename = $1:r
set rootname = $basename:t
17,1 6%
@
17,1 8%
set dbname =/mnt/data/BLASTCommon/db/nr.20160521/nr

# Where the NCBI programs have been installed
set ncbidir = /home/dangmingai/bin

17,1 7%
.1$ cd bin
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/bin$ ls
chkparse psipass2 psipred seq2mtx
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1/bin$ cd ..
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim
bin/ LICENSE src/
BLAST+/ README VERSION
data/ runpsipred
example/ runpsipred_single
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ vim runpsipred
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ ls
BLAST+ data example.ss2
LICENSE example runpsipred
README example.fasta runpsipred_single
VERSION example.horiz src
bin example.ss
dangmingai@PROTEIN:~/softwares/softwares/psipred-4.0.1$ cd ..
dangmingai@PROTEIN:~/softwares/softwares$ ls
CNFsearch1.66_release
PDB_Tool
TGT_Package
anaconda3
blast-2.2.26
cd-hit-v4.6.8-2017-0621
confold-v2.0
csblast-2.2.3_linux64
dDFIRE1.1-bin
dssp-3.0.0
fasta-36.3.8g
freecontact-1.0.21
gcc-7.1.0
glibc-2.23
hhomp-1.0-x86_64
hhsuite-2.0.16-linux-x86_64
hhsuite-3.0-beta.3-Linux
hhsuite-3.2.0-SSE2-Linux
hmmer-3.2.1
metapsicov-1.0.4
metapsicov-2.0.2
packages
psicov-2.4.0
psipred-4.0.1
rosetta_bin_linux_2017.08.59291_bundle
dangmingai@PROTEIN:~/softwares/softwares$ cd blast-2.2.26/
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26$ ls
VERSION bin data doc
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26$ cd bin
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26/bin$ l
bl2seq* fastacmd* megablast*
blastall* formatdb* rpsblast*
blastclust* formatrpsdb* seedtop*
blastpgp* impala*
copymat* makemat*
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26/bin$ sls
No command 'sls' found, but there are 22 similar ones
sls: command not found
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26/bin$ ls
bl2seq copymat impala seedtop
blastall fastacmd makemat
blastclust formatdb megablast
blastpgp formatrpsdb rpsblast
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26/bin$ blastpgp
The program 'blastpgp' is currently not installed. To run 'blastpgp' please ask your administrator to install the package 'blast2'
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26/bin$ ./blastpgp
^C
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26/bin$ pwd
/home/dangmingai/softwares/softwares/blast-2.2.26/bin
dangmingai@PROTEIN:~/softdangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26/bin$ cd ..
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26$ ls
VERSION bin data doc
dangmingai@PROTEIN:~/softwares/softwares/blast-2.2.26$ cd ..
dangmingai@PROTEIN:~/softwares/softwares$ ls
CNFsearch1.66_release
PDB_Tool
TGT_Package
anaconda3
blast-2.2.26
cd-hit-v4.6.8-2017-0621
confold-v2.0
csblast-2.2.3_linux64
dDFIRE1.1-bin
dssp-3.0.0
fasta-36.3.8g
freecontact-1.0.21
gcc-7.1.0
glibc-2.23
hhomp-1.0-x86_64
hhsuite-2.0.16-linux-x86_64
hhsuite-3.0-beta.3-Linux
hhsuite-3.2.0-SSE2-Linux
hmmer-3.2.1
metapsicov-1.0.4
metapsicov-2.0.2
packages
psicov-2.4.0
psipred-4.0.1
rosetta_bin_linux_2017.08.59291_bundle
dangmingai@PROTEIN:~/softwares/softwares$ ls
CNFsearch1.66_release
PDB_Tool
TGT_Package
anaconda3
blast-2.2.26
cd-hit-v4.6.8-2017-0621
confold-v2.0
csblast-2.2.3_linux64
dDFIRE1.1-bin
dssp-3.0.0
fasta-36.3.8g
freecontact-1.0.21
gcc-7.1.0
glibc-2.23
hhomp-1.0-x86_64
hhsuite-2.0.16-linux-x86_64
hhsuite-3.0-beta.3-Linux
hhsuite-3.2.0-SSE2-Linux
hmmer-3.2.1
metapsicov-1.0.4
metapsicov-2.0.2
packages
psicov-2.4.0
psipred-4.0.1
rosetta_bin_linux_2017.08.59291_bundle
