Job ID = 1295474 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 24,005,342 reads read : 48,010,684 reads written : 48,010,684 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:53:24 24005342 reads; of these: 24005342 (100.00%) were paired; of these: 5099546 (21.24%) aligned concordantly 0 times 13774325 (57.38%) aligned concordantly exactly 1 time 5131471 (21.38%) aligned concordantly >1 times ---- 5099546 pairs aligned concordantly 0 times; of these: 215967 (4.24%) aligned discordantly 1 time ---- 4883579 pairs aligned 0 times concordantly or discordantly; of these: 9767158 mates make up the pairs; of these: 8204072 (84.00%) aligned 0 times 685574 (7.02%) aligned exactly 1 time 877512 (8.98%) aligned >1 times 82.91% overall alignment rate Time searching: 00:53:24 Overall time: 00:53:24 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] 1205260 / 19102516 = 0.0631 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, 03 Jun 2019 15:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.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, 03 Jun 2019 15:12:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:12:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.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, 03 Jun 2019 15:12:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:12:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:12:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.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, 03 Jun 2019 15:12:30: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:12:30: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:12:38: 1000000 INFO @ Mon, 03 Jun 2019 15:12:39: 1000000 INFO @ Mon, 03 Jun 2019 15:12:39: 1000000 INFO @ Mon, 03 Jun 2019 15:12:45: 2000000 INFO @ Mon, 03 Jun 2019 15:12:47: 2000000 INFO @ Mon, 03 Jun 2019 15:12:48: 2000000 INFO @ Mon, 03 Jun 2019 15:12:52: 3000000 INFO @ Mon, 03 Jun 2019 15:12:55: 3000000 INFO @ Mon, 03 Jun 2019 15:12:56: 3000000 INFO @ Mon, 03 Jun 2019 15:13:00: 4000000 INFO @ Mon, 03 Jun 2019 15:13:03: 4000000 INFO @ Mon, 03 Jun 2019 15:13:05: 4000000 INFO @ Mon, 03 Jun 2019 15:13:07: 5000000 INFO @ Mon, 03 Jun 2019 15:13:12: 5000000 INFO @ Mon, 03 Jun 2019 15:13:14: 5000000 INFO @ Mon, 03 Jun 2019 15:13:16: 6000000 INFO @ Mon, 03 Jun 2019 15:13:21: 6000000 INFO @ Mon, 03 Jun 2019 15:13:24: 6000000 INFO @ Mon, 03 Jun 2019 15:13:24: 7000000 INFO @ Mon, 03 Jun 2019 15:13:30: 7000000 INFO @ Mon, 03 Jun 2019 15:13:32: 8000000 INFO @ Mon, 03 Jun 2019 15:13:33: 7000000 INFO @ Mon, 03 Jun 2019 15:13:38: 8000000 INFO @ Mon, 03 Jun 2019 15:13:40: 9000000 INFO @ Mon, 03 Jun 2019 15:13:42: 8000000 INFO @ Mon, 03 Jun 2019 15:13:46: 9000000 INFO @ Mon, 03 Jun 2019 15:13:47: 10000000 INFO @ Mon, 03 Jun 2019 15:13:51: 9000000 INFO @ Mon, 03 Jun 2019 15:13:55: 10000000 INFO @ Mon, 03 Jun 2019 15:13:55: 11000000 INFO @ Mon, 03 Jun 2019 15:14:00: 10000000 INFO @ Mon, 03 Jun 2019 15:14:03: 12000000 INFO @ Mon, 03 Jun 2019 15:14:04: 11000000 INFO @ Mon, 03 Jun 2019 15:14:09: 11000000 INFO @ Mon, 03 Jun 2019 15:14:11: 13000000 INFO @ Mon, 03 Jun 2019 15:14:13: 12000000 INFO @ Mon, 03 Jun 2019 15:14:18: 12000000 INFO @ Mon, 03 Jun 2019 15:14:19: 14000000 INFO @ Mon, 03 Jun 2019 15:14:21: 13000000 INFO @ Mon, 03 Jun 2019 15:14:27: 15000000 INFO @ Mon, 03 Jun 2019 15:14:27: 13000000 INFO @ Mon, 03 Jun 2019 15:14:30: 14000000 INFO @ Mon, 03 Jun 2019 15:14:34: 16000000 INFO @ Mon, 03 Jun 2019 15:14:36: 14000000 INFO @ Mon, 03 Jun 2019 15:14:38: 15000000 INFO @ Mon, 03 Jun 2019 15:14:42: 17000000 INFO @ Mon, 03 Jun 2019 15:14:45: 15000000 INFO @ Mon, 03 Jun 2019 15:14:47: 16000000 INFO @ Mon, 03 Jun 2019 15:14:50: 18000000 INFO @ Mon, 03 Jun 2019 