Job ID = 2590991 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 981,069 reads read : 1,962,138 reads written : 1,962,138 rm: cannot remove ‘[DSE]RR*’: No such file or directory fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:21 981069 reads; of these: 981069 (100.00%) were paired; of these: 307258 (31.32%) aligned concordantly 0 times 613200 (62.50%) aligned concordantly exactly 1 time 60611 (6.18%) aligned concordantly >1 times ---- 307258 pairs aligned concordantly 0 times; of these: 54178 (17.63%) aligned discordantly 1 time ---- 253080 pairs aligned 0 times concordantly or discordantly; of these: 506160 mates make up the pairs; of these: 313959 (62.03%) aligned 0 times 168485 (33.29%) aligned exactly 1 time 23716 (4.69%) aligned >1 times 84.00% overall alignment rate Time searching: 00:01:21 Overall time: 00:01:21 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 511607 / 725531 = 0.7051 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Tue, 13 Aug 2019 00:19:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-05 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 13 Aug 2019 00:19:50: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:19:50: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:19:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-10 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 13 Aug 2019 00:19:51: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:19:51: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:19:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.bam'] # control file = None # effective genome size = 1.20e+08 # band width = 300 # model fold = [5, 50] # qvalue cutoff = 1.00e-20 # Larger dataset will be scaled towards smaller dataset. # Range for calculating regional lambda is: 10000 bps # Broad region calling is off # Paired-End mode is off INFO @ Tue, 13 Aug 2019 00:19:52: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:19:52: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:19:57: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:19:57: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:19:57: #1 total tags in treatment: 194172 INFO @ Tue, 13 Aug 2019 00:19:57: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:19:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:19:57: #1 tags after filtering in treatment: 155584 INFO @ Tue, 13 Aug 2019 00:19:57: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 13 Aug 2019 00:19:57: #1 finished! INFO @ Tue, 13 Aug 2019 00:19:57: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:19:57: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:19:58: #2 number of paired peaks: 6664 INFO @ Tue, 13 Aug 2019 00:19:58: start model_add_line... INFO @ Tue, 13 Aug 2019 00:19:58: start X-correlation... INFO @ Tue, 13 Aug 2019 00:19:58: end of X-cor INFO @ Tue, 13 Aug 2019 00:19:58: #2 finished! INFO @ Tue, 13 Aug 2019 00:19:58: #2 predicted fragment length is 286 bps INFO @ Tue, 13 Aug 2019 00:19:58: #2 alternative fragment length(s) may be 7,247,286 bps INFO @ Tue, 13 Aug 2019 00:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.05_model.r INFO @ Tue, 13 Aug 2019 00:19:58: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:19:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:19:58: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:19:58: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:19:58: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:19:58: #1 total tags in treatment: 194172 INFO @ Tue, 13 Aug 2019 00:19:58: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:19:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:19:58: #1 tags after filtering in treatment: 155584 INFO @ Tue, 13 Aug 2019 00:19:58: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 13 Aug 2019 00:19:58: #1 finished! INFO @ Tue, 13 Aug 2019 00:19:58: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:19:58: #2 looking for paired plus/minus strand peaks... BedGraph に変換しました。 BigWig に変換中... INFO @ Tue, 13 Aug 2019 00:19:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:19:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:19:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.05_summits.bed INFO @ Tue, 13 Aug 2019 00:19:58: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (310 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:19:58: #2 number of paired peaks: 6664 INFO @ Tue, 13 Aug 2019 00:19:58: start model_add_line... INFO @ Tue, 13 Aug 2019 00:19:58: start X-correlation... INFO @ Tue, 13 Aug 2019 00:19:58: end of X-cor INFO @ Tue, 13 Aug 2019 00:19:58: #2 finished! INFO @ Tue, 13 Aug 2019 00:19:58: #2 predicted fragment length is 286 bps INFO @ Tue, 13 Aug 2019 00:19:58: #2 alternative fragment length(s) may be 7,247,286 bps INFO @ Tue, 13 Aug 2019 00:19:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.10_model.r INFO @ Tue, 13 Aug 2019 00:19:58: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:19:58: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:19:59: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:19:59: #1 tag size is determined as 75 bps INFO @ Tue, 13 Aug 2019 00:19:59: #1 tag size = 75 INFO @ Tue, 13 Aug 2019 00:19:59: #1 total tags in treatment: 194172 INFO @ Tue, 13 Aug 2019 00:19:59: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:19:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:19:59: #1 tags after filtering in treatment: 155584 INFO @ Tue, 13 Aug 2019 00:19:59: #1 Redundant rate of treatment: 0.20 INFO @ Tue, 13 Aug 2019 00:19:59: #1 finished! INFO @ Tue, 13 Aug 2019 00:19:59: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:19:59: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:19:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:19:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:19:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.10_summits.bed INFO @ Tue, 13 Aug 2019 00:19:59: Done! INFO @ Tue, 13 Aug 2019 00:19:59: #2 number of paired peaks: 6664 INFO @ Tue, 13 Aug 2019 00:19:59: start model_add_line... INFO @ Tue, 13 Aug 2019 00:19:59: start X-correlation... INFO @ Tue, 13 Aug 2019 00:19:59: end of X-cor INFO @ Tue, 13 Aug 2019 00:19:59: #2 finished! INFO @ Tue, 13 Aug 2019 00:19:59: #2 predicted fragment length is 286 bps INFO @ Tue, 13 Aug 2019 00:19:59: #2 alternative fragment length(s) may be 7,247,286 bps INFO @ Tue, 13 Aug 2019 00:19:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.20_model.r INFO @ Tue, 13 Aug 2019 00:19:59: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:19:59: #3 Pre-compute pvalue-qvalue table... pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (101 records, 4 fields): 2 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Tue, 13 Aug 2019 00:20:00: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:20:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:20:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:20:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6441120/SRX6441120.20_summits.bed INFO @ Tue, 13 Aug 2019 00:20:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (20 records, 4 fields): 2 millis CompletedMACS2peakCalling