dangmingai@PROTEIN:~/softwares/softwares$ ls
CNFsearch1.66_release
PDB_Tool
TGT_Package
anaconda3
blast-2.2.26
cd-hit-v4.6.8-2017-0621
confold-v2.0
csblast-2.2.3_linux64
dDFIRE1.1-bin
dssp-3.0.0
fasta-36.3.8g
freecontact-1.0.21
gcc-7.1.0
glibc-2.23
hhomp-1.0-x86_64
hhsuite-2.0.16-linux-x86_64
hhsuite-3.0-beta.3-Linux
hhsuite-3.2.0-SSE2-Linux
hmmer-3.2.1
metapsicov-1.0.4
metapsicov-2.0.2
packages
psicov-2.4.0
psipred-4.0.1
rosetta_bin_linux_2017.08.59291_bundle
dangmingai@PROTEIN:~/softwares/softwares$ pwd
/home/dangmingai/softwares/softwares
dangmingai@PROTEIN:~/softwares/softwares$ ls
CCMpred-0.3.2
CNFsearch1.66_release
PDB_Tool
TGT_Package
anaconda3
blast-2.2.26
cd-hit-v4.6.8-2017-0621
confold-v2.0
csblast-2.2.3_linux64
dDFIRE1.1-bin
dssp-3.0.0
fasta-36.3.8g
freecontact-1.0.21
gcc-7.1.0
glibc-2.23
hhomp-1.0-x86_64
hhsuite-2.0.16-linux-x86_64
hhsuite-3.0-beta.3-Linux
hhsuite-3.2.0-SSE2-Linux
hmmer-3.2.1
metapsicov-1.0.4
metapsicov-2.0.2
packages
psicov-2.4.0
psipred-4.0.1
rosetta_bin_linux_2017.08.59291_bundle
dangmingai@PROTEIN:~/softwares/softwares$ cd CCMpr
ed-0.3.2/
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2$ ls
bin lib
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2$ cd bin
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2/bin$ ls
ccmpred ccmpred_gpu
ccmpred_cpu
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2/bin$ cd ..
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2$ ls
bin lib
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2$ cd lib/
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2/lib$ ls
libconjugrad.a
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2/lib$ cd ..
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2$ ls
bin lib
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2$ cd bin
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2/bin$ ls
ccmpred ccmpred_gpu
ccmpred_cpu
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2/bin$ pwd
/home/dangmingai/softwares/softwares/CCMpred-0.3.2/bin
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2/bin$ cd ..
dangmingai@PROTEIN:~/softwares/softwares/CCMpred-0.3.2$ cd ..
dangmingai@PROTEIN:~/softwares/softwares$ ls
CCMpred-0.3.2
CNFsearch1.66_release
PDB_Tool
TGT_Package
anaconda3
blast-2.2.26
cd-hit-v4.6.8-2017-0621
confold-v2.0
csblast-2.2.3_linux64
dDFIRE1.1-bin
dssp-3.0.0
fasta-36.3.8g
freecontact-1.0.21
gcc-7.1.0
glibc-2.23
hhomp-1.0-x86_64
hhsuite-2.0.16-linux-x86_64
hhsuite-3.0-beta.3-Linux
hhsuite-3.2.0-SSE2-Linux
hmmer-3.2.1
metapsicov-1.0.4
metapsicov-2.0.2
packages
psicov-2.4.0
psipred-4.0.1
rosetta_bin_linux_2017.08.59291_bundle
dangmingai@PROTEIN:~/softwares/softwares$ cd packa
ges/
dangmingai@PROTEIN:~/soft00m$ lsoftwares/packages
Anaconda csblast
CNFsearch dssp
MRFsearch fasta
New_Uniform psicov
blast.blast+ psipred
cns qprob
dangmingai@PROTEIN:~/soft00m$ cd fastaes/packages
dangmingai@PROTEIN:~/softwares/softwares/packages/fasta$ ld
ld: no input files
dangmingai@PROTEIN:~/softwares/softwares/packages/fasta$ ls
fasta-36.3.8d-linux64.tar.gz
fasta-36.3.8d.tar.gz
fasta-36.3.8e-linux64.tar.gz
fasta-36.3.8e.tar.gz
fasta-36.3.8g-linux64.tar.gz
fasta-36.3.8g.tar.gz
dangmingai@PROTEIN:~/softwares/softwares/packages$ cd /mnt/data/FALCONCommon/@PROTEIN:~/softwares/softwares/packages/fasta$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP FALCON_softwares TrainingTestData
DSSP_series PDB_series hmmer
FALCON_databases SCOP_series uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ll
total 44
drwxr-xr-x 1 big-admin big-admin 4096 Jun 17 15:29 ./
