Job ID = 10487610 sra ファイルのダウンロード中... Completed: 1299354K bytes transferred in 82 seconds (128475K bits/sec), in 1 file. sra ファイルのダウンロードが完了しました。 Read layout: SINGLE fastq に変換中... Written 48757790 spots for /home/okishinya/chipatlas/results/rn6/SRX3087689/SRR5927325.sra Written 48757790 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:58:02 48757790 reads; of these: 48757790 (100.00%) were unpaired; of these: 1577876 (3.24%) aligned 0 times 34454853 (70.67%) aligned exactly 1 time 12725061 (26.10%) aligned >1 times 96.76% overall alignment rate Time searching: 00:58:04 Overall time: 00:58:04 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 20 files... [bam_rmdupse_core] 5948203 / 47179914 = 0.1261 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 @ Sun, 18 Mar 2018 11:15:19: # Command line: callpeak -t SRX3087689.bam -f BAM -g 2.15e9 -n SRX3087689.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087689.05 # format = BAM # ChIP-seq file = ['SRX3087689.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sun, 18 Mar 2018 11:15:19: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:15:19: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:15:19: # Command line: callpeak -t SRX3087689.bam -f BAM -g 2.15e9 -n SRX3087689.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087689.10 # format = BAM # ChIP-seq file = ['SRX3087689.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sun, 18 Mar 2018 11:15:19: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:15:19: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:15:19: # Command line: callpeak -t SRX3087689.bam -f BAM -g 2.15e9 -n SRX3087689.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087689.20 # format = BAM # ChIP-seq file = ['SRX3087689.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sun, 18 Mar 2018 11:15:19: #1 read tag files... INFO @ Sun, 18 Mar 2018 11:15:19: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 11:15:27: 1000000 INFO @ Sun, 18 Mar 2018 11:15:27: 1000000 INFO @ Sun, 18 Mar 2018 11:15:27: 1000000 INFO @ Sun, 18 Mar 2018 11:15:34: 2000000 INFO @ Sun, 18 Mar 2018 11:15:35: 2000000 INFO @ Sun, 18 Mar 2018 11:15:35: 2000000 INFO @ Sun, 18 Mar 2018 11:15:42: 3000000 INFO @ Sun, 18 Mar 2018 11:15:43: 3000000 INFO @ Sun, 18 Mar 2018 11:15:43: 3000000 INFO @ Sun, 18 Mar 2018 11:15:49: 4000000 INFO @ Sun, 18 Mar 2018 11:15:51: 4000000 INFO @ Sun, 18 Mar 2018 11:15:51: 4000000 INFO @ Sun, 18 Mar 2018 11:15:57: 5000000 INFO @ Sun, 18 Mar 2018 11:15:58: 5000000 INFO @ Sun, 18 Mar 2018 11:15:58: 5000000 INFO @ Sun, 18 Mar 2018 11:16:04: 6000000 INFO @ Sun, 18 Mar 2018 11:16:06: 6000000 INFO @ Sun, 18 Mar 2018 11:16:06: 6000000 INFO @ Sun, 18 Mar 2018 11:16:12: 7000000 INFO @ Sun, 18 Mar 2018 11:16:14: 7000000 INFO @ Sun, 18 Mar 2018 11:16:14: 7000000 INFO @ Sun, 18 Mar 2018 11:16:19: 8000000 INFO @ Sun, 18 Mar 2018 11:16:22: 8000000 INFO @ Sun, 18 Mar 2018 11:16:22: 8000000 INFO @ Sun, 18 Mar 2018 11:16:27: 9000000 INFO @ Sun, 18 Mar 2018 11:16:30: 9000000 INFO @ Sun, 18 Mar 2018 11:16:30: 9000000 INFO @ Sun, 18 Mar 2018 11:16:34: 10000000 INFO @ Sun, 18 Mar 2018 11:16:37: 10000000 INFO @ Sun, 18 Mar 2018 11:16:38: 10000000 INFO @ Sun, 18 Mar 2018 11:16:42: 11000000 INFO @ Sun, 18 Mar 2018 11:16:45: 