Difference between revisions of "Task2 Hemochromatosis Protocol"

From Bioinformatikpedia
(→‎Blast)
(→‎PSI-Blast)
Line 15: Line 15:
 
BIG="/mnt/project/pracstrucfunc12/data/big"
  
BIG="/mnt/project/pracstrucfunc12/data/big"
 
 
−
time blastpgp -C $TSK/h002j2.pbp -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 2 -b 1250 -v 1250 -o $TSK/align/blastpgp_h0.002_j2_1250.out
 +
time blastpgp -C $TSK/h002j2.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 2 -b 10000 -m 8 -o $TSK/align2/blastpgp_h0.002_j2_10000.out
 
 
−
real 3m2.887s
 +
real 3m21.031s
−
user 2m38.360s
 +
user 2m44.750s
−
sys 0m5.900s
 +
sys 0m10.270s
 
 
−
time blastpgp -C $TSK/h002j10.pbp -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 10 -b 1250 -v 1250 -o $TSK/align/blastpgp_h0.002_j10_1250.out
 +
time blastpgp -C $TSK/h002j10.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 10 -b 10000 -m 8 -o $TSK/align2/blastpgp_h0.002_j10_10000.out
 
 
−
real 14m9.579s
 +
real 16m39.699s
−
user 13m22.190s
 +
user 14m22.150s
−
sys 0m16.200s
 +
sys 0m41.310s
 
 
−
time blastpgp -C $TSK/h10e-10j2.pbp -d $BIG/big_80 -i $TSK/Q30201.fasta -h 10e-10 -j 2 -b 1250 -v 1250 -o $TSK/align/blastpgp_h10e-10_j2_1250.out
 +
time blastpgp -C $TSK/h1e-10j2.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 1e-10 -j 2 -b 10000 -m 8 -o $TSK/align2/blastpgp_h1e-10_j2_10000.out
 
 
−
real 2m42.516s
 +
real 3m6.093s
−
user 2m38.380s
 +
user 2m48.260s
−
sys 0m2.540s
 +
sys 0m6.020s
 
 
−
time blastpgp -C $TSK/h10e-10j10.pbp -d $BIG/big_80 -i $TSK/Q30201.fasta -h 10e-10 -j 10 -b 1250 -v 1250 -o $TSK/align/blastpgp_h10e-10_j10_1250.out
 +
time blastpgp -C $TSK/h1e-10j10.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 1e-10 -j 10 -b 10000 -m 8 -o $TSK/align2/blastpgp_h1e-10_j10_10000.out
 
 
−
real 11m23.359s
 +
real 16m41.797s
−
user 11m11.340s
 +
user 15m18.350s
−
sys 0m8.770s
 +
sys 0m28.890s
  +
  +
time blastpgp -R $TSK/h002j2.chk -d $BIG/big -i $TSK/Q30201.fasta -h 0.002 -j 2 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h0.002_j2_100000.out
  +
  +
real 28m17.459s
  +
user 18m26.930s
  +
sys 2m46.200s
  +
  +
time blastpgp -R $TSK/h002j10.chk -d $BIG/big -i $TSK/Q30201.fasta -h 0.002 -j 10 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h0.002_j10_100000.out
  +
  +
real 367m15.021s (srsly...)
  +
user 310m31.210s
  +
sys 14m39.460s
  +
...and some thousand "[blastpgp] ERROR: ncbiapi [000.000] ObjMgrNextAvailEntityID failed with idx 2048" messages
  +
  +
time blastpgp -R $TSK/h1e-10j2.chk -d $BIG/big -i $TSK/Q30201.fasta -h 1e-10 -j 2 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h1e-10_j2_100000.out
  +
  +
real 26m43.350s
  +
user 19m54.380s
  +
sys 2m3.900s
  +
  +
time blastpgp -R $TSK/h1e-10j10.chk -d $BIG/big -i $TSK/Q30201.fasta -h 1e-10 -j 10 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h1e-10_j10_100000.out
  +
  +
real 64m4.575s
  +
user 47m16.970s
  +
sys 4m54.890s
  +
...and some thousand "[blastpgp] ERROR: ncbiapi [000.000] ObjMgrNextAvailEntityID failed with idx 2048" messages
   
 
=== HHblits ===
  
=== HHblits ===

Revision as of 15:24, 6 May 2012

Sequence Searches

Blast

TSK="/mnt/home/student/bernhoferm/task2"
BIG="/mnt/project/pracstrucfunc12/data/big"

time blastall -p blastp -d $BIG/big_80 -i $TSK/Q30201.fasta -b 1500 -m 8 -o $TSK/align2/blast_default_1500.out

real	1m24.100s
user	1m5.950s
sys	0m3.500s

PSI-Blast

TSK="/mnt/home/student/bernhoferm/task2"
BIG="/mnt/project/pracstrucfunc12/data/big"

time blastpgp -C $TSK/h002j2.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 2 -b 10000 -m 8 -o $TSK/align2/blastpgp_h0.002_j2_10000.out

real	3m21.031s
user	2m44.750s
sys	0m10.270s

time blastpgp -C $TSK/h002j10.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 0.002 -j 10 -b 10000 -m 8 -o $TSK/align2/blastpgp_h0.002_j10_10000.out

real	16m39.699s
user	14m22.150s
sys	0m41.310s

time blastpgp -C $TSK/h1e-10j2.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 1e-10 -j 2 -b 10000 -m 8 -o $TSK/align2/blastpgp_h1e-10_j2_10000.out

real	3m6.093s
user	2m48.260s
sys	0m6.020s

time blastpgp -C $TSK/h1e-10j10.chk -d $BIG/big_80 -i $TSK/Q30201.fasta -h 1e-10 -j 10 -b 10000 -m 8 -o $TSK/align2/blastpgp_h1e-10_j10_10000.out

real	16m41.797s
user	15m18.350s
sys	0m28.890s

time blastpgp -R $TSK/h002j2.chk -d $BIG/big -i $TSK/Q30201.fasta -h 0.002 -j 2 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h0.002_j2_100000.out

real	28m17.459s
user	18m26.930s
sys	2m46.200s

time blastpgp -R $TSK/h002j10.chk -d $BIG/big -i $TSK/Q30201.fasta -h 0.002 -j 10 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h0.002_j10_100000.out

real	367m15.021s (srsly...)
user	310m31.210s
sys	14m39.460s
...and some thousand "[blastpgp] ERROR: ncbiapi [000.000]  ObjMgrNextAvailEntityID failed with idx 2048" messages

time blastpgp -R $TSK/h1e-10j2.chk -d $BIG/big -i $TSK/Q30201.fasta -h 1e-10 -j 2 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h1e-10_j2_100000.out

real	26m43.350s
user	19m54.380s
sys	2m3.900s

time blastpgp -R $TSK/h1e-10j10.chk -d $BIG/big -i $TSK/Q30201.fasta -h 1e-10 -j 10 -b 100000 -m 8 -o $TSK/align2/blastpgp_big_h1e-10_j10_100000.out

real	64m4.575s
user	47m16.970s
sys	4m54.890s
...and some thousand "[blastpgp] ERROR: ncbiapi [000.000]  ObjMgrNextAvailEntityID failed with idx 2048" messages

HHblits

TSK="/mnt/home/student/bernhoferm/task2"

time hhblits -d /mnt/project/pracstrucfunc12/data/hhblits/uniprot20_current -i $TSK/Q30201.fasta -Z 600 -B 600 -o $TSK/align/hhblits_default_600.out

real	20m46.643s
user	5m41.040s
sys	2m43.670s

MSA

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