Job ID = 2590450 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,251,358 reads read : 26,502,716 reads written : 13,251,358 reads 0-length : 13,251,358 spots read : 13,268,248 reads read : 26,536,496 reads written : 13,268,248 reads 0-length : 13,268,248 spots read : 13,176,365 reads read : 26,352,730 reads written : 13,176,365 reads 0-length : 13,176,365 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: 00:10:06 39695971 reads; of these: 39695971 (100.00%) were unpaired; of these: 2338995 (5.89%) aligned 0 times 31881532 (80.31%) aligned exactly 1 time 5475444 (13.79%) aligned >1 times 94.11% overall alignment rate Time searching: 00:10:06 Overall time: 00:10:06 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_rmdupse_core] 7773257 / 37356976 = 0.2081 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 @ Mon, 12 Aug 2019 22:13:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.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 @ Mon, 12 Aug 2019 22:13:21: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:13:21: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:13:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.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 @ Mon, 12 Aug 2019 22:13:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:13:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:13:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.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 @ Mon, 12 Aug 2019 22:13:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:13:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:13:28: 1000000 INFO @ Mon, 12 Aug 2019 22:13:32: 1000000 INFO @ Mon, 12 Aug 2019 22:13:33: 1000000 INFO @ Mon, 12 Aug 2019 22:13:35: 2000000 INFO @ Mon, 12 Aug 2019 22:13:42: 2000000 INFO @ Mon, 12 Aug 2019 22:13:42: 3000000 INFO @ Mon, 12 Aug 2019 22:13:43: 2000000 INFO @ Mon, 12 Aug 2019 22:13:50: 4000000 INFO @ Mon, 12 Aug 2019 22:13:52: 3000000 INFO @ Mon, 12 Aug 2019 22:13:53: 3000000 INFO @ Mon, 12 Aug 2019 22:13:58: 5000000 INFO @ Mon, 12 Aug 2019 22:14:02: 4000000 INFO @ Mon, 12 Aug 2019 22:14:03: 4000000 INFO @ Mon, 12 Aug 2019 22:14:05: 6000000 INFO @ Mon, 12 Aug 2019 22:14:11: 5000000 INFO @ Mon, 12 Aug 2019 22:14:12: 7000000 INFO @ Mon, 12 Aug 2019 22:14:12: 5000000 INFO @ Mon, 12 Aug 2019 22:14:18: 8000000 INFO @ Mon, 12 Aug 2019 22:14:21: 6000000 INFO @ Mon, 12 Aug 2019 22:14:22: 6000000 INFO @ Mon, 12 Aug 2019 22:14:25: 9000000 INFO @ Mon, 12 Aug 2019 22:14:30: 7000000 INFO @ Mon, 12 Aug 2019 22:14:31: 7000000 INFO @ Mon, 12 Aug 2019 22:14:32: 10000000 INFO @ Mon, 12 Aug 2019 22:14:39: 11000000 INFO @ Mon, 12 Aug 2019 22:14:40: 8000000 INFO @ Mon, 12 Aug 2019 22:14:41: 8000000 INFO @ Mon, 12 Aug 2019 22:14:46: 12000000 INFO @ Mon, 12 Aug 2019 22:14:49: 9000000 INFO @ Mon, 12 Aug 2019 22:14:50: 9000000 INFO @ Mon, 12 Aug 2019 22:14:53: 13000000 INFO @ Mon, 12 Aug 2019 22:14:59: 10000000 INFO @ Mon, 12 Aug 2019 22:14:59: 14000000 INFO @ Mon, 12 Aug 2019 22:15:00: 10000000 INFO @ Mon, 12 Aug 2019 22:15:06: 15000000 INFO @ Mon, 12 Aug 2019 22:15:08: 11000000 INFO @ Mon, 12 Aug 2019 22:15:09: 11000000 INFO @ Mon, 12 Aug 2019 22:15:13: 16000000 INFO @ Mon, 12 Aug 2019 22:15:18: 12000000 INFO @ Mon, 12 Aug 2019 22:15:19: 12000000 INFO @ Mon, 12 Aug 2019 22:15:20: 17000000 INFO @ Mon, 12 Aug 2019 22:15:27: 18000000 INFO @ Mon, 12 Aug 2019 22:15:27: 13000000 INFO @ Mon, 12 Aug 2019 22:15:28: 13000000 INFO @ Mon, 12 Aug 2019 22:15:34: 19000000 INFO @ Mon, 12 Aug 2019 22:15:35: 14000000 INFO @ Mon, 12 Aug 2019 22:15:37: 14000000 INFO @ Mon, 12 Aug 2019 22:15:41: 20000000 INFO @ Mon, 12 Aug 2019 22:15:42: 15000000 INFO @ Mon, 12 Aug 2019 22:15:46: 15000000 INFO @ Mon, 12 Aug 2019 22:15:47: 21000000 INFO @ Mon, 12 Aug 2019 22:15:50: 16000000 INFO @ Mon, 12 Aug 2019 22:15:54: 22000000 INFO @ Mon, 12 Aug 2019 22:15:54: 16000000 INFO @ Mon, 12 Aug 2019 22:15:57: 17000000 INFO @ Mon, 12 Aug 2019 22:16:01: 23000000 INFO @ Mon, 12 Aug 2019 22:16:03: 17000000 INFO @ Mon, 12 Aug 2019 22:16:05: 18000000 INFO @ Mon, 12 Aug 2019 22:16:08: 24000000 INFO @ Mon, 12 Aug 2019 22:16:12: 19000000 INFO @ Mon, 12 Aug 2019 22:16:12: 18000000 INFO @ Mon, 12 Aug 2019 22:16:15: 25000000 INFO @ Mon, 12 Aug 2019 22:16:19: 20000000 INFO @ Mon, 12 Aug 2019 22:16:21: 19000000 INFO @ Mon, 12 Aug 2019 22:16:22: 26000000 INFO @ Mon, 12 Aug 2019 22:16:27: 21000000 INFO @ Mon, 12 Aug 2019 22:16:29: 27000000 INFO @ Mon, 12 Aug 2019 22:16:30: 20000000 INFO @ Mon, 12 Aug 2019 22:16:34: 22000000 INFO @ Mon, 12 Aug 2019 22:16:36: 28000000 INFO @ Mon, 12 Aug 2019 22:16:38: 21000000 INFO @ Mon, 12 Aug 2019 22:16:42: 23000000 INFO @ Mon, 12 Aug 2019 22:16:43: 29000000 INFO @ Mon, 12 Aug 2019 22:16:47: 22000000 INFO @ Mon, 12 Aug 2019 22:16:47: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:16:47: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:16:47: #1 total tags in treatment: 29583719 INFO @ Mon, 12 Aug 2019 22:16:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:16:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:16:48: #1 tags