Job ID = 1295457 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 21,426,920 reads read : 42,853,840 reads written : 42,853,840 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: 00:00:01 Multiseed full-index search: 01:00:13 21426920 reads; of these: 21426920 (100.00%) were paired; of these: 2279430 (10.64%) aligned concordantly 0 times 12608472 (58.84%) aligned concordantly exactly 1 time 6539018 (30.52%) aligned concordantly >1 times ---- 2279430 pairs aligned concordantly 0 times; of these: 145344 (6.38%) aligned discordantly 1 time ---- 2134086 pairs aligned 0 times concordantly or discordantly; of these: 4268172 mates make up the pairs; of these: 3083235 (72.24%) aligned 0 times 592929 (13.89%) aligned exactly 1 time 592008 (13.87%) aligned >1 times 92.81% overall alignment rate Time searching: 01:00:14 Overall time: 01:00:14 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] 1088648 / 19215015 = 0.0567 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 15:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.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 15:09:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.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 15:09:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.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 15:09:34: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:09:34: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:09:42: 1000000 INFO @ Mon, 03 Jun 2019 15:09:43: 1000000 INFO @ Mon, 03 Jun 2019 15:09:43: 1000000 INFO @ Mon, 03 Jun 2019 15:09:50: 2000000 INFO @ Mon, 03 Jun 2019 15:09:51: 2000000 INFO @ Mon, 03 Jun 2019 15:09:52: 2000000 INFO @ Mon, 03 Jun 2019 15:09:57: 3000000 INFO @ Mon, 03 Jun 2019 15:09:59: 3000000 INFO @ Mon, 03 Jun 2019 15:10:00: 3000000 INFO @ Mon, 03 Jun 2019 15:10:05: 4000000 INFO @ Mon, 03 Jun 2019 15:10:07: 4000000 INFO @ Mon, 03 Jun 2019 15:10:09: 4000000 INFO @ Mon, 03 Jun 2019 15:10:14: 5000000 INFO @ Mon, 03 Jun 2019 15:10:15: 5000000 INFO @ Mon, 03 Jun 2019 15:10:16: 5000000 INFO @ Mon, 03 Jun 2019 15:10:22: 6000000 INFO @ Mon, 03 Jun 2019 15:10:23: 6000000 INFO @ Mon, 03 Jun 2019 15:10:24: 6000000 INFO @ Mon, 03 Jun 2019 15:10:30: 7000000 INFO @ Mon, 03 Jun 2019 15:10:31: 7000000 INFO @ Mon, 03 Jun 2019 15:10:31: 7000000 INFO @ Mon, 03 Jun 2019 15:10:38: 8000000 INFO @ Mon, 03 Jun 2019 15:10:38: 8000000 INFO @ Mon, 03 Jun 2019 15:10:39: 8000000 INFO @ Mon, 03 Jun 2019 15:10:45: 9000000 INFO @ Mon, 03 Jun 2019 15:10:45: 9000000 INFO @ Mon, 03 Jun 2019 15:10:47: 9000000 INFO @ Mon, 03 Jun 2019 15:10:51: 10000000 INFO @ Mon, 03 Jun 2019 15:10:52: 10000000 INFO @ Mon, 03 Jun 2019 15:10:55: 10000000 INFO @ Mon, 03 Jun 2019 15:10:58: 11000000 INFO @ Mon, 03 Jun 2019 15:11:00: 11000000 INFO @ Mon, 03 Jun 2019 15:11:04: 11000000 INFO @ Mon, 03 Jun 2019 15:11:05: 12000000 INFO @ Mon, 03 Jun 2019 15:11:07: 12000000 INFO @ Mon, 03 Jun 2019 15:11:13: 13000000 INFO @ Mon, 03 Jun 2019 15:11:14: 12000000 INFO @ Mon, 03 Jun 2019 15:11:15: 13000000 INFO @ Mon, 03 Jun 2019 15:11:20: 14000000 INFO @ Mon, 03 Jun 2019 15:11:22: 14000000 INFO @ Mon, 03 Jun 2019 15:11:23: 13000000 INFO @ Mon, 03 Jun 2019 15:11:26: 15000000 INFO @ Mon, 03 Jun 2019 15:11:29: 15000000 INFO @ Mon, 03 Jun 2019 15:11:31: 14000000 INFO @ Mon, 03 Jun 2019 15:11:33: 16000000 INFO @ Mon, 03 Jun 2019 15:11:36: 16000000 INFO @ Mon, 03 Jun 2019 15:11:40: 15000000 INFO @ Mon, 03 Jun 2019 15:11:40: 17000000 INFO @ Mon, 03 Jun 2019 15:11:43: 17000000 INFO @ Mon, 03 Jun 2019 15:11:46: 18000000 INFO @ Mon, 03 Jun 2019 15:11:48: 16000000 INFO @ Mon, 03 Jun 2019 15:11:51: 18000000 INFO @ Mon, 03 Jun 2019 15:11:53: 19000000 INFO @ Mon, 03 Jun 2019 15:11:56: 17000000 