Aimin Yan aiminy
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| 2019-01-16 11:36:18,622 INFO - MaterializeWorkflowDescriptorActor [UUID(0627e8c3)]: Parsing workflow as WDL draft-2 | |
| 2019-01-16 11:37:27,526 INFO - MaterializeWorkflowDescriptorActor [UUID(0627e8c3)]: Call-to-Backend assignments: chip.overlap -> Local, chip.macs2_ppr2 -> Local, chip.merge_fastq_ctl -> Local, chip.overlap_pr -> Local, chip.pool_ta_pr2 -> Local, chip.spp_ppr2 -> Local, chip.bam2ta -> Local, chip.xcor -> Local, chip.reproducibility_idr -> Local, chip.overlap_ppr -> Local, chip.bwa_ctl -> Local, chip.idr -> Local, chip.macs2_pr2 -> Local, chip.bam2ta_no_filt -> Local, chip.bwa_R1 -> Local, chip.reproducibility_overlap -> Local, chip.spp_pr1 -> Local, chip.bam2ta_ctl -> Local, chip.trim_fastq -> Local, chip.fraglen_mean -> Local, chip.idr_pr -> Local, chip.fingerprint -> Local, chip.read_genome_tsv -> Local, chip.spp_pooled -> Local, chip.filter -> Local, chip.macs2_pr1 -> Local, chip.bwa -> Local, chip.spp_ppr1 -> Local, chip.bam2ta_no_filt_R1 -> Local, chip.merge_fastq -> Local, chip.pool_ta_ct |
aiminy
/ gist:478b761dab90dc0325bb097e4cea1565
Created
April 27, 2018 21:06
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| [axy148@pegasus ~]$ .bds/bds -c .bds/bds_lsf.config -s local Aimin_project/AtacSeq/inst/bin/bds/test_4.bds | |
| Picked up _JAVA_OPTIONS: -Xms256M -Xmx728M -XX:ParallelGCThreads=1 | |
| Hi 8 | |
| Hi 12 | |
| Hi 10 | |
| Hi 9 | |
| Hi 11 | |
| Hi 2 | |
| Hi 3 | |
| Hi 1 |
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| [axy148@pegasus ~]$ ./Aimin_project/BigDataScript/scripts/install.sh | |
| + '[' -z ']' | |
| + BDS_HOME=/nethome/axy148/.bds | |
| + ORIGDIR=/nethome/axy148 | |
| ++ dirname ./Aimin_project/BigDataScript/scripts/install.sh | |
| + echo 'Changing dir' ./Aimin_project/BigDataScript/scripts | |
| Changing dir ./Aimin_project/BigDataScript/scripts | |
| ++ dirname ./Aimin_project/BigDataScript/scripts/install.sh | |
| + cd ./Aimin_project/BigDataScript/scripts | |
| + cd .. |
aiminy
/ sessionInfo for PathwaySplice_1.3.0
Created
April 10, 2018 20:00
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| > sessionInfo() | |
| R Under development (unstable) (2018-04-05 r74542) | |
| Platform: x86_64-apple-darwin15.6.0 (64-bit) | |
| Running under: OS X El Capitan 10.11.6 | |
| Matrix products: default | |
| BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib | |
| LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib | |
| locale: |
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| Picked up _JAVA_OPTIONS: -Xms256M | |
| /nethome/axy148/anaconda3/envs/bds_atac/lib/python2.7/site-packages/matplotlib/font_manager.py:273: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment. | |
| warnings.warn('Matplotlib is building the font cache using fc-list. This may take a moment.') | |
| Picked up _JAVA_OPTIONS: -Xms256M -Xmx20G -XX:ParallelGCThreads=1 -Djava.io.tmpdir=/nethome/axy148/tmp/ | |
| 00:01:32.523 ExecutionerLocal 'Local[64]': Tasks [Local[64]] Pending: 0 Running: 1 Done: 0 Failed: 0 | |
| | PID | Task state | Task name | Dependencies | Task definition | | |
