STAR: ultrafast universal RNA-seq aligner. Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, Batut P, Chaisson M, Gingeras TR. Bioinformatics. 2013 Jan 1;29(1):15-21. doi: 10.1093/bioinformatics/bts635.
The Genome Analysis Toolkit: a MapReduce framework for analyzing next-generation DNA sequencing data McKenna A, Hanna M, Banks E, Sivachenko A, Cibulskis K, Kernytsky A, Garimella K, Altshuler D, Gabriel S, Daly M, DePristo MA, 2010 GENOME RESEARCH 20:1297-303
http://broadinstitute.github.io/picard/
-rw-rw-r– 1 ubuntu ubuntu 9892774 Aug 20 2018 ctat_mutation_demo_1.fastq
-rw-rw-r– 1 ubuntu ubuntu 9892774 Aug 20 2018 ctat_mutation_demo_2.fastq
GRCh38_v27_CTAT_lib_Feb092018/ GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/AnnotFilterRule.pm GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/pfam_domains.dbm GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.fai GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_annot.gtf.mini.sortu GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/blast_pairs.idx GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_annot.gtf.gene_spans GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.gmap.ok GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/ GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/build.ok GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.fromGTF.out.tab GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonGeTrInfo.tab GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SAindex GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/transcriptInfo.tab GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/geneInfo.tab GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbInfo.txt GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/SA GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrStart.txt GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrName.txt GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrLength.txt GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/genomeParameters.txt GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/sjdbList.out.tab GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/Genome GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/chrNameLength.txt GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_genome.fa.star.idx/exonInfo.tab GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_annot.pep GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dat GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/trans.blast.align_coords.align_coords.dbm GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_annot.gtf GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_annot.cds GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/blast_pairs.idx.prev.1518217631 GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/fusion_annot_lib.idx GRCh38_v27_CTAT_lib_Feb092018/ctat_genome_lib_build_dir/ref_annot.prot_info.dbm
-rw-rw-r– 1 ubuntu ubuntu 2839 Feb 23 2018 AnnotFilterRule.pm
-rw-rw-r– 1 ubuntu ubuntu 1400848384 Feb 21 2018 blast_pairs.idx
-rw-rw-r– 1 ubuntu ubuntu 1400848384 Feb 21 2018 blast_pairs.idx.prev.1518217631
