I used to have issues with the pair99 program which have now been resolved. Now, the program stops at the wMUSTER step, where java throws a file not found error. Is the file supposed to be generated at a previous step? if so which one?
again, thank you for any help...
> ./runI-TASSER.pl -libdir ~/ITLIB/ -runstyle serial -seqname exmp1 -datadir ~/prot_struct_preds/alt_ryr2/ -java_home /usr
Your setting for running I-TASSER is:
-pkgdir = /home/sebastien/I-TASSER5.1
-libdir = /home/sebastien/ITLIB
-java_home = /usr
-seqname = exmp1
-datadir = /home/sebastien/prot_struct_preds/alt_ryr2
-outdir = /home/sebastien/prot_struct_preds/alt_ryr2
-runstyle = serial
-homoflag = real
-idcut = 1
-ntemp = 20
-nmodel = 5
-light = false
-hours = 50
-LBS = false
-EC = false
-GO = false
1. make seq.txt and rmsinp
Your protein contains 143 residues:
> exmp1
MYQLEKEPIVGAETFYVDGAANRETKLGKAGYVTNRGRQKVVTLTDTTNQKTELQAIYLA
LQDSGLEVNIVTDSQYALGIITQWIHNWKKRGWPVKNVDLVNQIIEQLIKKEKVYLAWVP
AHKGIGGNEQVDKLVSAGIRKVL
2.1 run Psi-blast
2.2 Predict secondary structure with PSSpred...
2.3 Predict solvent accessibility...
2.4 run pairmod
2.4.1 Use all templates
2.4.2 running pair ................
30000 6379375 total lib str & residues
number of observations 27.03459 1658491.
pair done
3.1 do threading
start serial threading PPAS
/tmp/sebastien/ITexmp1
/home/sebastien/prot_struct_preds/alt_ryr2/PPAS_exmp1
hostname: sebastien-GL553VD
starting time: Sun Aug 20 11:38:21 EDT 2017
pwd: /tmp/sebastien/ITexmp1
running zalign .....
ending time: Sun Aug 20 11:48:29 EDT 2017
start serial threading dPPAS
/tmp/sebastien/ITexmp1
/home/sebastien/prot_struct_preds/alt_ryr2/dPPAS_exmp1
hostname: sebastien-GL553VD
starting time: Sun Aug 20 11:48:31 EDT 2017
pwd: /tmp/sebastien/ITexmp1
running zalign .....
ending time: Sun Aug 20 12:11:19 EDT 2017
start serial threading dPPAS2
/tmp/sebastien/ITexmp1
/home/sebastien/prot_struct_preds/alt_ryr2/dPPAS2_exmp1
hostname: sebastien-GL553VD
starting time: Sun Aug 20 12:11:20 EDT 2017
pwd: /tmp/sebastien/ITexmp1
running zalign .....
ending time: Sun Aug 20 12:16:52 EDT 2017
start serial threading Env-PPAS
/tmp/sebastien/ITexmp1
/home/sebastien/prot_struct_preds/alt_ryr2/Env-PPAS_exmp1
hostname: sebastien-GL553VD
starting time: Sun Aug 20 12:16:53 EDT 2017
pwd: /tmp/sebastien/ITexmp1
running zalign .....
ending time: Sun Aug 20 12:37:17 EDT 2017
start serial threading MUSTER
/tmp/sebastien/ITexmp1
/home/sebastien/prot_struct_preds/alt_ryr2/MUSTER_exmp1
Illegal division by zero at /home/sebastien/prot_struct_preds/alt_ryr2/MUSTER_exmp1 line 599.
hostname: sebastien-GL553VD
starting time: Sun Aug 20 12:37:18 EDT 2017
pwd: /tmp/sebastien/ITexmp1
running Psi-blast .....
running zalign .....
start serial threading wPPAS
/tmp/sebastien/ITexmp1
/home/sebastien/prot_struct_preds/alt_ryr2/wPPAS_exmp1
hostname: sebastien-GL553VD
starting time: Sun Aug 20 12:39:50 EDT 2017
pwd: /tmp/sebastien/ITexmp1
running Psi-blast .....
ending time: Sun Aug 20 13:19:47 EDT 2017
start serial threading wdPPAS
/tmp/sebastien/ITexmp1
/home/sebastien/prot_struct_preds/alt_ryr2/wdPPAS_exmp1
hostname: sebastien-GL553VD
starting time: Sun Aug 20 13:19:49 EDT 2017
pwd: /tmp/sebastien/ITexmp1
running Psi-blast .....
ending time: Sun Aug 20 14:26:17 EDT 2017
start serial threading wMUSTER
/tmp/sebastien/ITexmp1
/home/sebastien/prot_struct_preds/alt_ryr2/wMUSTER_exmp1
Exception in thread "main" java.io.FileNotFoundException: seq.svr.psi (No such file or directory)
at java.io.FileInputStream.open0(java.base@9-internal/Native Method)
at java.io.FileInputStream.open(java.base@9-internal/FileInputStream.java:195)
at java.io.FileInputStream.(java.base@9-internal/FileInputStream.java:138)
at java.io.FileInputStream.(java.base@9-internal/FileInputStream.java:93)
at java.io.FileReader.(java.base@9-internal/FileReader.java:58)
at e.a(e.java)
at e.main(e.java)
Illegal division by zero at /home/sebastien/prot_struct_preds/alt_ryr2/wMUSTER_exmp1 line 570.
hostname: sebastien-GL553VD
starting time: Sun Aug 20 14:26:19 EDT 2017
pwd: /tmp/sebastien/ITexmp1
running Psi-blast .....
running Psi-blast .....
3.2 make restraints
missing some dat file after threading