Job ID = 10487597 sra ファイルのダウンロード中... Completed: 5302014K bytes transferred in 107 seconds (405731K 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 78853980 spots for /home/okishinya/chipatlas/results/rn6/SRX2611119/SRR5311163.sra Written 78853980 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: 04:20:47 78853980 reads; of these: 78853980 (100.00%) were unpaired; of these: 15647087 (19.84%) aligned 0 times 53914784 (68.37%) aligned exactly 1 time 9292109 (11.78%) aligned >1 times 80.16% overall alignment rate Time searching: 04:20:49 Overall time: 04:20:49 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 48 files... [bam_rmdupse_core] 20337789 / 63206893 = 0.3218 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 14:47:17: # Command line: callpeak -t SRX2611119.bam -f BAM -g 2.15e9 -n SRX2611119.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2611119.10 # format = BAM # ChIP-seq file = ['SRX2611119.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 14:47:17: # Command line: callpeak -t SRX2611119.bam -f BAM -g 2.15e9 -n SRX2611119.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2611119.05 # format = BAM # ChIP-seq file = ['SRX2611119.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 14:47:17: # Command line: callpeak -t SRX2611119.bam -f BAM -g 2.15e9 -n SRX2611119.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2611119.20 # format = BAM # ChIP-seq file = ['SRX2611119.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 14:47:17: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:47:17: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:47:17: #1 read tag files... INFO @ Sun, 18 Mar 2018 14:47:17: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:47:17: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:47:17: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 14:47:28: 1000000 INFO @ Sun, 18 Mar 2018 14:47:28: 1000000 INFO @ Sun, 18 Mar 2018 14:47:28: 1000000 INFO @ Sun, 18 Mar 2018 14:47:38: 2000000 INFO @ Sun, 18 Mar 2018 14:47:38: 2000000 INFO @ Sun, 18 Mar 2018 14:47:38: 2000000 INFO @ Sun, 18 Mar 2018 14:47:48: 3000000 INFO @ Sun, 18 Mar 2018 14:47:48: 3000000 INFO @ Sun, 18 Mar 2018 14:47:48: 3000000 INFO @ Sun, 18 Mar 2018 14:47:58: 4000000 INFO @ Sun, 18 Mar 2018 14:47:59: 4000000 INFO @ Sun, 18 Mar 2018 14:47:59: 4000000 INFO @ Sun, 18 Mar 2018 14:48:08: 5000000 INFO @ Sun, 18 Mar 2018 14:48:09: 5000000 INFO @ Sun, 18 Mar 2018 14:48:09: 5000000 INFO @ Sun, 18 Mar 2018 14:48:19: 6000000 INFO @ Sun, 18 Mar 2018 14:48:19: 6000000 INFO @ Sun, 18 Mar 2018 14:48:20: 6000000 INFO @ Sun, 18 Mar 2018 14:48:29: 7000000 INFO @ Sun, 18 Mar 2018 14:48:30: 7000000 INFO @ Sun, 18 Mar 2018 14:48:30: 7000000 INFO @ Sun, 18 Mar 2018 14:48:39: 8000000 INFO @ Sun, 18 Mar 2018 14:48:41: 8000000 INFO @ Sun, 18 Mar 2018 14:48:41: 8000000 INFO @ Sun, 18 Mar 2018 14:48:49: 9000000 INFO @ Sun, 18 Mar 2018 14:48:51: 9000000 INFO @ Sun, 18 Mar 2018 14:48:52: 9000000 INFO @ Sun, 18 Mar 2018 14:48:59: 10000000 INFO @ Sun, 18 Mar 2018 14:49:02: 10000000 INFO @ Sun, 18 Mar 2018 14:49:02: 10000000 INFO @ Sun, 18 Mar 2018 14:49:09: 11000000 INFO @ Sun, 18 Mar 2018 14:49:13: 11000000 INFO @ Sun, 18 Mar 2018 14:49:13: 11000000 INFO @ Sun, 18 Mar 2018 14:49:19: 12000000 INFO @ Sun, 18 Mar 2018 14:49:23: 12000000 