drwxr-xr-x 1 big-admin big-admin 4096 Jun 23 02:27 ../
drwxrwxr-x 1 big-admin big-admin 4096 Jan 22 2019 CASP/
drwxrwxr-x 1 big-admin big-admin 4096 Jun 17 17:00 DSSP_series/
drwxr-xr-x 1 big-admin big-admin 4096 Jun 17 15:31 FALCON_databases/
lrwxrwxrwx 1 big-admin big-admin 12 May 14 2018 FALCON_softwares -> ../softwares/
drwxr-xr-x 1 big-admin big-admin 4096 Jun 17 17:19 PDB_series/
drwxr-xr-x 1 big-admin big-admin 4096 May 28 2018 SCOP_series/
drwxr-xr-x 1 big-admin big-admin 4096 Jan 11 2019 TrainingTestData/
drwxrwxr-x 1 big-admin big-admin 4096 Jun 6 13:23 hmmer/
drwxrwxr-x 1 big-admin big-admin 4096 Apr 16 2018 uniprot/
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd FALCON_databases/
dangmingai@PROTEIN:/mnt/data/FALCONCommon/FALCON_databases$ ls
README nr100_pfilt.blastdb pdb70.hhsearchdb
SCOPe95.hhsearchdb nr90.blastdb relnotes.txt
nr.blastdb nr90_pfilt.blastdb uniclust30.hhblitsdb
nr100.blastdb nr_pfilt.blastdb uniprot20.hhblitsdb
dangmingai@PROTEIN:/mnt/data/FALCONCommon/FALCON_databases$ ll
total 60
drwxr-xr-x 1 big-admin big-admin 4096 Jun 17 15:31 ./
drwxr-xr-x 1 big-admin big-admin 4096 Jun 17 15:29 ../
-rw-rw-r-- 1 big-admin big-admin 29 Jun 6 13:35 README
lrwxrwxrwx 1 big-admin big-admin 47 Jun 6 13:34 SCOPe95.hhsearchdb -> ../../HHCommon/HHsearch/databases/SCOPe95_2.06//
lrwxrwxrwx 1 big-admin big-admin 33 Jun 17 15:30 nr.blastdb -> ../../BLASTCommon/db/nr.20190522//
lrwxrwxrwx 1 big-admin big-admin 36 Jun 17 15:30 nr100.blastdb -> ../../BLASTCommon/db/nr100.20190522//
lrwxrwxrwx 1 big-admin big-admin 42 Jun 17 15:30 nr100_pfilt.blastdb -> ../../BLASTCommon/db/nr100_pfilt.20190522//
lrwxrwxrwx 1 big-admin big-admin 35 Jun 17 15:31 nr90.blastdb -> ../../BLASTCommon/db/nr90.20190522//
lrwxrwxrwx 1 big-admin big-admin 41 Jun 17 15:31 nr90_pfilt.blastdb -> ../../BLASTCommon/db/nr90_pfilt.20190522//
lrwxrwxrwx 1 big-admin big-admin 39 Jun 17 15:30 nr_pfilt.blastdb -> ../../BLASTCommon/db/nr_pfilt.20190522//
lrwxrwxrwx 1 big-admin big-admin 48 Nov 13 2017 pdb70.hhsearchdb -> ../../HHCommon/HHsearch/databases/pdb70_04Jul16//
-rw-rw-r-- 1 big-admin big-admin 4272 Dec 7 2016 relnotes.txt
lrwxrwxrwx 1 big-admin big-admin 43 Jun 6 13:32 uniclust30.hhblitsdb -> ../../HHCommon/uniclust/uniclust30_2018_08//
lrwxrwxrwx 1 big-admin big-admin 45 Nov 13 2017 uniprot20.hhblitsdb -> ../../HHCommon/hhsuite_dbs/uniprot20_2016_02//
dangmingai@PROTEIN:/mnt/data/FALCONCommon/FALCON_databases$ ls
README nr100_pfilt.blastdb pdb70.hhsearchdb
SCOPe95.hhsearchdb nr90.blastdb relnotes.txt
nr.blastdb nr90_pfilt.blastdb uniclust30.hhblitsdb
nr100.blastdb nr_pfilt.blastdb uniprot20.hhblitsdb
dangmingai@PROTEIN:/mnt/data/FALCONCommon/FALCON_databases$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP FALCON_softwares TrainingTestData
DSSP_series PDB_series hmmer
FALCON_databases SCOP_series uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd hmmer
dangmingai@PROTEIN:/mnt/data/FALCONCommon/hmmer$ ls
uniclust30_2017_10 uniclust90_2017_10 uniref90_2018_03
dangmingai@PROTEIN:/mnt/data/FALCONCommon/hmmer$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP FALCON_softwares TrainingTestData
DSSP_series PDB_series hmmer
FALCON_databases SCOP_series uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot$ ls
bin release-2017_11 release-2018_03
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot$ ls
bin release-2017_11 release-2018_03
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP FALCON_softwares TrainingTestData
DSSP_series PDB_series hmmer
FALCON_databases SCOP_series uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd ..
