Hi,
I installed the stand alone version of the I-TASSER version 5.1 and all the libraries using the perl script provided without any problem.
Everything seems to run smoothly until it reaches the last step Step 7 where some errors are found when trying to copy some files in Fortran.
The command I am running:
/home/ubuntu/I-TASSER5.1/I-TASSERmod/runI-TASSER.pl -libdir /home/ubuntu/ITLIB -seqname etramp5 -datadir /home/ubuntu/etramp -runstyle gnuparallel -homoflag benchmark -idcut 0.3 -LBS true -EC true -GO true -java_home /usr/ -outdir /home/ubuntu/etramp_out/
The FASTA file:
>etramp5
MRFSKVFSFFAFFIALKYFNRCLGDQLDMGSVHNNNSVVGNSSSHSPSSSSSSPSSSSSSSSSSPSASSSSSSSSPASSS
SSPSSTSDDSKNASLDKIDEELQKKKKNEKLLLISSIATGLAVLVGGIIGTALYASRKSSKACKNNVDDLDSDVEEADVT
EESAVETKKDEVKTEEPKKEQ
The output with the errors in the screen:
....
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5.1 do clustering
No. of trajectory files: 54
8.000000 3.500000 12.00000
5.2 build full-atomic model
6 Estimate local accuracy of models and B-factor
7 run COACH to predict function: Ligand-binding site,EC number,GO terms...
/home/ubuntu/I-TASSER5.1/I-TASSERmod/runCOACH.pl -pkgdir /home/ubuntu/I-TASSER5.1 -libdir /home/ubuntu/ITLIB -runstyle gnuparallel -protname etramp5 -model model1.pdb -datadir /home/ubuntu/etramp -homoflag benchmark -idcut 0.3 -LBS true -EC true -GO true
Useless use of /d modifier in transliteration operator at /tmp/ubuntu/JSD_qury/parse_blast.pl line 314.
Academic tradition requires you to cite works you base your article on.
When using programs that use GNU Parallel to process data for publication
please cite:
O. Tange (2011): GNU Parallel - The Command-Line Power Tool,
;login: The USENIX Magazine, February 2011:42-47.
This helps funding further development; AND IT WON'T COST YOU A CENT.
If you pay 10000 EUR you should feel free to use GNU Parallel without citing.
To silence this citation notice: run 'parallel --citation'.
[blastpgp] WARNING: [000.000] posPurgeMatches: Due to purging near identical sequences, only the query is used to construct the position-specific score matrix
cp: cannot stat '/home/ubuntu/ITLIB/GO/MTX/2x4jA.mtx': No such file or directory
cp: cannot stat '/home/ubuntu/ITLIB/GO/PRF/2x4jA.prf': No such file or directory
At line 553 of file PRTMalign.f
Fortran runtime error: No such file or directory
cp: cannot stat '/home/ubuntu/ITLIB/GO/MTX/4f7aA.mtx': No such file or directory
cp: cannot stat '/home/ubuntu/ITLIB/GO/PRF/4f7aA.prf': No such file or directory
At line 553 of file PRTMalign.f
Fortran runtime error: No such file or directory
cp: cannot stat '/home/ubuntu/ITLIB/GO/MTX/5f21B.mtx': No such file or directory
cp: cannot stat '/home/ubuntu/ITLIB/GO/PRF/5f21B.prf': No such file or directory
At line 553 of file PRTMalign.f
Fortran runtime error: No such file or directory
At line 146 of file PRTMalign.f
Fortran runtime error: No such file or directory
Useless use of /d modifier in transliteration operator at ./parse_blast.pl line 314.