INFO @ Mon, 03 Jun 2019 15:11:58: 19000000 INFO @ Mon, 03 Jun 2019 15:12:00: 20000000 INFO @ Mon, 03 Jun 2019 15:12:05: 18000000 INFO @ Mon, 03 Jun 2019 15:12:05: 20000000 INFO @ Mon, 03 Jun 2019 15:12:06: 21000000 INFO @ Mon, 03 Jun 2019 15:12:12: 21000000 INFO @ Mon, 03 Jun 2019 15:12:13: 22000000 INFO @ Mon, 03 Jun 2019 15:12:14: 19000000 INFO @ Mon, 03 Jun 2019 15:12:19: 23000000 INFO @ Mon, 03 Jun 2019 15:12:20: 22000000 INFO @ Mon, 03 Jun 2019 15:12:23: 20000000 INFO @ Mon, 03 Jun 2019 15:12:27: 24000000 INFO @ Mon, 03 Jun 2019 15:12:27: 23000000 INFO @ Mon, 03 Jun 2019 15:12:31: 21000000 INFO @ Mon, 03 Jun 2019 15:12:34: 25000000 INFO @ Mon, 03 Jun 2019 15:12:34: 24000000 INFO @ Mon, 03 Jun 2019 15:12:40: 22000000 INFO @ Mon, 03 Jun 2019 15:12:42: 26000000 INFO @ Mon, 03 Jun 2019 15:12:42: 25000000 INFO @ Mon, 03 Jun 2019 15:12:48: 23000000 INFO @ Mon, 03 Jun 2019 15:12:48: 27000000 INFO @ Mon, 03 Jun 2019 15:12:49: 26000000 INFO @ Mon, 03 Jun 2019 15:12:54: 28000000 INFO @ Mon, 03 Jun 2019 15:12:56: 24000000 INFO @ Mon, 03 Jun 2019 15:12:56: 27000000 INFO @ Mon, 03 Jun 2019 15:13:01: 29000000 INFO @ Mon, 03 Jun 2019 15:13:04: 28000000 INFO @ Mon, 03 Jun 2019 15:13:04: 25000000 INFO @ Mon, 03 Jun 2019 15:13:07: 30000000 INFO @ Mon, 03 Jun 2019 15:13:11: 29000000 INFO @ Mon, 03 Jun 2019 15:13:13: 31000000 INFO @ Mon, 03 Jun 2019 15:13:14: 26000000 INFO @ Mon, 03 Jun 2019 15:13:18: 30000000 INFO @ Mon, 03 Jun 2019 15:13:20: 32000000 INFO @ Mon, 03 Jun 2019 15:13:23: 27000000 INFO @ Mon, 03 Jun 2019 15:13:25: 31000000 INFO @ Mon, 03 Jun 2019 15:13:26: 33000000 INFO @ Mon, 03 Jun 2019 15:13:31: 28000000 INFO @ Mon, 03 Jun 2019 15:13:32: 32000000 INFO @ Mon, 03 Jun 2019 15:13:33: 34000000 INFO @ Mon, 03 Jun 2019 15:13:39: 35000000 INFO @ Mon, 03 Jun 2019 15:13:39: 29000000 INFO @ Mon, 03 Jun 2019 15:13:40: 33000000 INFO @ Mon, 03 Jun 2019 15:13:45: 36000000 INFO @ Mon, 03 Jun 2019 15:13:47: 34000000 INFO @ Mon, 03 Jun 2019 15:13:48: 30000000 INFO @ Mon, 03 Jun 2019 15:13:52: 37000000 INFO @ Mon, 03 Jun 2019 15:13:54: 35000000 INFO @ Mon, 03 Jun 2019 15:13:56: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:13:56: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:13:56: #1 total tags in treatment: 18060004 INFO @ Mon, 03 Jun 2019 15:13:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:13:56: #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 15:13:56: #1 tags after filtering in treatment: 16379516 INFO @ Mon, 03 Jun 2019 15:13:56: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 15:13:56: #1 finished! INFO @ Mon, 03 Jun 2019 15:13:56: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:13:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:13:56: 31000000 INFO @ Mon, 03 Jun 2019 15:13:58: #2 number of paired peaks: 1319 INFO @ Mon, 03 Jun 2019 15:13:58: start model_add_line... INFO @ Mon, 03 Jun 2019 15:13:58: start X-correlation... INFO @ Mon, 03 Jun 2019 15:13:58: end of X-cor INFO @ Mon, 03 Jun 2019 15:13:58: #2 finished! INFO @ Mon, 03 Jun 2019 15:13:58: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 15:13:58: #2 alternative fragment length(s) may be 4,168 bps INFO @ Mon, 03 Jun 2019 15:13:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.05_model.r INFO @ Mon, 03 Jun 2019 15:13:58: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:13:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:14:02: 36000000 INFO @ Mon, 03 Jun 2019 15:14:05: 32000000 INFO @ Mon, 03 Jun 2019 15:14:09: 37000000 INFO @ Mon, 03 Jun 2019 15:14:13: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:14:13: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:14:13: #1 total tags in treatment: 18060004 INFO @ Mon, 03 Jun 2019 