Tim Sackton tsackton
tsackton
/ gist:6c1b024ddee18196e52cfc79e304d77e
Created
April 21, 2016 11:23
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <?xml version="1.0" ?> | |
| <multi_cactus inputSequences="/scratch1/tsackton/merged_aligns/refGenomes/croPor.fa /scratch1/tsackton/merged_aligns/refGenomes/gavGan.fa /scratch1/tsackton/merged_aligns/refGenomes/allSin.fa /scratch1/tsackton/merged_aligns/refGenomes/allMis.fa /scratch1/tsackton/merged_aligns/refGenomes/cheMyd.fa /scratch1/tsackton/merged_aligns/refGenomes/chrPic.fa /scratch1/tsackton/merged_aligns/refGenomes/pelSin.fa /scratch1/tsackton/merged_aligns/refGenomes/apaSpi.fa /scratch1/tsackton/merged_aligns/refGenomes/anoCar.fa /scratch1/tsackton/merged_aligns/refGenomes/thaSir.fa /scratch1/tsackton/merged_aligns/refGenomes/pytBiv.fa /scratch1/tsackton/merged_aligns/refGenomes/homSap.fa /scratch1/tsackton/merged_aligns/refGenomes/musMus.fa /scratch1/tsackton/merged_aligns/refGenomes/canLup.fa /scratch1/tsackton/merged_aligns/refGenomes/monDom.fa /scratch1/tsackton/merged_aligns/refGenomes/ornAna.fa /scratch1/tsackton/merged_aligns/refGenomes/xenTro.fa /scratch1/tsackton/merged_aligns/refGenomes/tetNig.fa |
tsackton
/ cactus2hal-error
Created
April 21, 2016 11:23
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| [tsackton@bioinf02 newRatite]$ cat cactus2hal.log | |
| real 32m6.430s | |
| user 31m7.563s | |
| sys 0m54.729s | |
| hal exception caught: Fatal Tree error. converter does not support adding more than one non-leaf:birdAnc06 | |
| real 7m33.713s | |
| user 7m11.973s | |
| sys 0m17.987s |
tsackton
/ Anc08_outgroup.xml
Created
April 19, 2016 00:38
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <?xml version="1.0" ?> | |
| <cactus_workflow_experiment config="/scratch1/tsackton/merged_aligns/eggDir/eggDir/progressiveAlignment/Anc08/Anc08_config.xml" outgroup_events="chrPic anoCar Anc06" outputSequenceDir="./eggDir/sequenceData" sequences="./eggDir/sequenceData/birdAnc.fa_0 /scratch1/tsackton/merged_aligns/eggDir/eggDir/progressiveAlignment/Anc12/Anc12.fa ./eggDir/sequenceData/chrPic.fa_6 ./eggDir/sequenceData/anoCar.fa_9 /scratch1/tsackton/merged_aligns/eggDir/eggDir/progressiveAlignment/Anc06/Anc06.fa" species_tree="(birdAnc:0.2381837697,Anc12:0.2052405704,chrPic:0.18022916961,anoCar:2.02848586505,Anc06:2.02848586505)Anc08;"> | |
| <cactus_disk> | |
| <st_kv_database_conf type="kyoto_tycoon"> | |
| <kyoto_tycoon database_dir="/scratch1/tsackton/merged_aligns/eggDir/eggDir/progressiveAlignment/Anc08/Anc08/Anc08_DB" database_name="Anc08.kch" in_memory="1" port="1987" snapshot="0"/> | |
| </st_kv_database_conf> | |
| </cactus_disk> | |
| <reference path="/scratch1/tsackton/merged_aligns/eggDir/eggDir/progressiveAlignment/Anc08/Anc08. |
tsackton
/ birdAnc.xml
Created
April 19, 2016 00:36
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <?xml version="1.0" ?> | |
| <cactus_workflow_experiment config="/scratch1/tsackton/merged_aligns/ratiteDir/progressiveAlignment/Anc03/Anc03_config.xml" outgroup_events="chrPic allMis anoCar" outputSequenceDir="./ratiteDir/sequenceData" sequences="/scratch1/tsackton/merged_aligns/ratiteDir/progressiveAlignment/Anc05/Anc05.fa /scratch1/tsackton/merged_aligns/ratiteDir/progressiveAlignment/Anc06/Anc06.fa ./ratiteDir/sequenceData/chrPic.fa_39 ./ratiteDir/sequenceData/allMis.fa_35 ./ratiteDir/sequenceData/anoCar.fa_41" species_tree="(birdAnc05:0.0575233,birdAnc06:0.0677528,chrPic:0.418413,allMis:0.4696778,anoCar:1.1811839)birdAnc;"> | |
| <cactus_disk> | |
| <st_kv_database_conf type="kyoto_tycoon"> | |
| <kyoto_tycoon database_dir="/scratch1/tsackton/merged_aligns/ratiteDir/progressiveAlignment/Anc03/Anc03/Anc03_DB" database_name="Anc03.kch" in_memory="1" port="1992" snapshot="0"/> | |
| </st_kv_database_conf> | |
| </cactus_disk> | |
| <reference path="/scratch1/tsackton/merged_aligns/ratiteDir/progressiveAlignment/Anc03/Anc03.fa"/> | |
| <hal fas |
tsackton
/ merged_alignment.xl
Created
April 19, 2016 00:28
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| <?xml version="1.0" ?> | |
| <multi_cactus inputSequences="/scratch1/tsackton/merged_aligns/refGenomes/croPor.fa /scratch1/tsackton/merged_aligns/refGenomes/gavGan.fa /scratch1/tsackton/merged_aligns/refGenomes/allSin.fa /scratch1/tsackton/merged_aligns/refGenomes/allMis.fa /scratch1/tsackton/merged_aligns/refGenomes/cheMyd.fa /scratch1/tsackton/merged_aligns/refGenomes/chrPic.fa /scratch1/tsackton/merged_aligns/refGenomes/pelSin.fa /scratch1/tsackton/merged_aligns/refGenomes/apaSpi.fa /scratch1/tsackton/merged_aligns/refGenomes/anoCar.fa /scratch1/tsackton/merged_aligns/refGenomes/thaSir.fa /scratch1/tsackton/merged_aligns/refGenomes/pytBiv.fa /scratch1/tsackton/merged_aligns/refGenomes/homSap.fa /scratch1/tsackton/merged_aligns/refGenomes/musMus.fa /scratch1/tsackton/merged_aligns/refGenomes/canLup.fa /scratch1/tsackton/merged_aligns/refGenomes/monDom.fa /scratch1/tsackton/merged_aligns/refGenomes/ornAna.fa /scratch1/tsackton/merged_aligns/refGenomes/xenTro.fa /scratch1/tsackton/merged_aligns/refGenomes/tetNig.fa |