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon I-TASSER SPARKS-X softwares
FALCONCommon ImageCommon lost+found
HHCommon RaptorXCommon original_databases
dangmingai@PROTEIN:/mnt/data$ cd BLASTCommon/
dangmingai@PROTEIN:/mnt/data/BLASTCommon$ ls
FASTA db
dangmingai@PROTEIN:/mnt/data/BLASTCommon$ cd FASTA/
dangmingai@PROTEIN:/mnt/data/BLASTCommon/FASTA$ ls
nr.20160521 nr70.20160521 nr90_pfilt.20160521
nr.20190522 nr70.20190522 nr90_pfilt.20190522
nr100.20160521 nr70_pfilt.20160521 nr_pfilt.20160521
nr100.20190522 nr70_pfilt.20190522 nr_pfilt.20190522
nr100_pfilt.20160521 nr90.20160521 pfilt
nr100_pfilt.20190522 nr90.20190522 pfilt1.5.tar.gz
dangmingai@PROTEIN:/mnt/data/BLASTCommon/FASTA$ cd ..
dangmingai@PROTEIN:/mnt/data/BLASTCommon$ ls
FASTA db
dangmingai@PROTEIN:/mnt/data/BLASTCommon$ cd db
dangmingai@PROTEIN:/mnt/data/BLASTCommon/db$ ls
nr.20160521 nr100_pfilt.20160521 nr90_pfilt.20160521
nr.20190522 nr100_pfilt.20190522 nr90_pfilt.20190522
nr100.20160521 nr90.20160521 nr_pfilt.20160521
nr100.20190522 nr90.20190522 nr_pfilt.20190522
dangmingai@PROTEIN:/mnt/data/BLASTCommon/db$ cd nr90.20190522/
dangmingai@PROTEIN:/mnt/data/BLASTCommon/db/nr90.20190522$ ls
nr90 nr90.15.phr nr90_pfilt nr90_pfilt.15.phr
nr90.00.phr nr90.15.pin nr90_pfilt.00.phr nr90_pfilt.15.pin
nr90.00.pin nr90.15.pog nr90_pfilt.00.pin nr90_pfilt.15.pog
nr90.00.pog nr90.15.psd nr90_pfilt.00.pog nr90_pfilt.15.psd
nr90.00.psd nr90.15.psi nr90_pfilt.00.psd nr90_pfilt.15.psi
nr90.00.psi nr90.15.psq nr90_pfilt.00.psi nr90_pfilt.15.psq
nr90.00.psq nr90.16.phr nr90_pfilt.00.psq nr90_pfilt.16.phr
nr90.01.phr nr90.16.pin nr90_pfilt.01.phr nr90_pfilt.16.pin
nr90.01.pin nr90.16.pog nr90_pfilt.01.pin nr90_pfilt.16.pog
nr90.01.pog nr90.16.psd nr90_pfilt.01.pog nr90_pfilt.16.psd
nr90.01.psd nr90.16.psi nr90_pfilt.01.psd nr90_pfilt.16.psi
nr90.01.psi nr90.16.psq nr90_pfilt.01.psi nr90_pfilt.16.psq
nr90.01.psq nr90.17.phr nr90_pfilt.01.psq nr90_pfilt.17.phr
nr90.02.phr nr90.17.pin nr90_pfilt.02.phr nr90_pfilt.17.pin
nr90.02.pin nr90.17.pog nr90_pfilt.02.pin nr90_pfilt.17.pog
nr90.02.pog nr90.17.psd nr90_pfilt.02.pog nr90_pfilt.17.psd
nr90.02.psd nr90.17.psi nr90_pfilt.02.psd nr90_pfilt.17.psi
nr90.02.psi nr90.17.psq nr90_pfilt.02.psi nr90_pfilt.17.psq
nr90.02.psq nr90.18.phr nr90_pfilt.02.psq nr90_pfilt.18.phr
nr90.03.phr nr90.18.pin nr90_pfilt.03.phr nr90_pfilt.18.pin
nr90.03.pin nr90.18.pog nr90_pfilt.03.pin nr90_pfilt.18.pog
nr90.03.pog nr90.18.psd nr90_pfilt.03.pog nr90_pfilt.18.psd
nr90.03.psd nr90.18.psi nr90_pfilt.03.psd nr90_pfilt.18.psi
nr90.03.psi nr90.18.psq nr90_pfilt.03.psi nr90_pfilt.18.psq
nr90.03.psq nr90.19.phr nr90_pfilt.03.psq nr90_pfilt.19.phr
nr90.04.phr nr90.19.pin nr90_pfilt.04.phr nr90_pfilt.19.pin
nr90.04.pin nr90.19.pog nr90_pfilt.04.pin nr90_pfilt.19.pog
nr90.04.pog nr90.19.psd nr90_pfilt.04.pog nr90_pfilt.19.psd
nr90.04.psd nr90.19.psi nr90_pfilt.04.psd nr90_pfilt.19.psi
nr90.04.psi nr90.19.psq nr90_pfilt.04.psi nr90_pfilt.19.psq
nr90.04.psq nr90.20.phr nr90_pfilt.04.psq nr90_pfilt.20.phr
nr90.05.phr nr90.20.pin nr90_pfilt.05.phr nr90_pfilt.20.pin
nr90.05.pin nr90.20.pog nr90_pfilt.05.pin nr90_pfilt.20.pog