-rw-rw-r– 1 ubuntu ubuntu 2320236544 Feb 21 2018 fusion_annot_lib.idx
-rw-rw-r– 1 ubuntu ubuntu 190857216 Feb 23 2018 pfam_domains.dbm
-rw-rw-r– 1 ubuntu ubuntu 108993409 Feb 21 2018 ref_annot.cds
-rw-rw-r– 1 ubuntu ubuntu 1150835305 Feb 21 2018 ref_annot.gtf
-rw-rw-r– 1 ubuntu ubuntu 3933998 Feb 21 2018 ref_annot.gtf.gene_spans
-rw-rw-r– 1 ubuntu ubuntu 49752053 Feb 21 2018 ref_annot.gtf.mini.sortu
-rw-rw-r– 1 ubuntu ubuntu 37597442 Feb 21 2018 ref_annot.pep
-rw-rw-r– 1 ubuntu ubuntu 719781888 Feb 21 2018 ref_annot.prot_info.dbm
-rw-rw-r– 1 ubuntu ubuntu 3139758082 Feb 21 2018 ref_genome.fa
-rw-rw-r– 1 ubuntu ubuntu 788 Feb 21 2018 ref_genome.fa.fai
-rw-rw-r– 1 ubuntu ubuntu 0 Feb 21 2018 ref_genome.fa.gmap.ok
drwxrwxr-x 2 ubuntu ubuntu 4096 Feb 21 2018 ref_genome.fa.star.idx
-rw-rw-r– 1 ubuntu ubuntu 1552146399 Feb 21 2018 trans.blast.align_coords.align_coords.dat
-rw-rw-r– 1 ubuntu ubuntu 4034531328 Feb 21 2018 trans.blast.align_coords.align_coords.dbm
Mar 30 17:12:42 ….. started STAR run
Mar 30 17:12:42 ….. loading genome
Mar 30 17:15:03 ….. started mapping
Mar 30 17:15:07 ….. finished successfully
-rw-rw-r– 1 ubuntu ubuntu 28318272 Mar 30 17:15 first_alAligned.out.sam
-rw-rw-r– 1 ubuntu ubuntu 1834 Mar 30 17:15 first_alLog.final.out
-rw-rw-r– 1 ubuntu ubuntu 18579 Mar 30 17:15 first_alLog.out
-rw-rw-r– 1 ubuntu ubuntu 246 Mar 30 17:15 first_alLog.progress.out
-rw-rw-r– 1 ubuntu ubuntu 36962 Mar 30 17:15 first_alSJ.out.tab
Started job on | Mar 30 17:12:42
Started mapping on | Mar 30 17:15:03
Finished on | Mar 30 17:15:07
Mapping speed, Million of reads per hour | 57.22
Number of input reads | 63580
Average input read length | 100
UNIQUE READS:
Uniquely mapped reads number | 59777
Uniquely mapped reads % | 94.02%
Mar 30 18:07:50 ….. started STAR run
Mar 30 18:07:50 … starting to generate Genome files
Mar 30 18:09:00 … starting to sort Suffix Array. This may take a long time…
Mar 30 18:09:15 … sorting Suffix Array chunks and saving them to disk…
Mar 30 19:04:16 … loading chunks from disk, packing SA…
Mar 30 19:05:31 … finished generating suffix array
Mar 30 19:05:31 … generating Suffix Array index
Mar 30 19:10:21 … completed Suffix Array index
Mar 30 19:10:21 ….. inserting junctions into the genome indices
Mar 30 19:11:35 … writing Genome to disk …
Mar 30 19:11:37 … writing Suffix Array to disk …
Mar 30 19:12:59 … writing SAindex to disk
Mar 30 19:13:06 ….. finished successfully
-rw-rw-r– 1 ubuntu ubuntu 3091663986 Mar 30 19:11 Genome
-rw-rw-r– 1 ubuntu ubuntu 20233 Mar 30 17:57 Log.out
-rw-rw-r– 1 ubuntu ubuntu 24237299472 Mar 30 19:12 SA
-rw-rw-r– 1 ubuntu ubuntu 1565873619 Mar 30 19:12 SAindex
drwx—— 2 ubuntu ubuntu 4096 Mar 30 17:40 _STARtmp
-rw-rw-r– 1 ubuntu ubuntu 238 Mar 30 18:08 chrLength.txt
-rw-rw-r– 1 ubuntu ubuntu 138 Mar 30 18:08 chrName.txt
-rw-rw-r– 1 ubuntu ubuntu 376 Mar 30 18:08 chrNameLength.txt
-rw-rw-r– 1 ubuntu ubuntu 273 Mar 30 18:08 chrStart.txt
-rw-rw-r– 1 ubuntu ubuntu 650 Mar 30 19:11 genomeParameters.txt
-rw-rw-r– 1 ubuntu ubuntu 29387 Mar 30 19:10 sjdbInfo.txt
-rw-rw-r– 1 ubuntu ubuntu 25835 Mar 30 19:10 sjdbList.out.tab
Mar 30 19:28:14 ….. started STAR run
