@HD VN:1.4 SO:coordinate @RG ID:22843_1#2 PL:ILLUMINA PU:170619_HS34_22843_A_CAYAAANXX_1#2 LB:19361351 DS:EGAS00001002325: We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney. DT:2017-06-19T01:00:00+0100 PG:SCS SM:EGAN00001549489 CN:SC @PG ID:SCS PN:RTA VN:1.18.66.3 DS:Controlling software on instrument @PG ID:basecalling PN:RTA PP:SCS VN:1.18.66.3 DS:Basecalling Package @PG ID:bambi PN:bambi PP:basecalling VN:0.9.4 DS:Convert Illumina BCL to BAM or SAM file CL:/software/solexa/pkg/bambi/0.9.4/bin/bambi i2b --intensity-dir=/nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities --basecalls-dir=/nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BaseCalls --lane=1 --platform-unit=170619_HS34_22843_A_CAYAAANXX_1 --read-group-id=22843_1 --study-name="EGAS00001002325: We intend to use single cell transcriptome analysis to explore the heterogenity of different cell types within the kidney." --sample-alias=EGAN00001549489,EGAN00001549489,EGAN00001549489,EGAN00001549489 --output-file=- --compression-level=0 @PG ID:bamadapterfind PN:bamadapterfind PP:bambi VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bamadapterfind level=0 @PG ID:bambi.1 PN:bambi PP:bamadapterfind VN:0.9.4 CL:/software/solexa/pkg/bambi/0.9.4/bin/bambi decode --metrics-file /nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BAM_basecalls_20170625-045447/22843_1.bam.tag_decode.metrics --barcode-file /nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BAM_basecalls_20170625-045447/metadata_cache_22843/lane_1.taglist --compression-level 0 - @PG ID:bamcollate2 PN:bamcollate2 PP:bambi.1 VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bamcollate2 collate=2 level=0 @PG ID:bwa PN:bwa PP:bamcollate2 VN:0.7.15-r1140 CL:/software/solexa/pkg/bwa/0.7.15/bwa sampe /lustre/scratch117/core/sciops_repository/references/PhiX/Sanger-SNPs/all/bwa0_6/phix_unsnipped_short_no_N.fa /tmp/tkCvb2bsZ6/alnphix_bwa_aln_1_out /tmp/mSlwmGJS2j/alnphix_bwa_aln_2_out /tmp/6MTxIs7kyj/alnphix_simple_cat1_out /tmp/887GLs0Zhb/alnphix_simple_cat2_out @PG ID:scramble PN:scramble PP:bwa VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -0 -t 1 -I sam -O bam @PG ID:bam12auxmerge PN:bam12auxmerge PP:scramble VN:2.0.72 CL:/software/solexa/pkg/biobambam/2.0.72/bin/bam12auxmerge level=0 rankstrip=1 ranksplit=1 zztoname=0 clipreinsert=1 /tmp/MnrxjKbb27/simple_cat_out @PG ID:scramble.1 PN:scramble PP:bam12auxmerge VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -I bam -O cram -x -3 @PG ID:scramble.2 PN:scramble PP:scramble.1 VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -I cram -O bam -0 @PG ID:spf PN:spatial_filter PP:scramble.2 DS:A program to apply a spatial filter VN:v10.27-dirty CL:/software/solexa/pkg/pb_calibration/10.27/bin/spatial_filter -c -F /dev/stdout -t /nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BAM_basecalls_20170625-045447/no_cal/archive/qc/tileviz/22843_1 --region_size 200 --region_mismatch_threshold 0.0160 --region_insertion_threshold 0.0160 --region_deletion_threshold 