Job ID = 1294359 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 24,311,725 reads read : 48,623,450 reads written : 48,623,450 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: 00:58:24 24311725 reads; of these: 24311725 (100.00%) were paired; of these: 2705944 (11.13%) aligned concordantly 0 times 15483937 (63.69%) aligned concordantly exactly 1 time 6121844 (25.18%) aligned concordantly >1 times ---- 2705944 pairs aligned concordantly 0 times; of these: 68230 (2.52%) aligned discordantly 1 time ---- 2637714 pairs aligned 0 times concordantly or discordantly; of these: 5275428 mates make up the pairs; of these: 4451326 (84.38%) aligned 0 times 575224 (10.90%) aligned exactly 1 time 248878 (4.72%) aligned >1 times 90.85% overall alignment rate Time searching: 00:58:24 Overall time: 00:58:24 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 20 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] 3819573 / 21651461 = 0.1764 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 08:21:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.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 08:21:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.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 08:21:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.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 08:21:40: #1 read tag files... INFO @ Mon, 03 Jun 2019 08:21:40: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 08:21:47: 1000000 INFO @ Mon, 03 Jun 2019 08:21:48: 1000000 INFO @ Mon, 03 Jun 2019 08:21:49: 1000000 INFO @ Mon, 03 Jun 2019 08:21:54: 2000000 INFO @ Mon, 03 Jun 2019 08:21:56: 2000000 INFO @ Mon, 03 Jun 2019 08:21:59: 2000000 INFO @ Mon, 03 Jun 2019 08:22:01: 3000000 INFO @ Mon, 03 Jun 2019 08:22:03: 3000000 INFO @ Mon, 03 Jun 2019 08:22:08: 3000000 INFO @ Mon, 03 Jun 2019 08:22:08: 4000000 INFO @ Mon, 03 Jun 2019 08:22:11: 4000000 INFO @ Mon, 03 Jun 2019 08:22:14: 5000000 INFO @ Mon, 03 Jun 2019 08:22:17: 4000000 INFO @ Mon, 03 Jun 2019 08:22:19: 5000000 INFO @ Mon, 03 Jun 2019 08:22:21: 6000000 INFO @ Mon, 03 Jun 2019 08:22:25: 5000000 INFO @ Mon, 03 Jun 2019 08:22:26: 6000000 INFO @ Mon, 03 Jun 2019 08:22:28: 7000000 INFO @ Mon, 03 Jun 2019 08:22:34: 7000000 INFO @ Mon, 03 Jun 2019 08:22:34: 6000000 INFO @ Mon, 03 Jun 2019 08:22:35: 8000000 INFO @ Mon, 03 Jun 2019 08:22:41: 9000000 INFO @ Mon, 03 Jun 2019 08:22:42: 8000000 INFO @ Mon, 03 Jun 2019 08:22:43: 7000000 INFO @ Mon, 03 Jun 2019 08:22:48: 10000000 INFO @ Mon, 03 Jun 2019 08:22:49: 9000000 INFO @ Mon, 03 Jun 2019 08:22:52: 8000000 INFO @ Mon, 03 Jun 2019 08:22:55: 11000000 INFO @ Mon, 03 Jun 2019 08:22:57: 10000000 INFO @ Mon, 03 Jun 2019 08:23:01: 9000000 INFO @ Mon, 03 Jun 2019 08:23:01: 12000000 INFO @ Mon, 03 Jun 2019 08:23:05: 11000000 INFO @ Mon, 03 Jun 2019 08:23:08: 13000000 INFO @ Mon, 03 Jun 2019 08:23:10: 10000000 INFO @ Mon, 03 Jun 2019 08:23:12: 12000000 INFO @ Mon, 03 Jun 2019 08:23:15: 14000000 INFO @ Mon, 03 Jun 2019 08:23:19: 11000000 INFO @ Mon, 03 Jun 2019 08:23:20: 13000000 INFO @ Mon, 03 Jun 2019 08:23:22: 15000000 INFO @ Mon, 03 Jun 2019 08:23:27: 14000000 INFO @ Mon, 03 Jun 2019 08:23:28: 12000000 INFO @ Mon, 03 Jun 2019 08:23:28: 16000000 INFO @ Mon, 03 Jun 2019 08:23:35: 15000000 INFO @ Mon, 03 Jun 2019 08:23:35: 17000000 INFO @ Mon, 03 Jun 2019 08:23:37: 13000000 INFO @ Mon, 03 Jun 2019 08:23:42: 18000000 INFO @ Mon, 03 Jun 2019 08:23:42: 16000000 INFO @ Mon, 03 Jun 2019 08:23:46: 14000000 INFO @ Mon, 03 Jun 2019 08:23:48: 19000000 INFO @ Mon, 03 Jun 2019 08:23:50: 17000000 INFO @ Mon, 03 Jun 2019 08:23:55: 15000000 INFO @ Mon, 03 Jun 2019 08:23:55: 20000000 INFO @ Mon, 03 Jun 2019 08:23:57: 18000000 INFO @ Mon, 03 Jun 2019 08:24:02: 21000000 INFO @ Mon, 03 Jun 2019 08:24:04: 16000000 INFO @ Mon, 03 