11000000 INFO @ Sun, 18 Mar 2018 11:16:45: 11000000 INFO @ Sun, 18 Mar 2018 11:16:49: 12000000 INFO @ Sun, 18 Mar 2018 11:16:53: 12000000 INFO @ Sun, 18 Mar 2018 11:16:53: 12000000 INFO @ Sun, 18 Mar 2018 11:16:57: 13000000 INFO @ Sun, 18 Mar 2018 11:17:01: 13000000 INFO @ Sun, 18 Mar 2018 11:17:01: 13000000 INFO @ Sun, 18 Mar 2018 11:17:04: 14000000 INFO @ Sun, 18 Mar 2018 11:17:08: 14000000 INFO @ Sun, 18 Mar 2018 11:17:09: 14000000 INFO @ Sun, 18 Mar 2018 11:17:12: 15000000 INFO @ Sun, 18 Mar 2018 11:17:16: 15000000 INFO @ Sun, 18 Mar 2018 11:17:16: 15000000 INFO @ Sun, 18 Mar 2018 11:17:19: 16000000 INFO @ Sun, 18 Mar 2018 11:17:24: 16000000 INFO @ Sun, 18 Mar 2018 11:17:24: 16000000 INFO @ Sun, 18 Mar 2018 11:17:27: 17000000 INFO @ Sun, 18 Mar 2018 11:17:32: 17000000 INFO @ Sun, 18 Mar 2018 11:17:32: 17000000 INFO @ Sun, 18 Mar 2018 11:17:34: 18000000 INFO @ Sun, 18 Mar 2018 11:17:39: 18000000 INFO @ Sun, 18 Mar 2018 11:17:40: 18000000 INFO @ Sun, 18 Mar 2018 11:17:42: 19000000 INFO @ Sun, 18 Mar 2018 11:17:47: 19000000 INFO @ Sun, 18 Mar 2018 11:17:48: 19000000 INFO @ Sun, 18 Mar 2018 11:17:49: 20000000 INFO @ Sun, 18 Mar 2018 11:17:55: 20000000 INFO @ Sun, 18 Mar 2018 11:17:55: 20000000 INFO @ Sun, 18 Mar 2018 11:17:57: 21000000 INFO @ Sun, 18 Mar 2018 11:18:03: 21000000 INFO @ Sun, 18 Mar 2018 11:18:03: 21000000 INFO @ Sun, 18 Mar 2018 11:18:04: 22000000 INFO @ Sun, 18 Mar 2018 11:18:11: 22000000 INFO @ Sun, 18 Mar 2018 11:18:11: 22000000 INFO @ Sun, 18 Mar 2018 11:18:12: 23000000 INFO @ Sun, 18 Mar 2018 11:18:18: 23000000 INFO @ Sun, 18 Mar 2018 11:18:19: 23000000 INFO @ Sun, 18 Mar 2018 11:18:19: 24000000 INFO @ Sun, 18 Mar 2018 11:18:26: 24000000 INFO @ Sun, 18 Mar 2018 11:18:27: 24000000 INFO @ Sun, 18 Mar 2018 11:18:27: 25000000 INFO @ Sun, 18 Mar 2018 11:18:34: 25000000 INFO @ Sun, 18 Mar 2018 11:18:34: 26000000 INFO @ Sun, 18 Mar 2018 11:18:34: 25000000 INFO @ Sun, 18 Mar 2018 11:18:42: 26000000 INFO @ Sun, 18 Mar 2018 11:18:42: 27000000 INFO @ Sun, 18 Mar 2018 11:18:42: 26000000 INFO @ Sun, 18 Mar 2018 11:18:50: 27000000 INFO @ Sun, 18 Mar 2018 11:18:51: 27000000 INFO @ Sun, 18 Mar 2018 11:18:52: 28000000 INFO @ Sun, 18 Mar 2018 11:18:59: 28000000 INFO @ Sun, 18 Mar 2018 11:18:59: 28000000 INFO @ Sun, 18 Mar 2018 11:19:01: 29000000 INFO @ Sun, 18 Mar 2018 11:19:08: 29000000 INFO @ Sun, 18 Mar 2018 11:19:08: 29000000 INFO @ Sun, 18 Mar 2018 11:19:11: 30000000 INFO @ Sun, 18 Mar 2018 11:19:17: 30000000 INFO @ Sun, 18 Mar 2018 11:19:17: 30000000 INFO @ Sun, 18 Mar 2018 11:19:21: 31000000 INFO @ Sun, 18 Mar 2018 11:19:26: 31000000 INFO @ Sun, 18 Mar 2018 11:19:27: 31000000 INFO @ Sun, 18 Mar 2018 11:19:31: 32000000 INFO @ Sun, 18 Mar 2018 11:19:35: 32000000 INFO @ Sun, 18 Mar 2018 11:19:36: 32000000 INFO @ Sun, 18 Mar 2018 11:19:41: 33000000 INFO @ Sun, 18 Mar 2018 11:19:44: 33000000 INFO @ Sun, 18 Mar 2018 11:19:45: 33000000 INFO @ Sun, 18 Mar 2018 11:19:51: 34000000 INFO @ Sun, 18 Mar 2018 11:19:53: 34000000 INFO @ Sun, 18 Mar 2018 11:19:54: 34000000 INFO @ Sun, 18 Mar 2018 11:20:00: 35000000 INFO @ Sun, 18 Mar 2018 11:20:01: 35000000 INFO @ Sun, 18 Mar 2018 11:20:02: 35000000 INFO @ Sun, 18 Mar 2018 11:20:10: 36000000 INFO @ Sun, 18 Mar 2018 11:20:10: 36000000 INFO @ Sun, 