15:14:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:14:13: #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 15:14:14: #1 tags after filtering in treatment: 16379516 INFO @ Mon, 03 Jun 2019 15:14:14: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 15:14:14: #1 finished! INFO @ Mon, 03 Jun 2019 15:14:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:14:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:14:14: 33000000 INFO @ Mon, 03 Jun 2019 15:14:15: #2 number of paired peaks: 1319 INFO @ Mon, 03 Jun 2019 15:14:15: start model_add_line... INFO @ Mon, 03 Jun 2019 15:14:15: start X-correlation... INFO @ Mon, 03 Jun 2019 15:14:16: end of X-cor INFO @ Mon, 03 Jun 2019 15:14:16: #2 finished! INFO @ Mon, 03 Jun 2019 15:14:16: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 15:14:16: #2 alternative fragment length(s) may be 4,168 bps INFO @ Mon, 03 Jun 2019 15:14:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.10_model.r INFO @ Mon, 03 Jun 2019 15:14:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:14:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:14:23: 34000000 INFO @ Mon, 03 Jun 2019 15:14:31: 35000000 INFO @ Mon, 03 Jun 2019 15:14:39: 36000000 INFO @ Mon, 03 Jun 2019 15:14:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:14:47: 37000000 INFO @ Mon, 03 Jun 2019 15:14:51: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:14:51: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:14:51: #1 total tags in treatment: 18060004 INFO @ Mon, 03 Jun 2019 15:14:51: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:14:51: #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 15:14:52: #1 tags after filtering in treatment: 16379516 INFO @ Mon, 03 Jun 2019 15:14:52: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 15:14:52: #1 finished! INFO @ Mon, 03 Jun 2019 15:14:52: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:14:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:14:53: #2 number of paired peaks: 1319 INFO @ Mon, 03 Jun 2019 15:14:53: start model_add_line... INFO @ Mon, 03 Jun 2019 15:14:54: start X-correlation... INFO @ Mon, 03 Jun 2019 15:14:54: end of X-cor INFO @ Mon, 03 Jun 2019 15:14:54: #2 finished! INFO @ Mon, 03 Jun 2019 15:14:54: #2 predicted fragment length is 168 bps INFO @ Mon, 03 Jun 2019 15:14:54: #2 alternative fragment length(s) may be 4,168 bps INFO @ Mon, 03 Jun 2019 15:14:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.20_model.r INFO @ Mon, 03 Jun 2019 15:14:54: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:14:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:15:03: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:15:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:15:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:15:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.05_summits.bed INFO @ Mon, 03 Jun 2019 15:15:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3136 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:15:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:15:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:15:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.10_summits.bed INFO @ Mon, 03 Jun 2019 15:15:25: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1899 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:15:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:16:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:16:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:16:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393661/SRX3393661.20_summits.bed INFO @ Mon, 03 Jun 2019 15:16:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1050 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。