For quick setup and methods testing, simply run install.py with the -nopicking option.
This bypasses installation of the VALL and genome databases and greatly reduces the size (and time) of the installation.
Hello, I have install the cs-rosetta. When I run the command pick_fragments -cs ntd_trim.tab >& pick.log, I got following errors in log file and no fragment files generated.
Expecting TALOS VERSION: post_2012
Command: bash talos.script
Finished running command: bash talos.script
Error: expected creation of ntd_trim.fasta.talos/predSS.tab after running 'bash talos.script'!
Command: /data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4
/data2/csrosetta3/frag_picker/blast/bin/blastpgp: 1: ELF: not found
/data2/csrosetta3/frag_picker/blast/bin/blastpgp: 1: @@*g@8: not found
/data2/csrosetta3/frag_picker/blast/bin/blastpgp: 2: Syntax error: ")" unexpected
Couldn't open ntd_trim.fasta.chk for reading.
Finished running command: /data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4
Error: expected creation of ntd_trim.fasta.chk after running '/data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4'!
---------------------------------------------------------------------------
--------- CS-Rosetta 3.0 (toolbox) -----------
----- -----
-- website: www.csrosetta.org --
-- copyright: Oliver Lange --
-- Reference: Lange et al. PNAS 2012, --
-- www.pnas.org/cgi/doi/10.1073/pnas.1203013109 --
-- --
-- program name: pick_fragments --
-- --
----- -----
-------- -------
---------------------------------------------------------------------------
Run TALOS+...
the flag -nohom should be enough do remove these sequences, but there is currently a bug in the fragment picker, which will be removed with the next release.
For now some useful commands to check and remove manually:
The file t000_.fasta.homologous is already generated by the fragment picker and should be found in the directory with your fragments:
write the following lines to a script: 'homs_grep.sh'
#!/bin/bash
frags=$1
homs=$2
cat $frags | gunzip | egrep "$( cat $homs | awk '{print $NF}' | sed 's/\(....\)\(.\)/\1 \2/ ' | awk '{printf("%s\\ %s|",$1,$2)}' | sed 's/|$//' )" | cut -f 2 -d " " | uniq
# then this command shows you the homologous that still appear in your fragments.
$ hom_grep.sh t000_.fasta.frags9.gz t000_.fasta.homologous
write the following lines to a script 'remove_homs.sh'
#!/bin/bash
frags=$1
homs=$2
cat $frags | gunzip | egrep -v "$( cat $homs | awk '{print $NF}' | sed 's/\(....\)\(.\)/\1 \2/ ' | awk '{printf("%s\\ %s|",$1,$2)}' | sed 's/|$//' )" | gzip > $(basename $frags .gz)_nohom.gz
# then this command should generate a new fragment file without any homs
$ remove_homs.sh 000_.fasta.frags9.gz t000_.fasta.homologous
This problem can arise when the input .tab file is in a different format than expected. Please see the File formats under CS Rosetta Manual
Hi,
The (Re-)Scoring of Structures link is now updated.
For quick setup and methods testing, simply run install.py with the -nopicking option.
This bypasses installation of the VALL and genome databases and greatly reduces the size (and time) of the installation.
Chemical shift-based fragments can be also made using the Robetta Fragment Server:
http://robetta.bakerlab.org/fragmentsubmit.jsp
Hello, I have install the cs-rosetta. When I run the command pick_fragments -cs ntd_trim.tab >& pick.log, I got following errors in log file and no fragment files generated.
Expecting TALOS VERSION: post_2012
Command: bash talos.script
Finished running command: bash talos.script
Error: expected creation of ntd_trim.fasta.talos/predSS.tab after running 'bash talos.script'!
Command: /data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4
/data2/csrosetta3/frag_picker/blast/bin/blastpgp: 1: ELF: not found
/data2/csrosetta3/frag_picker/blast/bin/blastpgp: 1: @@*g@8: not found
/data2/csrosetta3/frag_picker/blast/bin/blastpgp: 2: Syntax error: ")" unexpected
Couldn't open ntd_trim.fasta.chk for reading.
Finished running command: /data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4
Error: expected creation of ntd_trim.fasta.chk after running '/data2/csrosetta3/frag_picker/blast/bin/blastpgp -t T -i ntd_trim.fasta -F F -j2 -o ntd_trim.fasta.blast -d /data2/csrosetta3/frag_picker/genomes//nr -v10000 -b10000 -K1000 -h0.0009 -e0.0009 -C ntd_trim.fasta.chk -Q ntd_trim.fasta.pssm -a4'!
---------------------------------------------------------------------------
--------- CS-Rosetta 3.0 (toolbox) -----------
----- -----
-- website: www.csrosetta.org --
-- copyright: Oliver Lange --
-- Reference: Lange et al. PNAS 2012, --
-- www.pnas.org/cgi/doi/10.1073/pnas.1203013109 --
-- --
-- program name: pick_fragments --
-- --
----- -----
-------- -------
---------------------------------------------------------------------------
Run TALOS+...
Anyone can help? Thanks,
Xiaogang
Hi Brinda,
the flag -nohom should be enough do remove these sequences, but there is currently a bug in the fragment picker, which will be removed with the next release.
For now some useful commands to check and remove manually:
The file t000_.fasta.homologous is already generated by the fragment picker and should be found in the directory with your fragments:
write the following lines to a script: 'homs_grep.sh'
#!/bin/bash
frags=$1
homs=$2
cat $frags | gunzip | egrep "$( cat $homs | awk '{print $NF}' | sed 's/\(....\)\(.\)/\1 \2/ ' | awk '{printf("%s\\ %s|",$1,$2)}' | sed 's/|$//' )" | cut -f 2 -d " " | uniq
# then this command shows you the homologous that still appear in your fragments.
$ hom_grep.sh t000_.fasta.frags9.gz t000_.fasta.homologous
write the following lines to a script 'remove_homs.sh'
#!/bin/bash
frags=$1
homs=$2
cat $frags | gunzip | egrep -v "$( cat $homs | awk '{print $NF}' | sed 's/\(....\)\(.\)/\1 \2/ ' | awk '{printf("%s\\ %s|",$1,$2)}' | sed 's/|$//' )" | gzip > $(basename $frags .gz)_nohom.gz
# then this command should generate a new fragment file without any homs
$ remove_homs.sh 000_.fasta.frags9.gz t000_.fasta.homologous