Job ID = 11192589 sra ファイルのダウンロード中... Completed: 588399K bytes transferred in 8 seconds (566821K 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... Read 50288440 spots for /home/okishinya/chipatlas/results/rn6/SRX4014809/SRR7085058.sra Written 50288440 spots for /home/okishinya/chipatlas/results/rn6/SRX4014809/SRR7085058.sra 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: 00:00:03 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:57:36 50288440 reads; of these: 50288440 (100.00%) were unpaired; of these: 1485799 (2.95%) aligned 0 times 36229610 (72.04%) aligned exactly 1 time 12573031 (25.00%) aligned >1 times 97.05% overall alignment rate Time searching: 00:57:45 Overall time: 00:57:45 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] 5287992 / 48802641 = 0.1084 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 @ Sat, 15 Sep 2018 12:20:37: # Command line: callpeak -t SRX4014809.bam -f BAM -g 2.15e9 -n SRX4014809.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014809.05 # format = BAM # ChIP-seq file = ['SRX4014809.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 @ Sat, 15 Sep 2018 12:20:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 12:20:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 12:20:37: # Command line: callpeak -t SRX4014809.bam -f BAM -g 2.15e9 -n SRX4014809.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014809.10 # format = BAM # ChIP-seq file = ['SRX4014809.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 @ Sat, 15 Sep 2018 12:20:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 12:20:37: # Command line: callpeak -t SRX4014809.bam -f BAM -g 2.15e9 -n SRX4014809.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014809.20 # format = BAM # ChIP-seq file = ['SRX4014809.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 @ Sat, 15 Sep 2018 12:20:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 12:20:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 12:20:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 12:20:43: 1000000 INFO @ Sat, 15 Sep 2018 12:20:43: 1000000 INFO @ Sat, 15 Sep 2018 12:20:44: 1000000 INFO @ Sat, 15 Sep 2018 12:20:50: 2000000 INFO @ Sat, 15 Sep 2018 12:20:50: 2000000 INFO @ Sat, 15 Sep 2018 12:20:50: 2000000 INFO @ Sat, 15 Sep 2018 12:20:56: 3000000 INFO @ Sat, 15 Sep 2018 12:20:57: 3000000 INFO @ Sat, 15 Sep 2018 12:20:57: 3000000 INFO @ Sat, 15 Sep 2018 12:21:02: 4000000 INFO @ Sat, 15 Sep 2018 12:21:04: 4000000 INFO @ Sat, 15 Sep 2018 12:21:05: 4000000 INFO @ Sat, 15 Sep 2018 12:21:09: 5000000 INFO @ Sat, 15 Sep 2018 12:21:11: 5000000 INFO @ Sat, 15 Sep 2018 12:21:12: 5000000 INFO @ Sat, 15 Sep 2018 12:21:15: 6000000 INFO @ Sat, 15 Sep 2018 12:21:18: 6000000 INFO @ Sat, 15 Sep 2018 12:21:19: 6000000 INFO @ Sat, 15 Sep 2018 12:21:21: 7000000 INFO @ Sat, 15 Sep 2018 12:21:25: 7000000 INFO @ Sat, 15 Sep 2018 12:21:26: 7000000 INFO @ Sat, 15 Sep 2018 12:21:28: 8000000 INFO @ Sat, 15 Sep 2018 12:21:32: 8000000 INFO @ Sat, 15 Sep 2018 12:21:33: 8000000 INFO @ Sat, 15 Sep 2018 12:21:34: 9000000 INFO @ Sat, 15 Sep 2018 12:21:39: 9000000 INFO @ Sat, 15 Sep 2018 12:21:40: 10000000 INFO @ Sat, 15 Sep 2018 12:21:41: 9000000 INFO @ Sat, 15 Sep 2018 12:21:46: 10000000 INFO @ Sat, 15 Sep 2018 12:21:47: 11000000 INFO @ Sat, 15 Sep 2018 12:21:48: 10000000 INFO @ Sat, 15 Sep 2018 12:21:53: 11000000 INFO @ Sat, 15 Sep 