16070.70user 3053.68system 2:37:35elapsed 202%CPU (0avgtext+0avgdata 3588732maxresident)k
0inputs+1071904outputs (0major+483520186minor)pagefaults 0swaps
The input folder when the run stopped:
./
./profile_etramp5
./rep3.tra4M.bz2
./in1M.dd
./in3M.dd
./out5M
./rep4.tra1A.bz2
./rep2.tra3M.bz2
./rep3.tra1A.bz2
./out4M
./combo7.pdb
./closc7.pdb
./COACH_gnuparallel.sh
./exclude.lst
./rep1.tra1A.bz2
./cluster_CH.pl
./rep2.tra8M.bz2
./cscore
./init.wPPAS.old
./combo1.pdb
./PPAS_etramp5
./rep5.tra6A.bz2
./etramp5sim_3M
./dPPAS_etramp5
./g_template_0.3.lst
./JSD.dat
./rep3.tra6A.bz2
./in6A.dd
./rep4.tra5A.bz2
./Env-PPAS_etramp5
./etramp5sim_5A
./init.dPPAS2.old
./closc2.pdb
./threading_gnuparallel.sh
./rep1.tra3A.bz2
./rep1.tra4M.bz2
./fulinit.pdb
./rep4.tra4A.bz2
./rep4.tra6A.bz2
./in5A.dd
./Temlate_model1.score
./rep2.tra4M.bz2
./out2M
./rep3.tra2M.bz2
./init.wPPAS
./combo6.pdb
./rep2.tra2M.bz2
./combo10.pdb
./closc3.pdb
./JSD.pl
./str.txt
./rep5.tra3A.bz2
./etramp5sim_6A
./mtx
./wdPPAS_etramp5
./init.wdPPAS
./seq.ss
./out7M
./combo9.pdb
./in1A.dd
./model1.pdb
./lscore.txt
./rep3.tra7M.bz2
./out2A
./init.wMUSTER.old
./comb8CA.dat
./rep3.tra3M.bz2
./rep5.tra4A.bz2
./rep1.tra3M.bz2
./closc10.pdb
./out_COACH_model1
./in8M.dd
./out8M
./rep2.tra7M.bz2
./combo8.pdb
./rep3.tra5M.bz2
./seq.txt
./closc8.pdb
./out3A
./seq.fasta
./init.PPAS.old
./model5.pdb
./PDBsearchresult_model1.dat
./out5A
./etramp5sim_8M
./rep3.tra1M.bz2
./closc1.pdb
./out1A
./tra.in
./MUSTER_etramp5
./init.MUSTER.old
./PRF_etramp5
./etramp5sim_5M
./etramp5sim_6M
./rep2.tra1A.bz2
./out6M
./blast.out
./init.Env-PPAS
./rep4.tra2A.bz2
./init.dat
./combo4.pdb
./wPPAS_etramp5
./rep2.tra3A.bz2
./rep1.tra8M.bz2
./rep3.tra8M.bz2
./rep1.tra5M.bz2
./etramp5sim_1M
./model4.pdb
./JSD_coach.dat
./closc4.pdb
./etramp5sim_4A
./in2A.dd
./etramp5sim_3A
./etramp5sim_7M
./rep3.tra2A.bz2
./rep2.tra5M.bz2
./rmsinp
./in3A.dd
./init.dPPAS
./in6M.dd
./pair1.dat
./rep2.tra2A.bz2
./rep3.tra5A.bz2
./model1
./model1/tmsite
./model1/tmsite/complex3.pdb
./model1/tmsite/Bsites_prob.dat
./model1/tmsite/complex2.pdb
./model1/tmsite/Bsites_single.dat
./model1/tmsite/complex2_1zytA_BS03_HED.pdb
./model1/tmsite/pocket.dat
./model1/tmsite/Bsites_lig.clr
./model1/tmsite/Bsites.dat
./model1/tmsite/Bsites.clr
./model1/tmsite/TM_etramp5_model1.pl
./model1/tmsite/templates.inf
./model1/tmsite/complex1.pdb
./model1/tmsite/complex1_1li3A_BS01_3CH.pdb
./model1/tmsite/complex3_3gupA_BS02_CO3.pdb
./model1/tmsite/selected_templates.lst
./model1/cofactor
./model1/cofactor/GOsearchresult_model1_CC.dat
./model1/cofactor/CF_etramp5_model1.pl
./model1/cofactor/GOsearchresult_model1_MF.dat
./model1/cofactor/model1.pdb
./model1/cofactor/GOsearchresult_model1.dat
./model1/cofactor/ECsearchresult_model1.dat
./model1/cofactor/GOlocal_model1.dat
./model1/cofactor/similarpdb_model1.lst