after filtering in treatment: 29583719 INFO @ Mon, 12 Aug 2019 22:16:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:16:48: #1 finished! INFO @ Mon, 12 Aug 2019 22:16:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:16:49: 24000000 INFO @ Mon, 12 Aug 2019 22:16:51: #2 number of paired peaks: 1786 INFO @ Mon, 12 Aug 2019 22:16:51: start model_add_line... INFO @ Mon, 12 Aug 2019 22:16:51: start X-correlation... INFO @ Mon, 12 Aug 2019 22:16:51: end of X-cor INFO @ Mon, 12 Aug 2019 22:16:51: #2 finished! INFO @ Mon, 12 Aug 2019 22:16:51: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 22:16:51: #2 alternative fragment length(s) may be 4,139 bps INFO @ Mon, 12 Aug 2019 22:16:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.05_model.r INFO @ Mon, 12 Aug 2019 22:16:51: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:16:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:16:56: 23000000 INFO @ Mon, 12 Aug 2019 22:16:57: 25000000 INFO @ Mon, 12 Aug 2019 22:17:04: 26000000 INFO @ Mon, 12 Aug 2019 22:17:05: 24000000 INFO @ Mon, 12 Aug 2019 22:17:12: 27000000 INFO @ Mon, 12 Aug 2019 22:17:14: 25000000 INFO @ Mon, 12 Aug 2019 22:17:19: 28000000 INFO @ Mon, 12 Aug 2019 22:17:23: 26000000 INFO @ Mon, 12 Aug 2019 22:17:27: 29000000 INFO @ Mon, 12 Aug 2019 22:17:31: 27000000 INFO @ Mon, 12 Aug 2019 22:17:32: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:17:32: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:17:32: #1 total tags in treatment: 29583719 INFO @ Mon, 12 Aug 2019 22:17:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:17:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:17:32: #1 tags after filtering in treatment: 29583719 INFO @ Mon, 12 Aug 2019 22:17:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:17:32: #1 finished! INFO @ Mon, 12 Aug 2019 22:17:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:17:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:17:35: #2 number of paired peaks: 1786 INFO @ Mon, 12 Aug 2019 22:17:35: start model_add_line... INFO @ Mon, 12 Aug 2019 22:17:35: start X-correlation... INFO @ Mon, 12 Aug 2019 22:17:35: end of X-cor INFO @ Mon, 12 Aug 2019 22:17:35: #2 finished! INFO @ Mon, 12 Aug 2019 22:17:35: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 22:17:35: #2 alternative fragment length(s) may be 4,139 bps INFO @ Mon, 12 Aug 2019 22:17:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.10_model.r INFO @ Mon, 12 Aug 2019 22:17:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:17:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:17:40: 28000000 INFO @ Mon, 12 Aug 2019 22:17:49: 29000000 INFO @ Mon, 12 Aug 2019 22:17:54: #1 tag size is determined as 51 bps INFO @ Mon, 12 Aug 2019 22:17:54: #1 tag size = 51 INFO @ Mon, 12 Aug 2019 22:17:54: #1 total tags in treatment: 29583719 INFO @ Mon, 12 Aug 2019 22:17:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:17:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 22:17:55: #1 tags after filtering in treatment: 29583719 INFO @ Mon, 12 Aug 2019 22:17:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:17:55: #1 finished! INFO @ Mon, 12 Aug 2019 22:17:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:17:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:17:58: #2 number of paired peaks: 1786 INFO @ Mon, 12 Aug 2019 22:17:58: start model_add_line... INFO @ Mon, 12 Aug 2019 22:17:58: start X-correlation... INFO @ Mon, 12 Aug 2019 22:17:58: end of X-cor INFO @ Mon, 12 Aug 2019 22:17:58: #2 finished! INFO @ Mon, 12 Aug 2019 22:17:58: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 22:17:58: #2 alternative fragment length(s) may be 4,139 bps INFO @ Mon, 12 Aug 2019 22:17:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.20_model.r INFO @ Mon, 12 Aug 2019 22:17:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:17:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:18:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:18:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:18:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:18:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.05_summits.bed INFO @ Mon, 12 Aug 2019 22:18:43: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (11181 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:18:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:19:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:19:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:19:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:19:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.10_summits.bed INFO @ Mon, 12 Aug 2019 22:19:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7204 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:19:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:19:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:19:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3981683/SRX3981683.20_summits.bed INFO @ Mon, 12 Aug 2019 22:19:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3204 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。