0.0160 /dev/stdin ; /software/solexa/pkg/pb_calibration/10.27/bin/spatial_filter -a -f -u -l /nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BAM_basecalls_20170625-045447/no_cal/22843_1.bam.filter.stats -F /tmp/kesxLMli6k/tee_post_filter_creation:__APPLY_FILTER_OUT___out /dev/stdin @PG ID:samtools PN:samtools PP:spf VN:1.4 CL:/software/solexa/pkg/samtools/1.4/bin/samtools split -f /nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BAM_basecalls_20170625-045447/no_cal/lane1/%!.bam - @PG ID:AlignmentFilter PN:AlignmentFilter DS:Give a list of SAM/BAM files with the same set of records and in the same order but aligned with different references, split reads into different files according to alignments. You have option to put unaligned reads into one of output files or a separate file VN:V1.19 CL:uk.ac.sanger.npg.picard.AlignmentFilter INPUT_ALIGNMENT=[/nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BAM_basecalls_20170625-045447/no_cal/lane1/22843_1#2.bam] OUTPUT_ALIGNMENT=[/tmp/_2ESaQfJZf/alignment_filter:__PHIX_BAM_OUT___out] OUTPUT_UNALIGNED=/dev/stdout METRICS_FILE=22843_1#2.bam_alignment_filter_metrics.json VERBOSITY=INFO QUIET=false VALIDATION_STRINGENCY=SILENT COMPRESSION_LEVEL=0 MAX_RECORDS_IN_RAM=500000 CREATE_INDEX=false CREATE_MD5_FILE=false @PG ID:bamsormadup PN:bamsormadup CL:/software/solexa/pkg/biobambam/2.0.72/bin/bamsormadup threads=16 SO=coordinate level=0 verbose=0 fixmate=1 adddupmarksupport=1 tmpfile=/nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BAM_basecalls_20170625-045447/no_cal/archive/lane1/bsfopt_22843_1#2.tmp PP:AlignmentFilter VN:2.0.72 @PG ID:bamstreamingmarkduplicates PN:bamstreamingmarkduplicates CL:/software/solexa/pkg/biobambam/2.0.72/bin/bamstreamingmarkduplicates level=0 verbose=0 tmpfile=/nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BAM_basecalls_20170625-045447/no_cal/archive/lane1/bmdfopt_22843_1#2.tmp M=/nfs/sf50/ILorHSany_sf50/analysis/170619_HS34_22843_A_CAYAAANXX/Data/Intensities/BAM_basecalls_20170625-045447/no_cal/archive/lane1/22843_1#2.markdups_metrics.txt PP:bamsormadup VN:2.0.72 @PG ID:scramble.3 PN:scramble PP:samtools VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -t 7 -7 -I bam -O cram -x @PG ID:scramble.4 PN:scramble PP:bamstreamingmarkduplicates VN:1.14.9 CL:/software/solexa/pkg/scramble/1.14.9/bin/scramble -t 7 -7 -I bam -O cram -x @CO TY:checksum ST:all PA:all HA:crc32prod CO:2951624 BS:2475b3db NS:32ded074 SQ:4213b761 ST:BC,FI,QT,RT,TC:46befb56 @CO TY:checksum ST:all PA:pass HA:crc32prod CO:2951362 BS:72825714 NS:75d1deb3 SQ:279e5ddb ST:BC,FI,QT,RT,TC:39dad4d3 @CO TY:checksum ST: PA:all HA:crc32prod CO:0 BS:1 NS:1 SQ:1 ST:BC,FI,QT,RT,TC:1 @CO TY:checksum ST: PA:pass HA:crc32prod CO:0 BS:1 NS:1 SQ:1 ST:BC,FI,QT,RT,TC:1 @CO TY:checksum ST:22843_1#2 PA:all HA:crc32prod CO:2951624 BS:2475b3db NS:32ded074 SQ:4213b761 ST:BC,FI,QT,RT,TC:46befb56 @CO TY:checksum ST:22843_1#2 PA:pass HA:crc32prod CO:2951362 BS:72825714 NS:75d1deb3 SQ:279e5ddb ST:BC,FI,QT,RT,TC:39dad4d3