18 Mar 2018 11:20:11: 36000000 INFO @ Sun, 18 Mar 2018 11:20:18: 37000000 INFO @ Sun, 18 Mar 2018 11:20:19: 37000000 INFO @ Sun, 18 Mar 2018 11:20:20: 37000000 INFO @ Sun, 18 Mar 2018 11:20:27: 38000000 INFO @ Sun, 18 Mar 2018 11:20:28: 38000000 INFO @ Sun, 18 Mar 2018 11:20:29: 38000000 INFO @ Sun, 18 Mar 2018 11:20:35: 39000000 INFO @ Sun, 18 Mar 2018 11:20:37: 39000000 INFO @ Sun, 18 Mar 2018 11:20:38: 39000000 INFO @ Sun, 18 Mar 2018 11:20:44: 40000000 INFO @ Sun, 18 Mar 2018 11:20:46: 40000000 INFO @ Sun, 18 Mar 2018 11:20:48: 40000000 INFO @ Sun, 18 Mar 2018 11:20:53: 41000000 INFO @ Sun, 18 Mar 2018 11:20:55: 41000000 INFO @ Sun, 18 Mar 2018 11:20:55: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:20:55: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:20:55: #1 total tags in treatment: 41231711 INFO @ Sun, 18 Mar 2018 11:20:55: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:20:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:20:56: #1 tags after filtering in treatment: 41231640 INFO @ Sun, 18 Mar 2018 11:20:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:20:56: #1 finished! INFO @ Sun, 18 Mar 2018 11:20:56: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:20:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:20:57: 41000000 INFO @ Sun, 18 Mar 2018 11:20:57: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:20:57: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:20:57: #1 total tags in treatment: 41231711 INFO @ Sun, 18 Mar 2018 11:20:57: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:20:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:20:58: #1 tags after filtering in treatment: 41231640 INFO @ Sun, 18 Mar 2018 11:20:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:20:58: #1 finished! INFO @ Sun, 18 Mar 2018 11:20:58: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:20:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:20:59: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:20:59: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:20:59: #1 total tags in treatment: 41231711 INFO @ Sun, 18 Mar 2018 11:20:59: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:20:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 11:21:00: #1 tags after filtering in treatment: 41231640 INFO @ Sun, 18 Mar 2018 11:21:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:21:00: #1 finished! INFO @ Sun, 18 Mar 2018 11:21:00: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:21:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:21:00: #2 number of paired peaks: 5342 INFO @ Sun, 18 Mar 2018 11:21:00: start model_add_line... INFO @ Sun, 18 Mar 2018 11:21:01: start X-correlation... INFO @ Sun, 18 Mar 2018 11:21:01: end of X-cor INFO @ Sun, 18 Mar 2018 11:21:01: #2 finished! INFO @ Sun, 18 Mar 2018 11:21:01: #2 predicted fragment length is 61 bps INFO @ Sun, 18 Mar 2018 11:21:01: #2 alternative fragment length(s) may be 61 bps INFO @ Sun, 18 Mar 2018 11:21:01: #2.2 Generate R script for model : SRX3087689.10_model.r WARNING @ Sun, 18 Mar 2018 11:21:01: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:21:01: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sun, 18 Mar 2018 