| | ---- | ----------------- | ---------- | ------------ | ---------------------------------------------------------------------------- |
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| python /nethome/axy148/rMATS.3.2.2.beta -s1 /projects/scratch/bbc/Project/PJ/DATA/Trimmed_data/trimmed_76_S5R1.fastq:/projects/scratch/bbc/Project/PJ/DATA/Trimmed_data/trimmed_76_S5R2.fastq,/projects/scratch/bbc/Project/PJ/DATA/Trimmed_data/trimmed_91_S6R1.fastq:/projects/scratch/bbc/Project/PJ/DATA/Trimmed_data/trimmed_91_S6R2.fastq -s2 /projects/scratch/bbc/Project/PJ/DATA/Trimmed_data/trimmed_94_S3R1.fastq:/projects/scratch/bbc/Project/PJ/DATA/Trimmed_data/trimmed_94_S3R2.fastq,/projects/scratch/bbc/Project/PJ/DATA/Trimmed_data/trimmed_75_S1R1.fastq:/projects/scratch/bbc/Project/PJ/DATA/Trimmed_data/trimmed_75_S1R2.fastq -gtf /nethome/axy148/rMATS.3.2.2.beta/Mus_musculus.Ensembl.NCBIM37.65.gtf -bi /projects/scratch/bbc/STAR_mm10 -o /projects/scratch/bbc/PJ/out_rMAT -t paired -len 50 -a 8 -c 0.0001 -analysis P |
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| # LSBATCH: User input | |
| #!/bin/bash | |
| #BSUB -P bbc | |
| #BSUB -J CufflinksAnno | |
| #BSUB -o %J.CufflinksAnno.log | |
| #BSUB -e %J.CufflinksAnno.err | |
| #BSUB -W 48:00 | |
| #BSUB -n 16 | |
| #BSUB -q bigmem | |
| #BSUB -R 'rusage[mem=36864] span[ptile=8]' |
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| ==> devtools::check(cleanup = FALSE, build_args = c('--resave-data')) | |
| Updating PathwaySplice documentation | |
| Loading PathwaySplice | |
| Warning: @param [zzz.R#4]: requires name and description | |
| Warning: @return [zzz.R#7]: requires a value | |
| Warning: @examples [zzz.R#10]: requires a value | |
| Warning: The existing 'NAMESPACE' file was not generated by roxygen2, and will not be overwritten. |
aiminy
/ gist:1360bee7b4541796c42d8dca7055654e
Created
July 22, 2016 19:52
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| g++ -I/projects/scratch/bbc/R/src/R-3.3.0/builddir/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Alignment.cpp -o Alignment.o | |
| g++ -I/projects/scratch/bbc/R/src/R-3.3.0/builddir/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c ColumnComp.cpp -o ColumnComp.o | |
| g++ -I/projects/scratch/bbc/R/src/R-3.3.0/builddir/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c DeclareAll.cpp -o DeclareAll.o | |
| g++ -I/projects/scratch/bbc/R/src/R-3.3.0/builddir/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c Motif.cpp -o Motif.o | |
| g++ -I/projects/scratch/bbc/R/src/R-3.3.0/builddir/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c MotifDistances.cpp -o MotifDistances.o | |
| g++ -I/projects/scratch/bbc/R/src/R-3.3.0/builddir/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c MotifMatch.cpp -o MotifMatch.o | |
| g++ -I/projects/scratch/bbc/R/src/R-3.3.0/builddir/include -DNDEBUG -I/usr/local/include -fpic -g -O2 -c PlatformSupport.cpp -o PlatformSupport.o | |
| g++ -I/projects/scratch/ |
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| CKL09004; La Posta Seq C7-F71-1-2-1-1-B-B-B | |
| CML395 | |
| CML444 | |
| CML505 | |
| CML539 | |
| CZL02001 | |
| CZL03011 | |
| CZL04003 | |
| CZL04008 | |
| CZL0618 |
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