./model1/cofactor/GOsearchresult_model1_BP.dat
./model1/cofactor/status_report
./model1/cofactor/BSITE_model1
./model1/cofactor/BSITE_model1/complex3.pdb
./model1/cofactor/BSITE_model1/Bsites_prob.dat
./model1/cofactor/BSITE_model1/complex2.pdb
./model1/cofactor/BSITE_model1/complex4.pdb
./model1/cofactor/BSITE_model1/Bpockets_model1.dat
./model1/cofactor/BSITE_model1/process.lst
./model1/cofactor/BSITE_model1/Bsites_model1.dat
./model1/cofactor/BSITE_model1/record.dat
./model1/cofactor/BSITE_model1/complex1.pdb
./model1/cofactor/BSITE_model1/selected_templates.lst
./model1/cofactor/EClocal_model1.dat
./model1/cofactor/PDBsearchresult_ext_model1.dat
./model1/coach
./model1/coach/CH_CF_1c6aA_BS02_KR.pdb
./model1/coach/Bsites_prob.dat
./model1/coach/CH_complex2.pdb
./model1/coach/GO_BP.dat
./model1/coach/CH_protein.pdb
./model1/coach/CH_TM_3gupA_BS02_CO3.pdb
./model1/coach/CH_complex7.pdb
./model1/coach/Bsites.inf
./model1/coach/GO_MF.dat
./model1/coach/CH_complex4.pdb
./model1/coach/CH_complex3.pdb
./model1/coach/EC.dat
./model1/coach/CH_CF_2ou8A_BS01_MTN.pdb
./model1/coach/CH_TM_1li3A_BS01_3CH.pdb
./model1/coach/Bsites.dat
./model1/coach/GO_CC.dat
./model1/coach/CH_etramp5_model1.pl
./model1/coach/CH_TM_6lzmA_BS02_BME.pdb
./model1/coach/CH_complex1.pdb
./model1/coach/Bsites.clr
./model1/coach/templates_all.dat
./comb.dat
./wMUSTER_etramp5
./rst.dat
./init.dPPAS2
./rep3.tra4A.bz2
./rep1.tra7M.bz2
./pssm.txt
./psitmp.chk
./rep3.tra3A.bz2
./rep5.tra1A.bz2
./BFP.dat
./in4M.dd
./rep1.tra1M.bz2
./protein.mtx
./in2M.dd
./combo5.pdb
./combCA.dat
./remc_gnuparallel.sh
./in4A.dd
./model3.pdb
./rep3.tra6M.bz2
./distL.dat
./rep1.tra5A.bz2
./out3M
./dPPAS2_etramp5
./etramp5sim_4M
./SOP.dat
./init.Env-PPAS.old
./rep4.tra3A.bz2
./closc5.pdb
./out1M
./init.dPPAS.old
./rep5.tra5A.bz2
./out6A
./init.PPAS
./etramp5sim_1A
./init.wMUSTER
./ncaco.pdb
./rep5.tra2A.bz2
./init.wdPPAS.old
./closc9.pdb
./rep1.tra2A.bz2
./rep1.tra2M.bz2
./dist.dat
./closc6.pdb
./runpair.sh
./etramp5sim_2A
./in5M.dd
./exp.dat
./pair3.dat
./rep1.tra6A.bz2
./rep1.tra6M.bz2
./rep2.tra5A.bz2
./rep1.tra4A.bz2
./rep2.tra1M.bz2
./combo2.pdb
./ssite
./ssite/Bsites_prob_fpt.dat
./ssite/Bsites_fpt.clr
./ssite/Bsites_dis.clr
./ssite/SS_etramp5.pl
./ssite/Bsites_prob_dis.dat
./ssite/Bsites_fpt.dat
./ssite/Bsites_dis.dat
./ssite/sresult.dat
./combo3.pdb
./protein.prf
./in7M.dd
./seq.dat
./etramp5sim_2M
./rep2.tra6M.bz2
./par.dat
./init.MUSTER
./rep2.tra4A.bz2
./rep2.tra6A.bz2
./out4A
./model2.pdb
And the output folder as of the end of the run:
./
./rep3.tra4M.bz2
./rep4.tra1A.bz2
./rep2.tra3M.bz2
./rep3.tra1A.bz2
./rep1.tra1A.bz2
./rep2.tra8M.bz2
./cscore
./init.wPPAS.old
./rep5.tra6A.bz2
./rep3.tra6A.bz2
./rep4.tra5A.bz2
./init.dPPAS2.old
./rep1.tra3A.bz2
./rep1.tra4M.bz2
./rep4.tra4A.bz2
./rep4.tra6A.bz2
./rep2.tra4M.bz2
./rep3.tra2M.bz2
./init.wPPAS