INFO @ Sun, 18 Mar 2018 14:49:24: 12000000 INFO @ Sun, 18 Mar 2018 14:49:29: 13000000 INFO @ Sun, 18 Mar 2018 14:49:34: 13000000 INFO @ Sun, 18 Mar 2018 14:49:34: 13000000 INFO @ Sun, 18 Mar 2018 14:49:39: 14000000 INFO @ Sun, 18 Mar 2018 14:49:44: 14000000 INFO @ Sun, 18 Mar 2018 14:49:44: 14000000 INFO @ Sun, 18 Mar 2018 14:49:49: 15000000 INFO @ Sun, 18 Mar 2018 14:49:54: 15000000 INFO @ Sun, 18 Mar 2018 14:49:55: 15000000 INFO @ Sun, 18 Mar 2018 14:50:00: 16000000 INFO @ Sun, 18 Mar 2018 14:50:04: 16000000 INFO @ Sun, 18 Mar 2018 14:50:06: 16000000 INFO @ Sun, 18 Mar 2018 14:50:11: 17000000 INFO @ Sun, 18 Mar 2018 14:50:14: 17000000 INFO @ Sun, 18 Mar 2018 14:50:16: 17000000 INFO @ Sun, 18 Mar 2018 14:50:21: 18000000 INFO @ Sun, 18 Mar 2018 14:50:24: 18000000 INFO @ Sun, 18 Mar 2018 14:50:27: 18000000 INFO @ Sun, 18 Mar 2018 14:50:32: 19000000 INFO @ Sun, 18 Mar 2018 14:50:34: 19000000 INFO @ Sun, 18 Mar 2018 14:50:38: 19000000 INFO @ Sun, 18 Mar 2018 14:50:43: 20000000 INFO @ Sun, 18 Mar 2018 14:50:44: 20000000 INFO @ Sun, 18 Mar 2018 14:50:48: 20000000 INFO @ Sun, 18 Mar 2018 14:50:54: 21000000 INFO @ Sun, 18 Mar 2018 14:50:54: 21000000 INFO @ Sun, 18 Mar 2018 14:50:59: 21000000 INFO @ Sun, 18 Mar 2018 14:51:04: 22000000 INFO @ Sun, 18 Mar 2018 14:51:05: 22000000 INFO @ Sun, 18 Mar 2018 14:51:10: 22000000 INFO @ Sun, 18 Mar 2018 14:51:15: 23000000 INFO @ Sun, 18 Mar 2018 14:51:16: 23000000 INFO @ Sun, 18 Mar 2018 14:51:21: 23000000 INFO @ Sun, 18 Mar 2018 14:51:25: 24000000 INFO @ Sun, 18 Mar 2018 14:51:27: 24000000 INFO @ Sun, 18 Mar 2018 14:51:31: 24000000 INFO @ Sun, 18 Mar 2018 14:51:35: 25000000 INFO @ Sun, 18 Mar 2018 14:51:37: 25000000 INFO @ Sun, 18 Mar 2018 14:51:41: 25000000 INFO @ Sun, 18 Mar 2018 14:51:46: 26000000 INFO @ Sun, 18 Mar 2018 14:51:48: 26000000 INFO @ Sun, 18 Mar 2018 14:51:51: 26000000 INFO @ Sun, 18 Mar 2018 14:51:56: 27000000 INFO @ Sun, 18 Mar 2018 14:51:58: 27000000 INFO @ Sun, 18 Mar 2018 14:52:01: 27000000 INFO @ Sun, 18 Mar 2018 14:52:07: 28000000 INFO @ Sun, 18 Mar 2018 14:52:08: 28000000 INFO @ Sun, 18 Mar 2018 14:52:11: 28000000 INFO @ Sun, 18 Mar 2018 14:52:18: 29000000 INFO @ Sun, 18 Mar 2018 14:52:19: 29000000 INFO @ Sun, 18 Mar 2018 14:52:21: 29000000 INFO @ Sun, 18 Mar 2018 14:52:29: 30000000 INFO @ Sun, 18 Mar 2018 14:52:29: 30000000 INFO @ Sun, 18 Mar 2018 14:52:31: 30000000 INFO @ Sun, 18 Mar 2018 14:52:40: 31000000 INFO @ Sun, 18 Mar 2018 14:52:40: 31000000 INFO @ Sun, 18 Mar 2018 14:52:41: 31000000 INFO @ Sun, 18 Mar 2018 14:52:50: 32000000 INFO @ Sun, 18 Mar 2018 14:52:50: 32000000 INFO @ Sun, 18 Mar 2018 14:52:51: 32000000 INFO @ Sun, 18 Mar 2018 14:53:00: 33000000 INFO @ Sun, 18 Mar 2018 14:53:00: 33000000 INFO @ Sun, 18 Mar 2018 14:53:01: 33000000 INFO @ Sun, 18 Mar 2018 14:53:11: 34000000 INFO @ Sun, 18 Mar 2018 14:53:11: 34000000 INFO @ Sun, 18 Mar 2018 14:53:11: 34000000 INFO @ Sun, 18 Mar 2018 14:53:21: 35000000 INFO @ Sun, 18 Mar 2018 14:53:21: 35000000 INFO @ Sun, 18 Mar 2018 14:53:22: 35000000 INFO @ Sun, 18 Mar 2018 14:53:31: 36000000 INFO @ Sun, 18 Mar 2018 14:53:32: 36000000 INFO @ Sun, 18 Mar 2018 14:53:33: 36000000 INFO @ Sun, 18 Mar 2018 14:53:41: 37000000 INFO @ Sun, 18 Mar 2018 14:53:43: 37000000 INFO @ Sun, 18 Mar 2018 14:53:44: 37000000 INFO @ Sun, 18 Mar 2018 