nr90.05.pog nr90.20.psd nr90_pfilt.05.pog nr90_pfilt.20.psd
nr90.05.psd nr90.20.psi nr90_pfilt.05.psd nr90_pfilt.20.psi
nr90.05.psi nr90.20.psq nr90_pfilt.05.psi nr90_pfilt.20.psq
nr90.05.psq nr90.21.phr nr90_pfilt.05.psq nr90_pfilt.21.phr
nr90.06.phr nr90.21.pin nr90_pfilt.06.phr nr90_pfilt.21.pin
nr90.06.pin nr90.21.pog nr90_pfilt.06.pin nr90_pfilt.21.pog
nr90.06.pog nr90.21.psd nr90_pfilt.06.pog nr90_pfilt.21.psd
nr90.06.psd nr90.21.psi nr90_pfilt.06.psd nr90_pfilt.21.psi
nr90.06.psi nr90.21.psq nr90_pfilt.06.psi nr90_pfilt.21.psq
nr90.06.psq nr90.22.phr nr90_pfilt.06.psq nr90_pfilt.22.phr
nr90.07.phr nr90.22.pin nr90_pfilt.07.phr nr90_pfilt.22.pin
nr90.07.pin nr90.22.pog nr90_pfilt.07.pin nr90_pfilt.22.pog
nr90.07.pog nr90.22.psd nr90_pfilt.07.pog nr90_pfilt.22.psd
nr90.07.psd nr90.22.psi nr90_pfilt.07.psd nr90_pfilt.22.psi
nr90.07.psi nr90.22.psq nr90_pfilt.07.psi nr90_pfilt.22.psq
nr90.07.psq nr90.23.phr nr90_pfilt.07.psq nr90_pfilt.23.phr
nr90.08.phr nr90.23.pin nr90_pfilt.08.phr nr90_pfilt.23.pin
nr90.08.pin nr90.23.pog nr90_pfilt.08.pin nr90_pfilt.23.pog
nr90.08.pog nr90.23.psd nr90_pfilt.08.pog nr90_pfilt.23.psd
nr90.08.psd nr90.23.psi nr90_pfilt.08.psd nr90_pfilt.23.psi
nr90.08.psi nr90.23.psq nr90_pfilt.08.psi nr90_pfilt.23.psq
nr90.08.psq nr90.24.phr nr90_pfilt.08.psq nr90_pfilt.24.phr
nr90.09.phr nr90.24.pin nr90_pfilt.09.phr nr90_pfilt.24.pin
nr90.09.pin nr90.24.pog nr90_pfilt.09.pin nr90_pfilt.24.pog
nr90.09.pog nr90.24.psd nr90_pfilt.09.pog nr90_pfilt.24.psd
nr90.09.psd nr90.24.psi nr90_pfilt.09.psd nr90_pfilt.24.psi
nr90.09.psi nr90.24.psq nr90_pfilt.09.psi nr90_pfilt.24.psq
nr90.09.psq nr90.25.phr nr90_pfilt.09.psq nr90_pfilt.25.phr
nr90.10.phr nr90.25.pin nr90_pfilt.10.phr nr90_pfilt.25.pin
nr90.10.pin nr90.25.pog nr90_pfilt.10.pin nr90_pfilt.25.pog
nr90.10.pog nr90.25.psd nr90_pfilt.10.pog nr90_pfilt.25.psd
nr90.10.psd nr90.25.psi nr90_pfilt.10.psd nr90_pfilt.25.psi
nr90.10.psi nr90.25.psq nr90_pfilt.10.psi nr90_pfilt.25.psq
nr90.10.psq nr90.26.phr nr90_pfilt.10.psq nr90_pfilt.26.phr
nr90.11.phr nr90.26.pin nr90_pfilt.11.phr nr90_pfilt.26.pin
nr90.11.pin nr90.26.pog nr90_pfilt.11.pin nr90_pfilt.26.pog
nr90.11.pog nr90.26.psd nr90_pfilt.11.pog nr90_pfilt.26.psd
nr90.11.psd nr90.26.psi nr90_pfilt.11.psd nr90_pfilt.26.psi
nr90.11.psi nr90.26.psq nr90_pfilt.11.psi nr90_pfilt.26.psq
nr90.11.psq nr90.27.phr nr90_pfilt.11.psq nr90_pfilt.27.phr
nr90.12.phr nr90.27.pin nr90_pfilt.12.phr nr90_pfilt.27.pin
nr90.12.pin nr90.27.pog nr90_pfilt.12.pin nr90_pfilt.27.pog
nr90.12.pog nr90.27.psd nr90_pfilt.12.pog nr90_pfilt.27.psd
nr90.12.psd nr90.27.psi nr90_pfilt.12.psd nr90_pfilt.27.psi
nr90.12.psi nr90.27.psq nr90_pfilt.12.psi nr90_pfilt.27.psq
nr90.12.psq nr90.28.phr nr90_pfilt.12.psq nr90_pfilt.28.phr
nr90.13.phr nr90.28.pin nr90_pfilt.13.phr nr90_pfilt.28.pin
nr90.13.pin nr90.28.pog nr90_pfilt.13.pin nr90_pfilt.28.pog
nr90.13.pog nr90.28.psd nr90_pfilt.13.pog nr90_pfilt.28.psd
nr90.13.psd nr90.28.psi nr90_pfilt.13.psd nr90_pfilt.28.psi
nr90.13.psi nr90.28.psq nr90_pfilt.13.psi nr90_pfilt.28.psq
nr90.13.psq nr90.29.phr nr90_pfilt.13.psq nr90_pfilt.29.phr