Mar 30 19:28:14 ….. loading genome
Mar 30 19:28:58 ….. started mapping
Mar 30 19:29:11 ….. finished successfully
-rw-rw-r– 1 ubuntu ubuntu 17663 Mar 30 17:32 Log.out
drwx—— 2 ubuntu ubuntu 4096 Mar 30 17:30 _STARtmp
drwxrwxr-x 2 ubuntu ubuntu 4096 Mar 30 19:29 second_align
-rw-rw-r– 1 ubuntu ubuntu 28348992 Mar 30 19:29 Aligned.out.sam
-rw-rw-r– 1 ubuntu ubuntu 1835 Mar 30 19:29 Log.final.out
-rw-rw-r– 1 ubuntu ubuntu 18249 Mar 30 19:29 Log.out
-rw-rw-r– 1 ubuntu ubuntu 246 Mar 30 19:29 Log.progress.out
-rw-rw-r– 1 ubuntu ubuntu 36909 Mar 30 19:29 SJ.out.tab
Started job on | Mar 30 19:28:14
Started mapping on | Mar 30 19:28:58
Finished on | Mar 30 19:29:11
Mapping speed, Million of reads per hour | 17.61
Number of input reads | 63580
Average input read length | 100
UNIQUE READS:
Uniquely mapped reads number | 59810
Uniquely mapped reads % | 94.07%
@HD VN:1.4
@SQ SN:chr1 LN:248956422
@SQ SN:chr2 LN:242193529
@SQ SN:chr3 LN:198295559
@SQ SN:chr4 LN:190214555
@SQ SN:chr5 LN:181538259
@SQ SN:chr6 LN:170805979
@SQ SN:chr7 LN:159345973
@SQ SN:chr8 LN:145138636
@SQ SN:chr9 LN:138394717
INFO 2019-03-30 19:56:23 AddOrReplaceReadGroups
********** NOTE: Picard’s command line syntax is changing.
********** For more information, please see:
********** The command line looks like this in the new syntax: **********
********** AddOrReplaceReadGroups -I Aligned.out.sam -o ctat_mutation_rg_added_sorted.bam -SO coordinate -RGID 123 -RGLB Truseq_SS_Paired -RGPL Illumina -RGPU Hiseq4000 -RGSM ctat_mutation
-rw-rw-r– 1 ubuntu ubuntu 7330332 Mar 30 19:56 ctat_mutation_rg_added_sorted.bam
INFO 2019-03-30 20:03:45 MarkDuplicates
……………………………
[Sat Mar 30 20:03:53 UTC 2019] picard.sam.markduplicates.MarkDuplicates done. Elapsed time: 0.12 minutes.
Runtime.totalMemory()=649592832
-rw-rw-r– 1 ubuntu ubuntu 1437480 Mar 30 20:03 ctat_mutation_dedupped_rg_added_sorted.bai
-rw-rw-r– 1 ubuntu ubuntu 7450734 Mar 30 20:03 ctat_mutation_dedupped_rg_added_sorted.bam
-rw-rw-r– 1 ubuntu ubuntu 2900 Mar 30 20:03 output.metrics
142656 + 0 in total (QC-passed reads + QC-failed reads)
15522 + 0 secondary
0 + 0 supplementary
0 + 0 duplicates
142656 + 0 mapped (100.00% : N/A)
127134 + 0 paired in sequencing
63567 + 0 read1
63567 + 0 read2
127134 + 0 properly paired (100.00% : N/A)
127134 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
142656 + 0 in total (QC-passed reads + QC-failed reads)
15522 + 0 secondary
0 + 0 supplementary
2444 + 0 duplicates
142656 + 0 mapped (100.00% : N/A)
127134 + 0 paired in sequencing
63567 + 0 read1
63567 + 0 read2
127134 + 0 properly paired (100.00% : N/A)
127134 + 0 with itself and mate mapped
0 + 0 singletons (0.00% : N/A)
0 + 0 with mate mapped to a different chr
0 + 0 with mate mapped to a different chr (mapQ>=5)
-rw-rw-r– 1 ubuntu ubuntu 3139758082 Feb 21 2018 ref_genome.fa
-rw-rw-r– 1 ubuntu ubuntu 788 Mar 30 20:58 ref_genome.fa.fai
Using GATK jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar
Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar SplitNCigarReads -R ref_genome.fa -I ctat_mutation_dedupped_rg_added_sorted.bam -O ctat_mutation_split.bam
………………………………..