15:14:54: 16000000 INFO @ Mon, 03 Jun 2019 15:14:55: 17000000 INFO @ Mon, 03 Jun 2019 15:14:57: 19000000 INFO @ Mon, 03 Jun 2019 15:15:03: 17000000 INFO @ Mon, 03 Jun 2019 15:15:04: 18000000 INFO @ Mon, 03 Jun 2019 15:15:05: 20000000 INFO @ Mon, 03 Jun 2019 15:15:12: 18000000 INFO @ Mon, 03 Jun 2019 15:15:12: 19000000 INFO @ Mon, 03 Jun 2019 15:15:13: 21000000 INFO @ Mon, 03 Jun 2019 15:15:20: 22000000 INFO @ Mon, 03 Jun 2019 15:15:21: 19000000 INFO @ Mon, 03 Jun 2019 15:15:21: 20000000 INFO @ Mon, 03 Jun 2019 15:15:28: 23000000 INFO @ Mon, 03 Jun 2019 15:15:30: 20000000 INFO @ Mon, 03 Jun 2019 15:15:30: 21000000 INFO @ Mon, 03 Jun 2019 15:15:36: 24000000 INFO @ Mon, 03 Jun 2019 15:15:38: 22000000 INFO @ Mon, 03 Jun 2019 15:15:39: 21000000 INFO @ Mon, 03 Jun 2019 15:15:44: 25000000 INFO @ Mon, 03 Jun 2019 15:15:47: 23000000 INFO @ Mon, 03 Jun 2019 15:15:47: 22000000 INFO @ Mon, 03 Jun 2019 15:15:51: 26000000 INFO @ Mon, 03 Jun 2019 15:15:55: 24000000 INFO @ Mon, 03 Jun 2019 15:15:56: 23000000 INFO @ Mon, 03 Jun 2019 15:15:59: 27000000 INFO @ Mon, 03 Jun 2019 15:16:04: 25000000 INFO @ Mon, 03 Jun 2019 15:16:05: 24000000 INFO @ Mon, 03 Jun 2019 15:16:07: 28000000 INFO @ Mon, 03 Jun 2019 15:16:12: 26000000 INFO @ Mon, 03 Jun 2019 15:16:14: 25000000 INFO @ Mon, 03 Jun 2019 15:16:15: 29000000 INFO @ Mon, 03 Jun 2019 15:16:21: 27000000 INFO @ Mon, 03 Jun 2019 15:16:22: 30000000 INFO @ Mon, 03 Jun 2019 15:16:22: 26000000 INFO @ Mon, 03 Jun 2019 15:16:29: 28000000 INFO @ Mon, 03 Jun 2019 15:16:30: 31000000 INFO @ Mon, 03 Jun 2019 15:16:31: 27000000 INFO @ Mon, 03 Jun 2019 15:16:37: 32000000 INFO @ Mon, 03 Jun 2019 15:16:38: 29000000 INFO @ Mon, 03 Jun 2019 15:16:40: 28000000 INFO @ Mon, 03 Jun 2019 15:16:44: 33000000 INFO @ Mon, 03 Jun 2019 15:16:46: 30000000 INFO @ Mon, 03 Jun 2019 15:16:50: 29000000 INFO @ Mon, 03 Jun 2019 15:16:52: 34000000 INFO @ Mon, 03 Jun 2019 15:16:54: 31000000 INFO @ Mon, 03 Jun 2019 15:16:58: 30000000 INFO @ Mon, 03 Jun 2019 15:16:59: 35000000 INFO @ Mon, 03 Jun 2019 15:17:02: 32000000 INFO @ Mon, 03 Jun 2019 15:17:07: 36000000 INFO @ Mon, 03 Jun 2019 15:17:07: 31000000 INFO @ Mon, 03 Jun 2019 15:17:10: 33000000 INFO @ Mon, 03 Jun 2019 15:17:14: 37000000 INFO @ Mon, 03 Jun 2019 15:17:15: 32000000 INFO @ Mon, 03 Jun 2019 15:17:17: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:17:17: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:17:17: #1 total tags in treatment: 17704457 INFO @ Mon, 03 Jun 2019 15:17:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:17:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:17:18: #1 tags after filtering in treatment: 10736678 INFO @ Mon, 03 Jun 2019 15:17:18: #1 Redundant rate of treatment: 0.39 INFO @ Mon, 03 Jun 2019 15:17:18: #1 finished! INFO @ Mon, 03 Jun 2019 15:17:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:17:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:17:18: 34000000 INFO @ Mon, 03 Jun 2019 15:17:20: #2 number of paired peaks: 7895 INFO @ Mon, 03 Jun 2019 15:17:20: start model_add_line... INFO @ Mon, 03 Jun 2019 15:17:20: start X-correlation... INFO @ Mon, 03 Jun 2019 15:17:20: end of X-cor INFO @ Mon, 03 Jun 2019 15:17:20: #2 finished! INFO @ Mon, 03 Jun 2019 15:17:20: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 15:17:20: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 15:17:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.20_model.r INFO @ Mon, 03 Jun 2019 15:17:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:17:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:17:24: 33000000 INFO @ Mon, 03 Jun 2019 15:17:26: 35000000 INFO @ Mon, 03 Jun 2019 15:17:33: 34000000 INFO @ Mon, 03 Jun 2019 15:17:34: 36000000 INFO @ Mon, 03 Jun 