Galaxy History ' asp5 xylem example'


DatasetAnnotation
1: asp5_xylem_read1.P001.fq
142.5 Mb
format: fastq, database: Populus_unmasked
Info: uploaded fastq file
@SOLEXA14:2:1:1:234#0/1
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+SOLEXA14:2:1:1:234#0/1
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@SOLEXA14:2:1:2:1946#0/1
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2: asp5_xylem_read2.P001.fq
142.5 Mb
format: fastq, database: Populus_unmasked
Info: uploaded fastq file
@SOLEXA14:2:1:1:234#0/2
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+SOLEXA14:2:1:1:234#0/2
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3: FASTQ Groomer on data 1
142.5 Mb
format: fastqsanger, database: Populus_unmasked
Info: Groomed 937749 illumina reads into sanger reads.
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4: FASTQ Groomer on data 2
142.5 Mb
format: fastqsanger, database: Populus_unmasked
Info: Groomed 937749 illumina reads into sanger reads.
@SOLEXA14:2:1:1:234#0/2
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5: Map with BWA for Illumina on data 4 and data 3: mapped reads
~2,800,000 lines, 2,520 comments
format: sam, database: Populus_unmasked
Info: BWA Version: 0.5.9-r16
BWA run on paired-end data
1.QNAME2.FLAG3.RNAME4.POS5.MAPQ6.CIGAR7.MRNM8.MPOS9.ISIZE10.SEQ11.QUAL12.OPT
@SQ SN:scaffold_1 LN:48367220
@SQ SN:scaffold_2 LN:23562801
@SQ SN:scaffold_3 LN:20216605
@SQ SN:scaffold_4 LN:23188140
@SQ SN:scaffold_5 LN:25802683
@SQ SN:scaffold_6 LN:26894541
6: SAM-to-BAM on data 5: converted BAM
99.6 Mb
format: bam, database: Populus_unmasked
Info: Samtools Version: 0.1.18 (r982:295)
SAM file converted to BAM
Binary bam alignments file
7: flagstat on data 6
11 lines
format: txt, database: Populus_unmasked
1875498 + 0 in total (QC-passed reads + QC-failed reads)
0 + 0 duplicates
1448249 + 0 mapped (77.22%:-nan%)
1875498 + 0 paired in sequencing
937749 + 0 read1
937749 + 0 read2
18: Realigner Target Creator on data 6 (GATK intervals)
32,127 lines
format: gatk_interval, database: Populus_unmasked
scaffold_1:112937-112939
scaffold_1:113253
scaffold_1:114166
scaffold_1:116823-116824
scaffold_1:116902-116903
scaffold_1:128086
19: Realigner Target Creator on data 6 (log)
27 lines
format: txt, database: Populus_unmasked
INFO 14:07:44,061 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:07:44,063 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:07:44,063 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:07:44,064 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:07:44,064 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:07:44,064 HelpFormatter - Program Args: -T RealignerTargetCreator -o /mnt/spruce/storage/ftp/database/files/003/dataset_3740.dat -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa -I /tmp/tmpaaqhoJ/gatk_input.bam
20: Indel Realigner on data 18 and data 6 (BAM)
102.3 Mb
format: bam, database: Populus_unmasked
Binary bam alignments file
21: Indel Realigner on data 18 and data 6 (log)
18 lines
format: txt, database: Populus_unmasked
INFO 14:23:21,061 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:23:21,063 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:23:21,063 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:23:21,063 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:23:21,063 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:23:21,064 HelpFormatter - Program Args: -T IndelRealigner -o /mnt/spruce/storage/ftp/database/files/003/dataset_3742.dat -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa -LOD 5.0 --disable_bam_indexing -I /tmp/tmpY0umRN/gatk_input.ba
22: Count Covariates on data 20 (Covariate File)
40 lines, 4 comments
format: csv, database: Populus_unmasked
1
# Counted Sites 17573369
# Counted Bases 66698632
# Skipped Sites 0
# Fraction Skipped 1 / Infinity bp
ReadGroup,QualityScore,nObservations,nMismatches,Qempirical
Asp5,2,2502595,161983,12
23: Count Covariates on data 20 (log)
32 lines
format: txt, database: Populus_unmasked
INFO 14:26:09,154 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:26:09,156 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:26:09,156 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:26:09,157 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:26:09,157 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:26:09,157 HelpFormatter - Program Args: -T CountCovariates --num_threads 4 -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa --recal_file /mnt/spruce/storage/ftp/database/files/003/dataset_3744.dat -cov ReadGroupCovariate -cov Quality
24: Table Recalibration on data 22 and data 20 (BAM)
112.9 Mb
format: bam, database: Populus_unmasked
Binary bam alignments file
25: Table Recalibration on data 22 and data 20 (log)
25 lines
format: txt, database: Populus_unmasked
INFO 14:28:20,876 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:28:20,878 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:28:20,878 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:28:20,878 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:28:20,878 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:28:20,879 HelpFormatter - Program Args: -T TableRecalibration -o /mnt/spruce/storage/ftp/database/files/003/dataset_3756.dat -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa --recal_file /mnt/spruce/storage/ftp/database/files/003/dat
26: Unified Genotyper on data 24 (VCF)
90,983 lines, 2,544 comments
format: vcf, database: Populus_unmasked
1.Chrom2.Pos3.ID4.Ref5.Alt6.Qual7.Filter8.Info9.Format10.data
##fileformat=VCFv4.1
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Float,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
27: Unified Genotyper on data 24 (log)
42 lines
format: txt, database: Populus_unmasked
INFO 14:30:33,097 HelpFormatter - ---------------------------------------------------------------------------------
INFO 14:30:33,098 HelpFormatter - The Genome Analysis Toolkit (GATK) v1.6-13-g91f02df, Compiled 2012/06/26 20:27:56
INFO 14:30:33,099 HelpFormatter - Copyright (c) 2010 The Broad Institute
INFO 14:30:33,099 HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
INFO 14:30:33,099 HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
INFO 14:30:33,099 HelpFormatter - Program Args: -T UnifiedGenotyper -o /mnt/spruce/storage/ftp/database/files/003/dataset_3758.dat -R /mnt/spruce/storage/data/sequence/Populus_trichocarpa.v2.fa --standard_min_confidence_threshold_for_calling 30.0 --standa