nr90.14.phr nr90.29.pin nr90_pfilt.14.phr nr90_pfilt.29.pin
nr90.14.pin nr90.29.pog nr90_pfilt.14.pin nr90_pfilt.29.pog
nr90.14.pog nr90.29.psd nr90_pfilt.14.pog nr90_pfilt.29.psd
nr90.14.psd nr90.29.psi nr90_pfilt.14.psd nr90_pfilt.29.psi
nr90.14.psi nr90.29.psq nr90_pfilt.14.psi nr90_pfilt.29.psq
nr90.14.psq nr90.pal nr90_pfilt.14.psq nr90_pfilt.pal
dangmingai@PROTEIN:/mnt/data/BLASTCommon/db/nr90.20190522$ cd ..
dangmingai@PROTEIN:/mnt/data/BLASTCommon/db$ ls
nr.20160521 nr100_pfilt.20160521 nr90_pfilt.20160521
nr.20190522 nr100_pfilt.20190522 nr90_pfilt.20190522
nr100.20160521 nr90.20160521 nr_pfilt.20160521
nr100.20190522 nr90.20190522 nr_pfilt.20190522
dangmingai@PROTEIN:/mnt/data/BLASTCommon/db$ cd ..
dangmingai@PROTEIN:/mnt/data/BLASTCommon$ ls
FASTA db
dangmingai@PROTEIN:/mnt/data/BLASTCommon$ ls
FASTA db
dangmingai@PROTEIN:/mnt/data/BLASTCommon$ cd ..
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon I-TASSER SPARKS-X softwares
FALCONCommon ImageCommon lost+found
HHCommon RaptorXCommon original_databases
dangmingai@PROTEIN:/mnt/data$ cd FALCONCommon/
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ LS
The program 'LS' is currently not installed. To run 'LS' please ask your administrator to install the package 'sl'
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ LS
The program 'LS' is currently not installed. To run 'LS' please ask your administrator to install the package 'sl'
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP FALCON_softwares TrainingTestData
DSSP_series PDB_series hmmer
FALCON_databases SCOP_series uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd CASP
dangmingai@PROTEIN:/mnt/data/FALCONCommon/CASP$ ls
CASP12 casp12_domains
CASP12_FALCON casp12_predictions
casp10_domains casp12_predictions_trimmed_to_domains
casp10_targets casp12_targets
casp11_domains casp13_domains
casp11_targets casp13_targets
dangmingai@PROTEIN:/mnt/data/FALCONCommon/CASP$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP FALCON_softwares TrainingTestData
DSSP_series PDB_series hmmer
FALCON_databases SCOP_series uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd /home/casp/
dangmingai@PROTEIN:/home/casp$ ls
FORCASP anaconda2 anaconda3 workspace
dangmingai@PROTEIN:/home/casp$ cd FORCASP/
dangmingai@PROTEIN:/home/casp/FORCASP$ ls
BLAST4A3M quality_assessment send_email.py
align_fasta2pir.py run_TMalign.sh server.log
build_submitted_model.py run_casp.sh server.py
contact_assisted run_dDFIRE.sh threading
contact_prediction run_rosetta.sh
dangmingai@PROTEIN:/home/casp/FORCASP$ cd ..
dangmingai@PROTEIN:/home/casp$ ls
FORCASP anaconda2 anaconda3 workspace
dangmingai@PROTEIN:/home/casp$ cd workspace/
dangmingai@PROTEIN:/home/casp/workspace$ ls
jufusong konglupeng zhangqi zhujianwei
dangmingai@PROTEIN:/home/casp/workspace$ cd zhujianwei/
dangmingai@PROTEIN:/home/casp/workspace/zhujianwei$ ls
threading
dangmingai@PROTEIN:/home/casp/workspace/zhujianwei$ cd threading/
dangmingai@PROTEIN:/home/casp/workspace/zhujianwei/threading$ ls
README data examples models scripts third_party utils
dangmingai@PROTEIN:/home/casp/workspace/zhujianwei/threading$ cat README
Our protein threading pipeline.