2019 15:17:41: 35000000 INFO @ Mon, 03 Jun 2019 15:17:44: 37000000 INFO @ Mon, 03 Jun 2019 15:17:47: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:17:47: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:17:47: #1 total tags in treatment: 17704457 INFO @ Mon, 03 Jun 2019 15:17:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:17:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:17:48: #1 tags after filtering in treatment: 10736678 INFO @ Mon, 03 Jun 2019 15:17:48: #1 Redundant rate of treatment: 0.39 INFO @ Mon, 03 Jun 2019 15:17:48: #1 finished! INFO @ Mon, 03 Jun 2019 15:17:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:17:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:17:50: #2 number of paired peaks: 7895 INFO @ Mon, 03 Jun 2019 15:17:50: start model_add_line... INFO @ Mon, 03 Jun 2019 15:17:50: start X-correlation... INFO @ Mon, 03 Jun 2019 15:17:50: end of X-cor INFO @ Mon, 03 Jun 2019 15:17:50: #2 finished! INFO @ Mon, 03 Jun 2019 15:17:50: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 15:17:50: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 15:17:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.10_model.r INFO @ Mon, 03 Jun 2019 15:17:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:17:50: 36000000 INFO @ Mon, 03 Jun 2019 15:17:59: 37000000 INFO @ Mon, 03 Jun 2019 15:18:03: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:18:03: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:18:03: #1 total tags in treatment: 17704457 INFO @ Mon, 03 Jun 2019 15:18:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:18:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 15:18:04: #1 tags after filtering in treatment: 10736678 INFO @ Mon, 03 Jun 2019 15:18:04: #1 Redundant rate of treatment: 0.39 INFO @ Mon, 03 Jun 2019 15:18:04: #1 finished! INFO @ Mon, 03 Jun 2019 15:18:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:18:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:18:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:18:05: #2 number of paired peaks: 7895 INFO @ Mon, 03 Jun 2019 15:18:05: start model_add_line... INFO @ Mon, 03 Jun 2019 15:18:06: start X-correlation... INFO @ Mon, 03 Jun 2019 15:18:06: end of X-cor INFO @ Mon, 03 Jun 2019 15:18:06: #2 finished! INFO @ Mon, 03 Jun 2019 15:18:06: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 15:18:06: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 15:18:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.05_model.r INFO @ Mon, 03 Jun 2019 15:18:06: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:18:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:18:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:18:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.20_summits.bed INFO @ Mon, 03 Jun 2019 15:18:20: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7130 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:18:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:18:49: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:18:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:18:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:18:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.10_summits.bed INFO @ Mon, 03 Jun 2019 15:18:53: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8529 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:19:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:19:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:19:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393678/SRX3393678.05_summits.bed INFO @ Mon, 03 Jun 2019 15:19:08: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9699 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。