Jun 2019 08:24:05: 19000000 INFO @ Mon, 03 Jun 2019 08:24:08: 22000000 INFO @ Mon, 03 Jun 2019 08:24:12: 20000000 INFO @ Mon, 03 Jun 2019 08:24:14: 17000000 INFO @ Mon, 03 Jun 2019 08:24:15: 23000000 INFO @ Mon, 03 Jun 2019 08:24:20: 21000000 INFO @ Mon, 03 Jun 2019 08:24:21: 24000000 INFO @ Mon, 03 Jun 2019 08:24:23: 18000000 INFO @ Mon, 03 Jun 2019 08:24:27: 22000000 INFO @ Mon, 03 Jun 2019 08:24:28: 25000000 INFO @ Mon, 03 Jun 2019 08:24:32: 19000000 INFO @ Mon, 03 Jun 2019 08:24:34: 23000000 INFO @ Mon, 03 Jun 2019 08:24:34: 26000000 INFO @ Mon, 03 Jun 2019 08:24:41: 20000000 INFO @ Mon, 03 Jun 2019 08:24:41: 27000000 INFO @ Mon, 03 Jun 2019 08:24:42: 24000000 INFO @ Mon, 03 Jun 2019 08:24:48: 28000000 INFO @ Mon, 03 Jun 2019 08:24:49: 25000000 INFO @ Mon, 03 Jun 2019 08:24:49: 21000000 INFO @ Mon, 03 Jun 2019 08:24:54: 29000000 INFO @ Mon, 03 Jun 2019 08:24:56: 26000000 INFO @ Mon, 03 Jun 2019 08:24:58: 22000000 INFO @ Mon, 03 Jun 2019 08:25:01: 30000000 INFO @ Mon, 03 Jun 2019 08:25:03: 27000000 INFO @ Mon, 03 Jun 2019 08:25:06: 23000000 INFO @ Mon, 03 Jun 2019 08:25:07: 31000000 INFO @ Mon, 03 Jun 2019 08:25:10: 28000000 INFO @ Mon, 03 Jun 2019 08:25:14: 32000000 INFO @ Mon, 03 Jun 2019 08:25:15: 24000000 INFO @ Mon, 03 Jun 2019 08:25:18: 29000000 INFO @ Mon, 03 Jun 2019 08:25:20: 33000000 INFO @ Mon, 03 Jun 2019 08:25:23: 25000000 INFO @ Mon, 03 Jun 2019 08:25:25: 30000000 INFO @ Mon, 03 Jun 2019 08:25:27: 34000000 INFO @ Mon, 03 Jun 2019 08:25:32: 26000000 INFO @ Mon, 03 Jun 2019 08:25:32: 31000000 INFO @ Mon, 03 Jun 2019 08:25:34: 35000000 INFO @ Mon, 03 Jun 2019 08:25:39: 32000000 INFO @ Mon, 03 Jun 2019 08:25:40: 36000000 INFO @ Mon, 03 Jun 2019 08:25:40: 27000000 INFO @ Mon, 03 Jun 2019 08:25:44: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:25:44: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:25:44: #1 total tags in treatment: 17791640 INFO @ Mon, 03 Jun 2019 08:25:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:25:44: #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 08:25:44: #1 tags after filtering in treatment: 15869348 INFO @ Mon, 03 Jun 2019 08:25:44: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:25:44: #1 finished! INFO @ Mon, 03 Jun 2019 08:25:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:25:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:25:46: #2 number of paired peaks: 466 WARNING @ Mon, 03 Jun 2019 08:25:46: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Mon, 03 Jun 2019 08:25:46: start model_add_line... INFO @ Mon, 03 Jun 2019 08:25:46: start X-correlation... INFO @ Mon, 03 Jun 2019 08:25:46: end of X-cor INFO @ Mon, 03 Jun 2019 08:25:46: #2 finished! INFO @ Mon, 03 Jun 2019 08:25:46: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 08:25:46: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 08:25:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.20_model.r INFO @ Mon, 03 Jun 2019 08:25:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:25:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:25:47: 33000000 INFO @ Mon, 03 Jun 2019 08:25:49: 28000000 INFO @ Mon, 03 Jun 2019 08:25:54: 34000000 INFO @ Mon, 03 Jun 2019 08:25:57: 29000000 INFO @ Mon, 03 Jun 2019 08:26:01: 35000000 INFO @ Mon, 03 Jun 2019 08:26:06: 30000000 INFO @ Mon, 03 Jun 2019 08:26:09: 36000000 INFO @ Mon, 03 Jun 2019 08:26:13: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:26:13: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:26:13: #1 total tags in treatment: 17791640 INFO @ Mon, 03 Jun 2019 08:26:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:26:13: #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 08:26:13: #1 tags after filtering in treatment: 15869348 INFO @ Mon, 03 Jun 2019 08:26:13: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:26:13: #1 finished! INFO @ Mon, 03 Jun 2019 08:26:13: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:26:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:26:14: 31000000 INFO @ Mon, 03 Jun 2019 08:26:15: #2 number of paired peaks: 466 WARNING @ Mon, 03 Jun 2019 08:26:15: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Mon, 03 Jun 2019 08:26:15: start model_add_line... INFO @ Mon, 03 Jun 2019 08:26:15: start X-correlation... INFO @ Mon, 03 Jun 2019 08:26:15: end of X-cor INFO @ Mon, 03 Jun 2019 08:26:15: #2 finished! INFO @ Mon, 03 Jun 2019 08:26:15: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 08:26:15: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 08:26:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.05_model.r INFO @ Mon, 03 Jun 2019 08:26:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:26:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:26:23: 32000000 INFO @ Mon, 03 Jun 2019 08:26:29: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:26:31: 33000000 INFO @ Mon, 03 Jun 2019 08:26:39: 34000000 INFO @ Mon, 03 Jun 2019 08:26:47: 35000000 INFO @ Mon, 03 Jun 2019 08:26:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.20_peaks.xls INFO @ Mon, 03 Jun 2019 08:26:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:26:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.20_summits.bed INFO @ Mon, 03 Jun 2019 08:26:50: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (975 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:26:56: 36000000 INFO @ Mon, 03 Jun 2019 08:26:58: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:27:00: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 08:27:00: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 08:27:00: #1 total tags in treatment: 17791640 INFO @ Mon, 03 Jun 2019 08:27:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 08:27:00: #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 08:27:01: #1 tags after filtering in treatment: 15869348 INFO @ Mon, 03 Jun 2019 08:27:01: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 08:27:01: #1 finished! INFO @ Mon, 03 Jun 2019 08:27:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 08:27:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 08:27:02: #2 number of paired peaks: 466 WARNING @ Mon, 03 Jun 2019 08:27:02: Fewer paired peaks (466) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 466 pairs to build model! INFO @ Mon, 03 Jun 2019 08:27:02: start model_add_line... INFO @ Mon, 03 Jun 2019 08:27:02: start X-correlation... INFO @ Mon, 03 Jun 2019 08:27:02: end of X-cor INFO @ Mon, 03 Jun 2019 08:27:02: #2 finished! INFO @ Mon, 03 Jun 2019 08:27:02: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 08:27:02: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 08:27:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.10_model.r INFO @ Mon, 03 Jun 2019 08:27:02: #3 Call peaks... INFO @ Mon, 03 Jun 2019 08:27:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 08:27:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.05_peaks.xls INFO @ Mon, 03 Jun 2019 08:27:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:27:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.05_summits.bed INFO @ Mon, 03 Jun 2019 08:27:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2734 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 08:27:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 08:28:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.10_peaks.xls INFO @ Mon, 03 Jun 2019 08:28:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 08:28:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2612524/SRX2612524.10_summits.bed INFO @ Mon, 03 Jun 2019 08:28:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1689 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。