dangmingai@PROTEIN:/home/casp/workspace/zhujianwei/threading$ cd /mnt/data
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon I-TASSER SPARKS-X softwares
FALCONCommon ImageCommon lost+found
HHCommon RaptorXCommon original_databases
dangmingai@PROTEIN:/mnt/data$ cd HHCommon/
dangmingai@PROTEIN:/mnt/data/HHCommon$ ls
HHsearch hhomp hhsuite_dbs uniclust
dangmingai@PROTEIN:/mnt/data/HHCommon$ cd hhsuite_dbs/
dangmingai@PROTEIN:/mnt/data/HHCommon/hhsuite_dbs$ ls
pdb70_02Apr16 pdb70_from_mmcif_180411 uniprot20_2013_03
pdb70_06Sep14 pdb70_from_mmcif_180808 uniprot20_2015_06
pdb70_14Sep16 pdb70_from_mmcif_190522 uniprot20_2016_02
dangmingai@PROTEIN:/mnt/data/HHCommon/hhsuite_dbs$ cd ..
dangmingai@PROTEIN:/mnt/data/HHCommon$ ls
HHsearch hhomp hhsuite_dbs uniclust
dangmingai@PROTEIN:/mnt/data/HHCommon$ cd hh
hhomp/ hhsuite_dbs/
dangmingai@PROTEIN:/mnt/data/HHCommon$ cd hhomp/
dangmingai@PROTEIN:/mnt/data/HHCommon/hhomp$ ls
benchmark bin_32bit bin_64bit db
dangmingai@PROTEIN:/mnt/data/HHCommon/hhomp$ cd ..
dangmingai@PROTEIN:/mnt/data/HHCommon$ ls
HHsearch hhomp hhsuite_dbs uniclust
dangmingai@PROTEIN:/mnt/data/HHCommon$ cd HHsearch/
dangmingai@PROTEIN:/mnt/data/HHCommon/HHsearch$ ls
databases
dangmingai@PROTEIN:/mnt/data/HHCommon/HHsearch$ cd databases/
dangmingai@PROTEIN:/mnt/data/HHCommon/HHsearch/databases$ ls
SCOPe95_2.06 pdb70_04Jul16
dangmingai@PROTEIN:/mnt/data/HHCommon/HHsearch/databases$ cd ..
dangmingai@PROTEIN:/mnt/data/HHCommon/HHsearch$ ls
databases
dangmingai@PROTEIN:/mnt/data/HHCommon/HHsearch$ ls
databases
dangmingai@PROTEIN:/mnt/data/HHCommon/HHsearch$ cd ..
dangmingai@PROTEIN:/mnt/data/HHCommon$ ls
HHsearch hhomp hhsuite_dbs uniclust
dangmingai@PROTEIN:/mnt/data/HHCommon$ cd hhsuite_dbs/
dangmingai@PROTEIN:/mnt/data/HHCommon/hhsuite_dbs$ ls
pdb70_02Apr16 pdb70_from_mmcif_180411 uniprot20_2013_03
pdb70_06Sep14 pdb70_from_mmcif_180808 uniprot20_2015_06
pdb70_14Sep16 pdb70_from_mmcif_190522 uniprot20_2016_02
dangmingai@PROTEIN:/mnt/data/HHCommon/hhsuite_dbs$ cd ..
dangmingai@PROTEIN:/mnt/data/HHCommon$ ks
ks: command not found
dangmingai@PROTEIN:/mnt/data/HHCommon$ ls
HHsearch hhomp hhsuite_dbs uniclust
dangmingai@PROTEIN:/mnt/data/HHCommon$ cd ..
