Job ID = 9371956 sra ファイルのダウンロード中... Completed: 1509893K bytes transferred in 24 seconds (504974K bits/sec), in 2 files, 3 directories. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 8411107 spots for /home/okishinya/chipatlas/results/dm3/SRX2548349/SRR5241494.sra Written 8411107 spots total Written 8972428 spots for /home/okishinya/chipatlas/results/dm3/SRX2548349/SRR5241493.sra Written 8972428 spots total 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: 04:44:20 17383535 reads; of these: 17383535 (100.00%) were paired; of these: 3804023 (21.88%) aligned concordantly 0 times 4614220 (26.54%) aligned concordantly exactly 1 time 8965292 (51.57%) aligned concordantly >1 times ---- 3804023 pairs aligned concordantly 0 times; of these: 707962 (18.61%) aligned discordantly 1 time ---- 3096061 pairs aligned 0 times concordantly or discordantly; of these: 6192122 mates make up the pairs; of these: 2326864 (37.58%) aligned 0 times 494589 (7.99%) aligned exactly 1 time 3370669 (54.43%) aligned >1 times 93.31% overall alignment rate Time searching: 04:44:20 Overall time: 04:44:20 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_sort_core] merging from 16 files... [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] 539341 / 14213831 = 0.0379 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 @ Fri, 04 Aug 2017 20:13:38: # Command line: callpeak -t SRX2548349.bam -f BAM -g dm -n SRX2548349.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2548349.20 # format = BAM # ChIP-seq file = ['SRX2548349.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 @ Fri, 04 Aug 2017 20:13:38: # Command line: callpeak -t SRX2548349.bam -f BAM -g dm -n SRX2548349.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2548349.10 # format = BAM # ChIP-seq file = ['SRX2548349.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 @ Fri, 04 Aug 2017 20:13:38: #1 read tag files... INFO @ Fri, 04 Aug 2017 20:13:38: #1 read tag files... INFO @ Fri, 04 Aug 2017 20:13:38: # Command line: callpeak -t SRX2548349.bam -f BAM -g dm -n SRX2548349.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2548349.05 # format = BAM # ChIP-seq file = ['SRX2548349.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 @ Fri, 04 Aug 2017 20:13:38: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 20:13:38: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 20:13:38: #1 read tag files... INFO @ Fri, 04 Aug 2017 20:13:38: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 20:13:50: 1000000 INFO @ Fri, 04 Aug 2017 20:13:51: 1000000 INFO @ Fri, 04 Aug 2017 20:13:54: 1000000 INFO @ Fri, 04 Aug 2017 20:14:02: 2000000 INFO @ Fri, 04 Aug 2017 20:14:04: 2000000 INFO @ Fri, 04 Aug 2017 20:14:08: 2000000 INFO @ Fri, 04 Aug 2017 20:14:13: 3000000 INFO @ Fri, 04 Aug 2017 20:14:18: 3000000 INFO @ Fri, 04 Aug 2017 20:14:22: 3000000 INFO @ Fri, 04 Aug 2017 20:14:25: 4000000 INFO @ Fri, 04 Aug 2017 20:14:31: 4000000 INFO @ Fri, 04 Aug 2017 20:14:35: 4000000 INFO @ Fri, 04 Aug 2017 20:14:36: 5000000 INFO @ Fri, 04 Aug 2017 20:14:44: 5000000 INFO @ Fri, 04 Aug 2017 20:14:46: 5000000 INFO @ Fri, 04 Aug 2017 20:14:47: 6000000 INFO @ Fri, 04 Aug 2017 20:14:57: 6000000 INFO @ Fri, 04 Aug 2017 20:14:57: 6000000 INFO @ Fri, 04 Aug 2017 20:14:58: 7000000 INFO @ Fri, 04 Aug 2017 20:15:09: 7000000 INFO @ Fri, 04 Aug 2017 20:15:09: 8000000 INFO @ Fri, 04 Aug 2017 20:15:09: 7000000 INFO @ Fri, 04 Aug 2017 20:15:20: 9000000 INFO @ Fri, 04 Aug 2017 20:15:20: 8000000 INFO @ Fri, 04 Aug 2017 20:15:22: 8000000 INFO @ Fri, 04 Aug 2017 20:15:30: 10000000 INFO @ Fri, 04 Aug 2017 20:15:31: 9000000 INFO @ Fri, 04 Aug 2017 20:15:35: 9000000 INFO @ Fri, 04 Aug 2017 20:15:41: 11000000 INFO @ Fri, 04 Aug 2017 20:15:42: 10000000 INFO @ Fri, 04 Aug 2017 20:15:47: 10000000 INFO @ Fri, 04 Aug 2017 20:15:52: 12000000 INFO @ Fri, 04 Aug 2017 20:15:53: 11000000 INFO @ Fri, 04 Aug 2017 20:16:00: 11000000 INFO @ Fri, 04 Aug 2017 20:16:02: 13000000 INFO @ Fri, 04 Aug 2017 20:16:04: 12000000 INFO @ Fri, 04 Aug 2017 20:16:12: 12000000 INFO @ Fri, 04 Aug 2017 20:16:13: 14000000 INFO @ Fri, 04 Aug 2017 20:16:14: 13000000 INFO @ Fri, 04 Aug 2017 20:16:23: 15000000 INFO @ Fri, 04 Aug 2017 20:16:25: 14000000 INFO @ Fri, 04 Aug 2017 20:16:25: 13000000 INFO @ Fri, 04 Aug 2017 20:16:34: 16000000 INFO @ Fri, 04 Aug 2017 20:16:36: 15000000 INFO @ Fri, 04 Aug 2017 20:16:37: 14000000 INFO @ Fri, 04 Aug 2017 20:16:45: 17000000 INFO @ Fri, 04 Aug 2017 20:16:46: 16000000 INFO @ Fri, 04 Aug 2017 20:16:49: 15000000 INFO @ Fri, 04 Aug 2017 20:16:55: 18000000 INFO @ Fri, 04 Aug 2017 20:16:57: 17000000 INFO @ Fri, 04 Aug 2017 20:17:02: 16000000 INFO @ Fri, 04 Aug 2017 20:17:06: 19000000 INFO @ Fri, 04 Aug 2017 20:17:08: 18000000 INFO @ Fri, 04 Aug 2017 20:17:15: 17000000 INFO @ Fri, 04 Aug 2017 20:17:16: 20000000 INFO @ Fri, 04 Aug 2017 20:17:19: 19000000 INFO @ Fri, 04 Aug 2017 20:17:27: 21000000 INFO @ Fri, 04 Aug 2017 20:17:27: 18000000 INFO @ Fri, 04 Aug 2017 20:17:30: 20000000 INFO @ Fri, 04 Aug 2017 20:17:37: 22000000 INFO @ Fri, 04 Aug 2017 20:17:39: 19000000 INFO @ Fri, 04 Aug 2017 20:17:40: 21000000 INFO @ Fri, 04 Aug 2017 20:17:47: 23000000 INFO @ Fri, 04 Aug 2017 20:17:51: 22000000 INFO @ Fri, 04 Aug 2017 20:17:51: 20000000 INFO @ Fri, 04 Aug 2017 20:17:57: 24000000 INFO @ Fri, 04 Aug 2017 20:18:02: 23000000 INFO @ Fri, 04 Aug 2017 20:18:03: 21000000 INFO @ Fri, 04 Aug 2017 20:18:08: 25000000 INFO @ Fri, 04 Aug 2017 20:18:12: 24000000 INFO @ Fri, 04 Aug 2017 20:18:15: 22000000 INFO @ Fri, 04 Aug 2017 20:18:18: 26000000 INFO @ Fri, 04 Aug 2017 20:18:23: 25000000 INFO @ Fri, 04 Aug 2017 20:18:27: 23000000 INFO @ Fri, 04 Aug 2017 20:18:28: 27000000 INFO @ Fri, 04 Aug 2017 20:18:34: 26000000 INFO @ Fri, 04 Aug 2017 20:18:39: 28000000 INFO @ Fri, 04 Aug 2017 20:18:39: 24000000 INFO @ Fri, 04 Aug 2017 20:18:44: 27000000 INFO @ Fri, 04 Aug 2017 20:18:49: 29000000 INFO @ Fri, 04 Aug 2017 20:18:51: 25000000 INFO @ Fri, 04 Aug 2017 20:18:55: 28000000 INFO @ Fri, 04 Aug 2017 20:19:00: 30000000 INFO @ Fri, 04 Aug 2017 20:19:03: 26000000 INFO @ Fri, 04 Aug 2017 20:19:07: 29000000 INFO @ Fri, 04 Aug 2017 20:19:11: 31000000 INFO @ Fri, 04 Aug 2017 20:19:14: 27000000 INFO @ Fri, 04 Aug 2017 20:19:15: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 20:19:15: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 20:19:15: #1 total tags in treatment: 13043571 INFO @ Fri, 04 Aug 2017 20:19:15: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 20:19:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 20:19:15: #1 tags after filtering in treatment: 10962302 INFO @ Fri, 04 Aug 2017 20:19:15: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 04 Aug 2017 20:19:15: #1 finished! INFO @ Fri, 04 Aug 2017 20:19:15: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 20:19:15: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 20:19:16: #2 number of paired peaks: 2983 INFO @ Fri, 04 Aug 2017 20:19:16: start model_add_line... INFO @ Fri, 04 Aug 2017 20:19:17: start X-correlation... INFO @ Fri, 04 Aug 2017 20:19:17: end of X-cor INFO @ Fri, 04 Aug 2017 20:19:17: #2 finished! INFO @ Fri, 04 Aug 2017 20:19:17: #2 predicted fragment length is 215 bps INFO @ Fri, 04 Aug 2017 20:19:17: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 04 Aug 2017 20:19:17: #2.2 Generate R script for model : SRX2548349.20_model.r INFO @ Fri, 04 Aug 2017 20:19:17: #3 Call peaks... INFO @ Fri, 04 Aug 2017 20:19:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 20:19:18: 30000000 INFO @ Fri, 04 Aug 2017 20:19:26: 28000000 INFO @ Fri, 04 Aug 2017 20:19:31: 31000000 INFO @ Fri, 04 Aug 2017 20:19:36: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 20:19:36: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 20:19:36: #1 total tags in treatment: 13043571 INFO @ Fri, 04 Aug 2017 