tsackton
/ sra_test.fq
Created
May 5, 2015 16:00
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| @SRR488565.1 HWI-ST344_0078:1:1101:1204:2041 length=100 | |
| GATGAACTTGTGTGCATGGTAGAGCAGCCGCTGTGCACTCTTGCTGAGTGGGATATCTGAGGATGTTGGAGAGAGCTGGAGATACTGTAGGAGCCTGTAG | |
| +SRR488565.1 HWI-ST344_0078:1:1101:1204:2041 length=100 | |
| GGGGDGGGFGGGFFGGGFGDFGEGGGGGGGGGGDGGGEGGFGG@FFDEEGGGBGB?DEGDFG>EGCFFF??5<739:>99EBC=EFGDDFFEF?GDDA?D | |
| @SRR488565.2 HWI-ST344_0078:1:1101:1191:2067 length=100 | |
| CCTGGTGTTAAGGTTAATTGGTTGTAGACTGCAGTGGTTTATCACGCTATGCACACTATGAGAAACGTTTATTAAATTGACTTTTGTTTTGTTTCTTTAA | |
| +SRR488565.2 HWI-ST344_0078:1:1101:1191:2067 length=100 | |
| GGGGFEGGGEFGGDGGFGGGGBGGDGGGGBGGEFFGG3FFEECDEFDBGGD:EFFGFGFEEFDEFFF9FD69=;DGFGEDFGGGFE0=B=;<=>9FFG=A | |
| @SRR488565.3 HWI-ST344_0078:1:1101:1171:2102 length=100 | |
| ATGGTCTCTGAAATGTCTGCTGAGGGCTGTCTCTCAGGTGACAGTGCTGATGACAGATGCCCATCCTGCTGGAGGGGAATCTGAGCCCTCAGGAGAGCTC |
tsackton
/ jobTree_failedLoop
Last active
August 29, 2015 14:19
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Logging set at level: DEBUG | |
| Logging to file: None | |
| The job tree appears to already exist, so we'll reload it | |
| Written the config file | |
| Got the maxCPU: 0 | |
| Setting up the thread pool with 60 threads given the max threads 60 and the max cpus 9000 | |
| Reloaded the jobtree | |
| Written the environment for the jobs to the environment file | |
| Got parameters,rescue jobs frequency: 1800.0 max job duration: 9.22337203685e+18 | |
| Checked batch system has no running jobs and no updated jobs |
tsackton
/ fullalign.log
Last active
August 29, 2015 14:19
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Logging set at level: DEBUG | |
| Logging to file: ratite_align.log | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/ratite_align_sr2/refGenomes/pseHum.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/ratite_align_sr2/refGenomes/taeGut.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/ratite_align_sr2/refGenomes/ficAlb.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/ratite_align_sr2/refGenomes/corBra.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/ratite_align_sr2/refGenomes/melUnd.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/ratite_align_sr2/refGenomes/falPer.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/ratite_align_sr2/refGenomes/picPub.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/ratite_align_sr2/refGenomes/lepDis.fa |
tsackton
/ 6sp-test.log
Last active
August 29, 2015 14:19
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Logging set at level: DEBUG | |
| Logging to file: test_align.log | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/test_birds/refGenomes/strCam.20130116.OM.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/test_birds/refGenomes/galGal.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/test_birds/refGenomes/melGal.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/test_birds/refGenomes/taeGut.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/test_birds/refGenomes/ficAlb.fa | |
| Running the command: cactus_analyseAssembly /n/regal/edwards_lab/ratites/wga/test_birds/refGenomes/pseHum.fa | |
| Running the command: rm -rf ./testDir/jobTree | |
| Running the command: cactus_createMultiCactusProject.py "/n/home12/tsackton/ratite_scratch/wga/test_birds/testDir/expTemplate.xml" "./testDir/progressiveAlignment" --fixNames=0 |
tsackton
/ blanchette.log
Last active
August 29, 2015 14:19
This file contains bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| Logging set at level: DEBUG | |
| Logging to file: test_align.log | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/HUMAN | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/CHIMP | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/BABOON | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/MOUSE | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/RAT | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/DOG | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/CAT | |
| Running the command: cactus_analyseAssembly ./cactusTestData/blanchettesSimulation/00.job/PIG |
NewerOlder