11:21:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:21:01: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:21:02: #2 number of paired peaks: 5342 INFO @ Sun, 18 Mar 2018 11:21:02: start model_add_line... INFO @ Sun, 18 Mar 2018 11:21:03: start X-correlation... INFO @ Sun, 18 Mar 2018 11:21:03: end of X-cor INFO @ Sun, 18 Mar 2018 11:21:03: #2 finished! INFO @ Sun, 18 Mar 2018 11:21:03: #2 predicted fragment length is 61 bps INFO @ Sun, 18 Mar 2018 11:21:03: #2 alternative fragment length(s) may be 61 bps INFO @ Sun, 18 Mar 2018 11:21:03: #2.2 Generate R script for model : SRX3087689.05_model.r WARNING @ Sun, 18 Mar 2018 11:21:03: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:21:03: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sun, 18 Mar 2018 11:21:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:21:03: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:21:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:21:04: #2 number of paired peaks: 5342 INFO @ Sun, 18 Mar 2018 11:21:04: start model_add_line... INFO @ Sun, 18 Mar 2018 11:21:04: start X-correlation... INFO @ Sun, 18 Mar 2018 11:21:04: end of X-cor INFO @ Sun, 18 Mar 2018 11:21:04: #2 finished! INFO @ Sun, 18 Mar 2018 11:21:04: #2 predicted fragment length is 61 bps INFO @ Sun, 18 Mar 2018 11:21:04: #2 alternative fragment length(s) may be 61 bps INFO @ Sun, 18 Mar 2018 11:21:04: #2.2 Generate R script for model : SRX3087689.20_model.r WARNING @ Sun, 18 Mar 2018 11:21:04: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 11:21:04: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sun, 18 Mar 2018 11:21:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 18 Mar 2018 11:21:04: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:21:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:22:36: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:22:40: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:22:42: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:23:34: #4 Write output xls file... SRX3087689.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:23:34: #4 Write peak in narrowPeak format file... SRX3087689.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:23:34: #4 Write summits bed file... SRX3087689.05_summits.bed INFO @ Sun, 18 Mar 2018 11:23:34: Done! pass1 - making usageList (54 chroms): 1 millis pass2 - checking and writing primary data (2055 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:23:35: #4 Write output xls file... SRX3087689.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:23:35: #4 Write peak in narrowPeak format file... SRX3087689.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:23:35: #4 Write summits bed file... SRX3087689.20_summits.bed INFO @ Sun, 18 Mar 2018 11:23:35: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (575 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:23:35: #4 Write output xls file... SRX3087689.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:23:35: #4 Write peak in narrowPeak format file... SRX3087689.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:23:36: #4 Write summits bed file... SRX3087689.10_summits.bed INFO @ Sun, 18 Mar 2018 11:23:36: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (1155 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。