14:53:51: 38000000 INFO @ Sun, 18 Mar 2018 14:53:54: 38000000 INFO @ Sun, 18 Mar 2018 14:53:54: 38000000 INFO @ Sun, 18 Mar 2018 14:54:02: 39000000 INFO @ Sun, 18 Mar 2018 14:54:04: 39000000 INFO @ Sun, 18 Mar 2018 14:54:04: 39000000 INFO @ Sun, 18 Mar 2018 14:54:13: 40000000 INFO @ Sun, 18 Mar 2018 14:54:14: 40000000 INFO @ Sun, 18 Mar 2018 14:54:15: 40000000 INFO @ Sun, 18 Mar 2018 14:54:23: 41000000 INFO @ Sun, 18 Mar 2018 14:54:25: 41000000 INFO @ Sun, 18 Mar 2018 14:54:25: 41000000 INFO @ Sun, 18 Mar 2018 14:54:34: 42000000 INFO @ Sun, 18 Mar 2018 14:54:35: 42000000 INFO @ Sun, 18 Mar 2018 14:54:35: 42000000 INFO @ Sun, 18 Mar 2018 14:54:43: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:54:43: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:54:43: #1 total tags in treatment: 42869104 INFO @ Sun, 18 Mar 2018 14:54:43: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:54:43: #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 14:54:44: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:54:44: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:54:44: #1 total tags in treatment: 42869104 INFO @ Sun, 18 Mar 2018 14:54:44: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:54:44: #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 14:54:44: #1 tags after filtering in treatment: 42869005 INFO @ Sun, 18 Mar 2018 14:54:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:54:44: #1 finished! INFO @ Sun, 18 Mar 2018 14:54:44: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:54:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:54:45: #1 tag size is determined as 151 bps INFO @ Sun, 18 Mar 2018 14:54:45: #1 tag size = 151 INFO @ Sun, 18 Mar 2018 14:54:45: #1 total tags in treatment: 42869104 INFO @ Sun, 18 Mar 2018 14:54:45: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 14:54:45: #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 14:54:45: #1 tags after filtering in treatment: 42869005 INFO @ Sun, 18 Mar 2018 14:54:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:54:45: #1 finished! INFO @ Sun, 18 Mar 2018 14:54:45: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:54:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:54:46: #1 tags after filtering in treatment: 42869005 INFO @ Sun, 18 Mar 2018 14:54:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 14:54:46: #1 finished! INFO @ Sun, 18 Mar 2018 14:54:46: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 14:54:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 14:54:48: #2 number of paired peaks: 6976 INFO @ Sun, 18 Mar 2018 14:54:48: start model_add_line... INFO @ Sun, 18 Mar 2018 14:54:49: start X-correlation... INFO @ Sun, 18 Mar 2018 14:54:49: end of X-cor INFO @ Sun, 18 Mar 2018 14:54:49: #2 finished! INFO @ Sun, 18 Mar 2018 14:54:49: #2 predicted fragment length is 160 bps INFO @ Sun, 18 Mar 2018 14:54:49: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 18 Mar 2018 14:54:49: #2.2 Generate R script for model : SRX2611119.05_model.r WARNING @ Sun, 18 Mar 2018 14:54:49: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:54:49: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sun, 18 Mar 2018 14:54:49: #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 