20:19:36: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 20:19:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 20:19:36: #1 tags after filtering in treatment: 10962302 INFO @ Fri, 04 Aug 2017 20:19:36: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 04 Aug 2017 20:19:36: #1 finished! INFO @ Fri, 04 Aug 2017 20:19:36: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 20:19:36: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 20:19:38: #2 number of paired peaks: 2983 INFO @ Fri, 04 Aug 2017 20:19:38: start model_add_line... INFO @ Fri, 04 Aug 2017 20:19:38: start X-correlation... INFO @ Fri, 04 Aug 2017 20:19:38: end of X-cor INFO @ Fri, 04 Aug 2017 20:19:38: #2 finished! INFO @ Fri, 04 Aug 2017 20:19:38: #2 predicted fragment length is 215 bps INFO @ Fri, 04 Aug 2017 20:19:38: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 04 Aug 2017 20:19:38: #2.2 Generate R script for model : SRX2548349.05_model.r INFO @ Fri, 04 Aug 2017 20:19:38: #3 Call peaks... INFO @ Fri, 04 Aug 2017 20:19:38: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 20:19:41: 29000000 INFO @ Fri, 04 Aug 2017 20:19:53: 30000000 INFO @ Fri, 04 Aug 2017 20:20:03: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 20:20:04: 31000000 INFO @ Fri, 04 Aug 2017 20:20:08: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 20:20:08: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 20:20:08: #1 total tags in treatment: 13043571 INFO @ Fri, 04 Aug 2017 20:20:08: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 20:20:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 20:20:08: #1 tags after filtering in treatment: 10962302 INFO @ Fri, 04 Aug 2017 20:20:08: #1 Redundant rate of treatment: 0.16 INFO @ Fri, 04 Aug 2017 20:20:08: #1 finished! INFO @ Fri, 04 Aug 2017 20:20:08: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 20:20:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 20:20:10: #2 number of paired peaks: 2983 INFO @ Fri, 04 Aug 2017 20:20:10: start model_add_line... INFO @ Fri, 04 Aug 2017 20:20:10: start X-correlation... INFO @ Fri, 04 Aug 2017 20:20:10: end of X-cor INFO @ Fri, 04 Aug 2017 20:20:10: #2 finished! INFO @ Fri, 04 Aug 2017 20:20:10: #2 predicted fragment length is 215 bps INFO @ Fri, 04 Aug 2017 20:20:10: #2 alternative fragment length(s) may be 215 bps INFO @ Fri, 04 Aug 2017 20:20:10: #2.2 Generate R script for model : SRX2548349.10_model.r INFO @ Fri, 04 Aug 2017 20:20:10: #3 Call peaks... INFO @ Fri, 04 Aug 2017 20:20:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 20:20:19: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 20:20:25: #4 Write output xls file... SRX2548349.20_peaks.xls INFO @ Fri, 04 Aug 2017 20:20:25: #4 Write peak in narrowPeak format file... SRX2548349.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 20:20:25: #4 Write summits bed file... SRX2548349.20_summits.bed INFO @ Fri, 04 Aug 2017 20:20:25: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4211 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 20:20:42: #4 Write output xls file... SRX2548349.05_peaks.xls INFO @ Fri, 04 Aug 2017 20:20:42: #4 Write peak in narrowPeak format file... SRX2548349.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 20:20:42: #4 Write summits bed file... SRX2548349.05_summits.bed INFO @ Fri, 04 Aug 2017 20:20:42: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (10796 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 20:20:52: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 20:21:14: #4 Write output xls file... SRX2548349.10_peaks.xls INFO @ Fri, 04 Aug 2017 20:21:14: #4 Write peak in narrowPeak format file... SRX2548349.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 20:21:14: #4 Write summits bed file... SRX2548349.10_summits.bed INFO @ Fri, 04 Aug 2017 20:21:14: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7078 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。