[March 30, 2019 8:59:26 PM UTC] org.broadinstitute.hellbender.tools.walkers.rnaseq.SplitNCigarReads done. Elapsed time: 0.09 minutes.
Runtime.totalMemory()=1422393344
-rw-rw-r– 1 ubuntu ubuntu 1439384 Mar 30 20:59 ctat_mutation_split.bai
-rw-rw-r– 1 ubuntu ubuntu 10714092 Mar 30 20:59 ctat_mutation_split.bam
……………………………..
common_all_20180418.vcf.gz 100%[=========================================================================================================>] 1.49G 136MB/s in 13s
………………………………..
common_all_20180418.vcf.gz.tbi 100%[=========================================================================================================>] 2.15M 13.1MB/s in 0.2s
-rw-rw-r– 1 ubuntu ubuntu 1595848625 Mar 30 21:35 common_all_20180418.vcf.gz
-rw-rw-r– 1 ubuntu ubuntu 2258664 Mar 30 21:36 common_all_20180418.vcf.gz.tbi
Using GATK jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar BaseRecalibrator -R ref_genome.fa -I ctat_mutation_split.bam --known-sites gatk-vcf/common_all_20180418.vcf.gz -O ctat_mutation_recal_data.table
21:37:23.730 INFO NativeLibraryLoader - Loading libgkl_compression.so from
21:37:23.875 INFO BaseRecalibrator - ————————————————————
21:37:23.875 INFO BaseRecalibrator - The Genome Analysis Toolkit (GATK) v4.1.1.0
………………………………….
[March 30, 2019 9:37:28 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.BaseRecalibrator done. Elapsed time: 0.08 minutes.
Runtime.totalMemory()=1,452,277,760
-rw-rw-r– 1 ubuntu ubuntu 364976 Mar 30 21:37 ctat_mutation_recal_data.table
:GATKReport.v1.1:5
:GATKTable:2:17:%s:%s:;
:GATKTable:Arguments:Recalibration argument collection values used in this run
Argument Value
binary_tag_name null
covariate ReadGroupCovariate,QualityScoreCovariate,ContextCovariate,CycleCovariate
default_platform null
deletions_default_quality 45
force_platform null
indels_context_size 3
insertions_default_quality 45
low_quality_tail 2
maximum_cycle_value 500
mismatches_context_size 2
mismatches_default_quality -1
no_standard_covs false
quantizing_levels 16
recalibration_report null
run_without_dbsnp false
solid_nocall_strategy THROW_EXCEPTION
Using GATK jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar
Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar ApplyBQSR -R ref_genome.fa -I ctat_mutation_split.bam –bqsr-recal-file ctat_mutation_recal_data.table -O ctat_mutation_recal_split.bam
………………………………………….
[March 30, 2019 9:49:10 PM UTC] org.broadinstitute.hellbender.tools.walkers.bqsr.ApplyBQSR done. Elapsed time: 0.04 minutes.