2018 12:21:53: 12000000 INFO @ Sat, 15 Sep 2018 12:21:55: 11000000 INFO @ Sat, 15 Sep 2018 12:21:59: 13000000 INFO @ Sat, 15 Sep 2018 12:22:00: 12000000 INFO @ Sat, 15 Sep 2018 12:22:02: 12000000 INFO @ Sat, 15 Sep 2018 12:22:06: 14000000 INFO @ Sat, 15 Sep 2018 12:22:07: 13000000 INFO @ Sat, 15 Sep 2018 12:22:10: 13000000 INFO @ Sat, 15 Sep 2018 12:22:12: 15000000 INFO @ Sat, 15 Sep 2018 12:22:14: 14000000 INFO @ Sat, 15 Sep 2018 12:22:17: 14000000 INFO @ Sat, 15 Sep 2018 12:22:18: 16000000 INFO @ Sat, 15 Sep 2018 12:22:21: 15000000 INFO @ Sat, 15 Sep 2018 12:22:24: 15000000 INFO @ Sat, 15 Sep 2018 12:22:25: 17000000 INFO @ Sat, 15 Sep 2018 12:22:28: 16000000 INFO @ Sat, 15 Sep 2018 12:22:31: 18000000 INFO @ Sat, 15 Sep 2018 12:22:31: 16000000 INFO @ Sat, 15 Sep 2018 12:22:35: 17000000 INFO @ Sat, 15 Sep 2018 12:22:38: 19000000 INFO @ Sat, 15 Sep 2018 12:22:39: 17000000 INFO @ Sat, 15 Sep 2018 12:22:42: 18000000 INFO @ Sat, 15 Sep 2018 12:22:44: 20000000 INFO @ Sat, 15 Sep 2018 12:22:46: 18000000 INFO @ Sat, 15 Sep 2018 12:22:49: 19000000 INFO @ Sat, 15 Sep 2018 12:22:50: 21000000 INFO @ Sat, 15 Sep 2018 12:22:53: 19000000 INFO @ Sat, 15 Sep 2018 12:22:57: 22000000 INFO @ Sat, 15 Sep 2018 12:22:57: 20000000 INFO @ Sat, 15 Sep 2018 12:23:00: 20000000 INFO @ Sat, 15 Sep 2018 12:23:03: 23000000 INFO @ Sat, 15 Sep 2018 12:23:04: 21000000 INFO @ Sat, 15 Sep 2018 12:23:07: 21000000 INFO @ Sat, 15 Sep 2018 12:23:09: 24000000 INFO @ Sat, 15 Sep 2018 12:23:11: 22000000 INFO @ Sat, 15 Sep 2018 12:23:15: 22000000 INFO @ Sat, 15 Sep 2018 12:23:16: 25000000 INFO @ Sat, 15 Sep 2018 12:23:18: 23000000 INFO @ Sat, 15 Sep 2018 12:23:22: 23000000 INFO @ Sat, 15 Sep 2018 12:23:22: 26000000 INFO @ Sat, 15 Sep 2018 12:23:25: 24000000 INFO @ Sat, 15 Sep 2018 12:23:28: 27000000 INFO @ Sat, 15 Sep 2018 12:23:29: 24000000 INFO @ Sat, 15 Sep 2018 12:23:32: 25000000 INFO @ Sat, 15 Sep 2018 12:23:34: 28000000 INFO @ Sat, 15 Sep 2018 12:23:36: 25000000 INFO @ Sat, 15 Sep 2018 12:23:39: 26000000 INFO @ Sat, 15 Sep 2018 12:23:41: 29000000 INFO @ Sat, 15 Sep 2018 12:23:43: 26000000 INFO @ Sat, 15 Sep 2018 12:23:46: 27000000 INFO @ Sat, 15 Sep 2018 12:23:47: 30000000 INFO @ Sat, 15 Sep 2018 12:23:50: 27000000 INFO @ Sat, 15 Sep 2018 12:23:53: 28000000 INFO @ Sat, 15 Sep 2018 12:23:53: 31000000 INFO @ Sat, 15 Sep 2018 12:23:57: 28000000 INFO @ Sat, 15 Sep 2018 12:24:00: 29000000 INFO @ Sat, 15 Sep 2018 12:24:00: 32000000 INFO @ Sat, 15 Sep 2018 12:24:04: 29000000 INFO @ Sat, 15 Sep 2018 12:24:06: 33000000 INFO @ Sat, 15 Sep 2018 12:24:06: 30000000 INFO @ Sat, 15 Sep 2018 12:24:11: 30000000 INFO @ Sat, 15 Sep 2018 12:24:12: 34000000 INFO @ Sat, 15 Sep 2018 12:24:13: 31000000 INFO @ Sat, 15 Sep 2018 12:24:18: 31000000 INFO @ Sat, 15 Sep 2018 12:24:19: 35000000 INFO @ Sat, 15 Sep 2018 12:24:20: 32000000 INFO @ Sat, 15 Sep 2018 12:24:25: 32000000 INFO @ Sat, 15 Sep 2018 12:24:25: 36000000 INFO @ Sat, 15 Sep 2018 12:24:27: 33000000 INFO @ Sat, 15 Sep 2018 12:24:32: 37000000 INFO @ Sat, 15 Sep 2018 12:24:32: 33000000 INFO @ Sat, 15 Sep 2018 12:24:33: 34000000 INFO @ Sat, 15 Sep 2018 12:24:38: 38000000 INFO @ Sat, 15 Sep 2018 12:24:39: 34000000 INFO @ Sat, 15 Sep 2018 12:24:40: 35000000 INFO @ Sat, 15 Sep 2018 12:24:45: 39000000 INFO @ Sat, 15 Sep 2018 12:24:46: 35000000 INFO @ Sat, 15 Sep 2018 12:24:47: 36000000 INFO @ Sat, 15 Sep 2018 12:24:51: 40000000 