14:54:49: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:54:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:54:49: #2 number of paired peaks: 6976 INFO @ Sun, 18 Mar 2018 14:54:49: start model_add_line... INFO @ Sun, 18 Mar 2018 14:54:50: start X-correlation... INFO @ Sun, 18 Mar 2018 14:54:50: end of X-cor INFO @ Sun, 18 Mar 2018 14:54:50: #2 finished! INFO @ Sun, 18 Mar 2018 14:54:50: #2 predicted fragment length is 160 bps INFO @ Sun, 18 Mar 2018 14:54:50: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 18 Mar 2018 14:54:50: #2.2 Generate R script for model : SRX2611119.20_model.r WARNING @ Sun, 18 Mar 2018 14:54:50: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:54:50: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sun, 18 Mar 2018 14:54:50: #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 14:54:50: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:54:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:54:50: #2 number of paired peaks: 6976 INFO @ Sun, 18 Mar 2018 14:54:50: start model_add_line... INFO @ Sun, 18 Mar 2018 14:54:51: start X-correlation... INFO @ Sun, 18 Mar 2018 14:54:51: end of X-cor INFO @ Sun, 18 Mar 2018 14:54:51: #2 finished! INFO @ Sun, 18 Mar 2018 14:54:51: #2 predicted fragment length is 160 bps INFO @ Sun, 18 Mar 2018 14:54:51: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 18 Mar 2018 14:54:51: #2.2 Generate R script for model : SRX2611119.10_model.r WARNING @ Sun, 18 Mar 2018 14:54:51: #2 Since the d (160) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 18 Mar 2018 14:54:51: #2 You may need to consider one of the other alternative d(s): 160 WARNING @ Sun, 18 Mar 2018 14:54:51: #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 14:54:51: #3 Call peaks... INFO @ Sun, 18 Mar 2018 14:54:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 14:56:31: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:56:31: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:56:39: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 14:57:28: #4 Write output xls file... SRX2611119.05_peaks.xls INFO @ Sun, 18 Mar 2018 14:57:28: #4 Write peak in narrowPeak format file... SRX2611119.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:57:28: #4 Write summits bed file... SRX2611119.05_summits.bed INFO @ Sun, 18 Mar 2018 14:57:28: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (4601 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:57:35: #4 Write output xls file... SRX2611119.10_peaks.xls INFO @ Sun, 18 Mar 2018 14:57:35: #4 Write peak in narrowPeak format file... SRX2611119.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:57:35: #4 Write summits bed file... SRX2611119.10_summits.bed INFO @ Sun, 18 Mar 2018 14:57:35: Done! pass1 - making usageList (45 chroms): 1 millis pass2 - checking and writing primary data (1178 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 14:57:38: #4 Write output xls file... SRX2611119.20_peaks.xls INFO @ Sun, 18 Mar 2018 14:57:38: #4 Write peak in narrowPeak format file... SRX2611119.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 14:57:38: #4 Write summits bed file... SRX2611119.20_summits.bed INFO @ Sun, 18 Mar 2018 14:57:38: Done! pass1 - making usageList (35 chroms): 2 millis pass2 - checking and writing primary data (504 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。