Runtime.totalMemory()=1231552512
HWI-EAS418:5:8:639:1002 163 chr1 633375 1 1S49M = 633415 590361 CGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCC ?;99;==>9==<><?=>=><?=>>=<=><==>==>>>>>====<>==;:;PG:Z:MarkDuplicates RG:Z:123 HI:i:1 nM:i:0 AS:i:86
HWI-EAS418:5:8:639:1002 419 chr1 633375 1 1S49M = 633415 78 CGCCCATCGTCCTAGAATTAATTCCCCTAAAAATCTTTGAAATAGGGCCC ?;99;==>9==<><?=>=><?=>>=<=><==>==>>>>>====<>==;:;PG:Z:MarkDuplicates RG:Z:123 HI:i:2 nM:i:0 AS:i:85
HWI-EAS418:5:8:639:1002 83 chr1 633415 1 35M15S = 633375 -590361 ATAGGGCCCGTATTTACCCTATAGCACCCCCTCTACCCACCGCCCGTCCC <9<<<==;;=<===<8<=>:=<>=>8;<;;?;>;:;<>:;9=;:7;<7:=<>=>8;<;;?;>;:;<>:;9=;:7;<7:;=6;><>>7<><;>=><98=<:>>:=<:>;<;95=;<=;7&19:<6<PG:Z:MarkDuplicates RG:Z:123 HI:i:1 nM:i:1 AS:i:90
HWI-EAS418:3:91:1122:13 147 chr1 891893 60 33M17S = 891886 -227226 CAAGTAATTCTCCTGCCTCAGCCTCCCGAGCAGCTGGGACCACAGGTGTG 19/28::;=<;<5<>;55<8;;5(.:8>;>>>=>>==>5;><>>;<;9@?SA:Z:chr1,1119095,-,33S17M,60,*; PG:Z:MarkDuplicates RG:Z:123 HI:i:1 nM:i:1 AS:i:90
HWI-EAS418:3:87:1409:52 163 chr1 1025555 60 50M = 1025732 245083 TCCTCCCCATTCCTGCCACCCTCTCCTGCCCCCTCCTGACTCCAGGTTCT ?:8;==:<>=>==??=;>>8<>>>>=;>;4<<<==:;>=5=>.:>=:=<=PG:Z:MarkDuplicates RG:Z:123 HI:i:1 nM:i:1 AS:i:86
HWI-EAS418:3:87:1409:52 83 chr1 1025732 60 37M13S = 1025555 -245083 GAGGGCGGAGGGCCTACCTCTGTCCCTCCCCACTCACCCCAACTCCCCCC 5:90/:379306<><8=<:>6=9==>:;;6>:<=>8<==>==>;9=87=?SA:Z:chr1,1270625,-,37S13M,60,*; PG:Z:MarkDuplicates RG:Z:123 HI:i:1 nM:i:1 AS:i:86
HWI-EAS418:3:100:1425:750 99 chr1 1044211 3 48M2S = 1044406 956 GGCCGTGTGTCTGTGACTTCAGCTGCCAGAGTGTCCCAGGCAGCCCGGGG ==997:=<>=>>><>=>>>=>>=:>><>>=<<<:>=<;>==:>=<=:;/< PG:Z:MarkDuplicates RG:Z:123 HI:i:1 nM:i:0 AS:i:88
HWI-EAS418:3:100:1425:750 355 chr1 1044211 3 48M2S = 1044406 254443 GGCCGTGTGTCTGTGACTTCAGCTGCCAGAGTGTCCCAGGCAGCCCGGGG ==997:=<>=>>><>=>>>=>>=:>><>>=<<<:>=<;>==:>=<=:;/< PG:Z:MarkDuplicates RG:Z:123 HI:i:2 nM:i:0 AS:i:88
Using GATK jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar Running: java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar HaplotypeCaller -R ref_genome.fa -I ctat_mutation_recal_split.bam –dont-use-soft-clipped-bases -stand-call-conf 20 -O ctat_mutation_called_variants.vcf
……………………………………..
22:05:17.737 INFO IntelPairHmm - Available threads: 8
22:05:17.737 INFO IntelPairHmm - Requested threads: 4
22:05:17.737 INFO PairHMM - Using the OpenMP multi-threaded AVX-accelerated native PairHMM implementation
22:05:17.763 INFO ProgressMeter - Starting traversal
22:05:17.764 INFO ProgressMeter - Current Locus Elapsed Minutes Regions Processed Regions/Minute
22:05:27.764 INFO ProgressMeter - chr1:46181894 0.2 154050 924300.0
22:05:37.764 INFO ProgressMeter - chr1:109433646 0.3 364890 1094670.0
22:05:47.764 INFO ProgressMeter - chr1:169209679 0.5 564200 1128400.0
22:05:57.764 INFO ProgressMeter - chr1:230721420 0.7 769280 1153920.0
22:06:07.764 INFO ProgressMeter - chr2:38880301 0.8 959690 1151628.0
22:06:17.764 INFO ProgressMeter - chr2:101685747 1.0 1169080 1169080.0
22:06:27.764 INFO ProgressMeter - chr2:165356603 1.2 1381340 1184005.7
22:06:37.764 INFO ProgressMeter - chr2:228231360 1.3 1590930 1193197.5
……………………………………….