INFO @ Sat, 15 Sep 2018 12:24:53: 36000000 INFO @ Sat, 15 Sep 2018 12:24:54: 37000000 INFO @ Sat, 15 Sep 2018 12:24:58: 41000000 INFO @ Sat, 15 Sep 2018 12:25:00: 37000000 INFO @ Sat, 15 Sep 2018 12:25:01: 38000000 INFO @ Sat, 15 Sep 2018 12:25:04: 42000000 INFO @ Sat, 15 Sep 2018 12:25:07: 38000000 INFO @ Sat, 15 Sep 2018 12:25:08: 39000000 INFO @ Sat, 15 Sep 2018 12:25:11: 43000000 INFO @ Sat, 15 Sep 2018 12:25:14: 39000000 INFO @ Sat, 15 Sep 2018 12:25:14: 40000000 INFO @ Sat, 15 Sep 2018 12:25:14: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 12:25:14: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 12:25:14: #1 total tags in treatment: 43514649 INFO @ Sat, 15 Sep 2018 12:25:14: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 12:25:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 12:25:16: #1 tags after filtering in treatment: 43514590 INFO @ Sat, 15 Sep 2018 12:25:16: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 12:25:16: #1 finished! INFO @ Sat, 15 Sep 2018 12:25:16: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 12:25:16: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 12:25:19: #2 number of paired peaks: 5913 INFO @ Sat, 15 Sep 2018 12:25:19: start model_add_line... INFO @ Sat, 15 Sep 2018 12:25:20: start X-correlation... INFO @ Sat, 15 Sep 2018 12:25:20: end of X-cor INFO @ Sat, 15 Sep 2018 12:25:20: #2 finished! INFO @ Sat, 15 Sep 2018 12:25:20: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Sep 2018 12:25:20: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Sep 2018 12:25:20: #2.2 Generate R script for model : SRX4014809.10_model.r WARNING @ Sat, 15 Sep 2018 12:25:20: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 12:25:20: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Sep 2018 12:25:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 12:25:20: #3 Call peaks... INFO @ Sat, 15 Sep 2018 12:25:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 12:25:21: 40000000 INFO @ Sat, 15 Sep 2018 12:25:21: 41000000 INFO @ Sat, 15 Sep 2018 12:25:28: 41000000 INFO @ Sat, 15 Sep 2018 12:25:28: 42000000 INFO @ Sat, 15 Sep 2018 12:25:35: 42000000 INFO @ Sat, 15 Sep 2018 12:25:35: 43000000 INFO @ Sat, 15 Sep 2018 12:25:39: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 12:25:39: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 12:25:39: #1 total tags in treatment: 43514649 INFO @ Sat, 15 Sep 2018 12:25:39: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 12:25:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 12:25:40: #1 tags after filtering in treatment: 43514590 INFO @ Sat, 15 Sep 2018 12:25:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 12:25:40: #1 finished! INFO @ Sat, 15 Sep 2018 12:25:40: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 12:25:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 12:25:42: 43000000 INFO @ Sat, 15 Sep 2018 12:25:44: #2 number of paired peaks: 5913 INFO @ Sat, 15 Sep 2018 12:25:44: start model_add_line... INFO @ Sat, 15 Sep 2018 12:25:44: start X-correlation... INFO @ Sat, 15 Sep 2018 12:25:44: end of X-cor INFO @ Sat, 15 Sep 2018 12:25:44: #2 finished! INFO @ Sat, 15 Sep 2018 12:25:44: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Sep 2018 12:25:44: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Sep 2018 12:25:44: #2.2 Generate R script for model : SRX4014809.20_model.r WARNING @ Sat, 15 Sep 2018 12:25:44: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 12:25:44: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Sep 2018 12:25:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 12:25:44: #3 Call peaks... INFO @ Sat, 15 Sep 2018 12:25:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 12:25:45: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 12:25:45: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 12:25:45: #1 total tags in treatment: 43514649 INFO @ Sat, 15 Sep 2018 12:25:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 12:25:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 12:25:47: #1 tags after filtering in treatment: 43514590 INFO @ Sat, 15 Sep 2018 12:25:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 12:25:47: #1 finished! INFO @ Sat, 15 Sep 2018 12:25:47: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 12:25:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 12:25:50: #2 number of paired peaks: 5913 INFO @ Sat, 15 Sep 2018 12:25:50: start model_add_line... INFO @ Sat, 15 Sep 2018 12:25:51: start X-correlation... INFO @ Sat, 15 Sep 2018 12:25:51: end of X-cor INFO @ Sat, 15 Sep 2018 12:25:51: #2 finished! INFO @ Sat, 15 Sep 2018 12:25:51: #2 predicted fragment length is 75 bps INFO @ Sat, 15 Sep 2018 12:25:51: #2 alternative fragment length(s) may be 75 bps INFO @ Sat, 15 Sep 2018 12:25:51: #2.2 Generate R script for model : SRX4014809.05_model.r WARNING @ Sat, 15 Sep 2018 12:25:51: #2 Since the d (75) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 15 Sep 2018 12:25:51: #2 You may need to consider one of the other alternative d(s): 75 WARNING @ Sat, 15 Sep 2018 12:25:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 15 Sep 2018 12:25:51: #3 Call peaks... INFO @ Sat, 15 Sep 2018 12:25:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 12:27:03: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 12:27:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 12:27:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 12:28:02: #4 Write output xls file... SRX4014809.10_peaks.xls INFO @ Sat, 15 Sep 2018 12:28:02: #4 Write peak in narrowPeak format file... SRX4014809.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 12:28:02: #4 Write summits bed file... SRX4014809.10_summits.bed INFO @ Sat, 15 Sep 2018 12:28:02: Done! pass1 - making usageList (47 chroms): 1 millis pass2 - checking and writing primary data (1278 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 12:28:32: #4 Write output xls file... SRX4014809.20_peaks.xls INFO @ Sat, 15 Sep 2018 12:28:32: #4 Write peak in narrowPeak format file... SRX4014809.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 12:28:32: #4 Write summits bed file... SRX4014809.20_summits.bed INFO @ Sat, 15 Sep 2018 12:28:32: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (594 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 12:28:49: #4 Write output xls file... SRX4014809.05_peaks.xls INFO @ Sat, 15 Sep 2018 12:28:49: #4 Write peak in narrowPeak format file... SRX4014809.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 12:28:49: #4 Write summits bed file... SRX4014809.05_summits.bed INFO @ Sat, 15 Sep 2018 12:28:49: Done! pass1 - making usageList (66 chroms): 1 millis pass2 - checking and writing primary data (2615 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。