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon I-TASSER SPARKS-X softwares
FALCONCommon ImageCommon lost+found
HHCommon RaptorXCommon original_databases
dangmingai@PROTEIN:/mnt/data$ cd FALCONCommon/
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP FALCON_softwares TrainingTestData
DSSP_series PDB_series hmmer
FALCON_databases SCOP_series uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd uniprot/
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot$ ls
bin release-2017_11 release-2018_03
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot$ cd bin
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot/bin$ ls
xml2fasta.py
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot/bin$ cd ,,
-bash: cd: ,,: No such file or directory
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot/bin$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot$ ls
bin release-2017_11 release-2018_03
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot$ cd release-2018_03/
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot/release-2018_03$ ls
md5sum uniref100.fasta uniref50.fasta uniref90.fasta
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot/release-2018_03$ vim md5sum
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot/release-2018_03$ ls
md5sum uniref100.fasta uniref50.fasta uniref90.fasta
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot/release-2018_03$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot$ ls
bin release-2017_11 release-2018_03
dangmingai@PROTEIN:/mnt/data/FALCONCommon/uniprot$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP FALCON_softwares TrainingTestData
DSSP_series PDB_series hmmer
FALCON_databases SCOP_series uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd TrainingTestData/
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData$ ls
12404_PDB25_Training_Data DeepFR PSICOV
CASP12 DeepThreader SCOPe-2.06
DeepCNF_SS_Training_Data EigenTHREADER
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData$ cd DeepFR
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR$ ls
Approaches LINDAHL Models Others SCOP_TEST
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR$ ls
Approaches LINDAHL Models Others SCOP_TEST
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR$ cd Models/
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR/Models$ ls
backup.20160901 backup.20160923 backup.20161214 backup.20170803
backup.20160911 backup.20161005 backup.20170408 databases
backup.20160920 backup.20161206 backup.20170620 fold.baseline
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR/Models$ x
x: command not found
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR/Models$ cd backup.201
-bash: cd: backup.201: No such file or directory
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR/Models$ cd backup.20160923
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR/Models/backup.20160923$ ls
caffemodel.family.1111test.bak
caffemodel.family.bak
caffemodel.fold.1111test.bak
caffemodel.fold.bak
caffemodel.superfamily.1111test.bak
caffemodel.superfamily.bak
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR/Models/backup.20160923$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR/Models$ ls
backup.20160901 backup.20160923 backup.20161214 backup.20170803
backup.20160911 backup.20161005 backup.20170408 databases
backup.20160920 backup.20161206 backup.20170620 fold.baseline
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR/Models$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR$ ls
Approaches LINDAHL Models Others SCOP_TEST
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData/DeepFR$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData$ ls
12404_PDB25_Training_Data DeepFR PSICOV
CASP12 DeepThreader SCOPe-2.06
DeepCNF_SS_Training_Data EigenTHREADER
dangmingai@PROTEIN:/mnt/data/FALCONCommon/TrainingTestData$ cd ..
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ ls
CASP FALCON_softwares TrainingTestData
DSSP_series PDB_series hmmer
FALCON_databases SCOP_series uniprot
dangmingai@PROTEIN:/mnt/data/FALCONCommon$ cd SCOP_series/
dangmingai@PROTEIN:/mnt/data/FALCONCommon/SCOP_series$ ls
astral pdbstyle scripts
dangmingai@PROTEIN:/mnt/data/FALCONCommon/SCOP_series$ cd astral/
dangmingai@PROTEIN:/mnt/data/FALCONCommon/SCOP_series/astral$ ls
scopeseq-2.06 scopseq-1.75
dangmingai@PROTEIN:/mnt/data/FALCONCommon/SCOP_series/astral$ cd scop-2.06
-bash: cd: scop-2.06: No such file or directory
dangmingai@PROTEIN:/mnt/data/FALCONCommon/SCOP_series/astral$ cd scopeseq-2.06/
dangmingai@PROTEIN:/mnt/data/FALCONCommon/SCOP_series/astral/scopeseq-2.06$ ls
astral-scopedom-seqres-gd-all-2.06-stable.fa fasta40
astral-scopedom-seqres-gd-sel-gs-bib-40-2.06.fa fasta70
astral-scopedom-seqres-gd-sel-gs-bib-70-2.06.fa fasta95
astral-scopedom-seqres-gd-sel-gs-bib-95-2.06.fa lists
fasta100 scope_list
dangmingai@PROTEIN:/mnt/data/FALCONCommon/SCOP_series/astral/scopeseq-2.06$ cd lists
dangmingai@PROTEIN:/mnt/data/FALCONCommon/SCOP_series/astral/scopeseq-2.06/lists$ ls
common list_fold repeat_fold
family.txt list_fold_test repeat_superfamily
filelist list_fold_train superfamily.txt
fold.txt list_label test_family.txt
identity_gt99 list_superfamily test_fold.txt
labellist list_superfamily_test test_superfamily.txt
labels list_superfamily_train train_family.txt
list_family list_test train_fold.txt
list_family_test list_train train_superfamily.txt
list_family_train repeat_family
dangmingai@PROTEIN:/mnt/data/FALCONCommon/SCOP_series/astral/scopeseq-2.06/lists$ cd /mnt
dangmingai@PROTEIN:/mnt$ ls
data home
dangmingai@PROTEIN:/mnt$ cd data
dangmingai@PROTEIN:/mnt/data$ ls
BLASTCommon I-TASSER SPARKS-X softwares
FALCONCommon ImageCommon lost+found
HHCommon RaptorXCommon original_databases
dangmingai@PROTEIN:/mnt/data$

workbench environment analysis----directly saved analysis after

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