./rep2.tra2M.bz2
./rep5.tra3A.bz2
./init.wdPPAS
./seq.ss
./model1.pdb
./lscore.txt
./rep3.tra7M.bz2
./init.wMUSTER.old
./rep3.tra3M.bz2
./rep5.tra4A.bz2
./rep1.tra3M.bz2
./rep2.tra7M.bz2
./rep3.tra5M.bz2
./seq.fasta
./init.PPAS.old
./model5.pdb
./rep3.tra1M.bz2
./init.MUSTER.old
./rep2.tra1A.bz2
./init.Env-PPAS
./rep4.tra2A.bz2
./init.dat
./rep2.tra3A.bz2
./rep1.tra8M.bz2
./rep3.tra8M.bz2
./rep1.tra5M.bz2
./model4.pdb
./rep3.tra2A.bz2
./rep2.tra5M.bz2
./init.dPPAS
./rep2.tra2A.bz2
./rep3.tra5A.bz2
./model1
./model1/tmsite
./model1/tmsite/complex3.pdb
./model1/tmsite/complex2.pdb
./model1/tmsite/complex2_1zytA_BS03_HED.pdb
./model1/tmsite/Bsites.dat
./model1/tmsite/Bsites.clr
./model1/tmsite/complex1.pdb
./model1/tmsite/complex1_1li3A_BS01_3CH.pdb
./model1/tmsite/complex3_3gupA_BS02_CO3.pdb
./model1/cofactor
./model1/cofactor/GOsearchresult_model1_CC.dat
./model1/cofactor/GOsearchresult_model1_MF.dat
./model1/cofactor/GOsearchresult_model1.dat
./model1/cofactor/ECsearchresult_model1.dat
./model1/cofactor/similarpdb_model1.lst
./model1/cofactor/GOsearchresult_model1_BP.dat
./model1/cofactor/BSITE_model1
./model1/cofactor/BSITE_model1/complex3.pdb
./model1/cofactor/BSITE_model1/Bsites_prob.dat
./model1/cofactor/BSITE_model1/complex2.pdb
./model1/cofactor/BSITE_model1/complex4.pdb
./model1/cofactor/BSITE_model1/Bpockets_model1.dat
./model1/cofactor/BSITE_model1/Bsites_model1.dat
./model1/cofactor/BSITE_model1/complex1.pdb
./model1/coach
./model1/coach/CH_CF_1c6aA_BS02_KR.pdb
./model1/coach/CH_complex2.pdb
./model1/coach/GO_BP.dat
./model1/coach/CH_protein.pdb
./model1/coach/CH_TM_3gupA_BS02_CO3.pdb
./model1/coach/CH_complex7.pdb
./model1/coach/Bsites.inf
./model1/coach/GO_MF.dat
./model1/coach/CH_complex4.pdb
./model1/coach/CH_complex3.pdb
./model1/coach/EC.dat
./model1/coach/CH_CF_2ou8A_BS01_MTN.pdb
./model1/coach/CH_TM_1li3A_BS01_3CH.pdb
./model1/coach/Bsites.dat
./model1/coach/GO_CC.dat
./model1/coach/CH_TM_6lzmA_BS02_BME.pdb
./model1/coach/CH_complex1.pdb
./model1/coach/Bsites.clr
./rst.dat
./init.dPPAS2
./rep3.tra4A.bz2
./rep1.tra7M.bz2
./rep3.tra3A.bz2
./rep5.tra1A.bz2
./rep1.tra1M.bz2
./model3.pdb
./rep3.tra6M.bz2
./rep1.tra5A.bz2
./init.Env-PPAS.old
./rep4.tra3A.bz2
./init.dPPAS.old
./rep5.tra5A.bz2
./init.PPAS
./init.wMUSTER
./rep5.tra2A.bz2
./init.wdPPAS.old
./rep1.tra2A.bz2
./rep1.tra2M.bz2
./exp.dat
./rep1.tra6A.bz2
./rep1.tra6M.bz2
./rep2.tra5A.bz2
./rep1.tra4A.bz2
./rep2.tra1M.bz2
./ssite
./ssite/Bsites_prob_fpt.dat
./ssite/Bsites_fpt.clr
./ssite/Bsites_dis.clr
./ssite/Bsites_prob_dis.dat
./ssite/Bsites_fpt.dat
./ssite/Bsites_dis.dat
./rep2.tra6M.bz2
./init.MUSTER
./rep2.tra4A.bz2
./rep2.tra6A.bz2
./model2.pdb
I would appreciate some help if possible as I am not sure what is actually going wrong.
Regards,
Ernest Diez Benavente
Research Fellow
London School of Hygiene and Tropical Medicine