22:12:57.783 INFO ProgressMeter - chr21:35043601 7.7 9377230 1223066.4
22:13:07.783 INFO ProgressMeter - chr22:48149126 7.8 9576660 1222502.9
22:13:17.783 INFO ProgressMeter - chrX:60279636 8.0 9786500 1223264.1
22:13:27.783 INFO ProgressMeter - chrX:123588891 8.2 9997540 1224141.1
22:13:37.783 INFO ProgressMeter - chrY:27365701 8.3 10196940 1223586.3
22:13:43.059 INFO HaplotypeCaller - 25014 read(s) filtered by:
…………………
22:13:43.059 INFO ProgressMeter - chrM:15001 8.4 10296535 1222636.5
……………………………………………
[March 30, 2019 10:13:43 PM UTC] org.broadinstitute.hellbender.tools.walkers.haplotypecaller.HaplotypeCaller done. Elapsed time: 8.43 minutes.
Runtime.totalMemory()=1260388352
-rw-rw-r– 1 ubuntu ubuntu 120104 Mar 30 22:13 ctat_mutation_called_variants.vcf
-rw-rw-r– 1 ubuntu ubuntu 23566 Mar 30 22:13 ctat_mutation_called_variants.vcf.idx
Using GATK jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar
Running:
java -Dsamjdk.use_async_io_read_samtools=false -Dsamjdk.use_async_io_write_samtools=true -Dsamjdk.use_async_io_write_tribble=false -Dsamjdk.compression_level=2 -jar /home/ubuntu/miniconda3/share/gatk4-4.1.1.0-0/gatk-package-4.1.1.0-local.jar VariantFiltration -R ref_genome.fa -V ctat_mutation_called_variants.vcf -window 35 -cluster 3 --filter-name FS -filter FS > 30.0 -O ctat_mutation_filtered_called_variants.vcf
……………………………
22:25:49.987 INFO ProgressMeter - Traversal complete. Processed 586 total variants in 0.0 minutes.
22:25:50.093 INFO VariantFiltration - Shutting down engine
[March 30, 2019 10:25:50 PM UTC] org.broadinstitute.hellbender.tools.walkers.filters.VariantFiltration done. Elapsed time: 0.01 minutes.
Runtime.totalMemory()=1164967936
-rw-rw-r– 1 ubuntu ubuntu 123563 Mar 30 22:25 ctat_mutation_filtered_called_variants.vcf
-rw-rw-r– 1 ubuntu ubuntu 23575 Mar 30 22:25 ctat_mutation_filtered_called_variants.vcf.idx
SN, Summary numbers:
SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 586
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 567
SN 0 number of MNPs: 0
SN 0 number of indels: 19
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1
SN 0 number of multiallelic SNP sites: 0
TSTV, transitions/transversions:
TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
TSTV 0 449 118 3.81 449 118 3.81
SN, Summary numbers:
SN [2]id [3]key [4]value
SN 0 number of samples: 1
SN 0 number of records: 586
SN 0 number of no-ALTs: 0
SN 0 number of SNPs: 567
SN 0 number of MNPs: 0
SN 0 number of indels: 19
SN 0 number of others: 0
SN 0 number of multiallelic sites: 1
SN 0 number of multiallelic SNP sites: 0
TSTV, transitions/transversions:
TSTV [2]id [3]ts [4]tv [5]ts/tv [6]ts (1st ALT) [7]tv (1st ALT) [8]ts/tv (1st ALT)
TSTV 0 449 118 3.81 449 118 3.81