Job ID = 10194939 sra ファイルのダウンロード中... Completed: 697766K bytes transferred in 10 seconds (534398K bits/sec), in 1 file. Completed: 574798K bytes transferred in 10 seconds (460402K 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 30006657 spots for /home/okishinya/chipatlas/results/rn6/SRX2512949/SRR5197465.sra Written 30006657 spots total Written 31374949 spots for /home/okishinya/chipatlas/results/rn6/SRX2512949/SRR5197464.sra Written 31374949 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 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:55:25 61381606 reads; of these: 61381606 (100.00%) were unpaired; of these: 14133961 (23.03%) aligned 0 times 30788997 (50.16%) aligned exactly 1 time 16458648 (26.81%) aligned >1 times 76.97% overall alignment rate Time searching: 00:55:29 Overall time: 00:55:29 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 12 files... [bam_rmdupse_core] 4843478 / 47247645 = 0.1025 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, 11 Nov 2017 01:07:55: # Command line: callpeak -t SRX2512949.bam -f BAM -g 2.15e9 -n SRX2512949.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2512949.05 # format = BAM # ChIP-seq file = ['SRX2512949.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, 11 Nov 2017 01:07:55: # Command line: callpeak -t SRX2512949.bam -f BAM -g 2.15e9 -n SRX2512949.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2512949.10 # format = BAM # ChIP-seq file = ['SRX2512949.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, 11 Nov 2017 01:07:55: # Command line: callpeak -t SRX2512949.bam -f BAM -g 2.15e9 -n SRX2512949.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2512949.20 # format = BAM # ChIP-seq file = ['SRX2512949.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, 11 Nov 2017 01:07:55: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:07:55: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:07:55: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:07:55: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:07:55: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:07:55: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:08:04: 1000000 INFO @ Sat, 11 Nov 2017 01:08:04: 1000000 INFO @ Sat, 11 Nov 2017 01:08:04: 1000000 INFO @ Sat, 11 Nov 2017 01:08:12: 2000000 INFO @ Sat, 11 Nov 2017 01:08:13: 2000000 INFO @ Sat, 11 Nov 2017 01:08:13: 2000000 INFO @ Sat, 11 Nov 2017 01:08:20: 3000000 INFO @ Sat, 11 Nov 2017 01:08:21: 3000000 INFO @ Sat, 11 Nov 2017 01:08:22: 3000000 INFO @ Sat, 11 Nov 2017 01:08:28: 4000000 INFO @ Sat, 11 Nov 2017 01:08:29: 4000000 INFO @ Sat, 11 Nov 2017 01:08:30: 4000000 INFO @ Sat, 11 Nov 2017 01:08:36: 5000000 INFO @ Sat, 11 Nov 2017 01:08:37: 5000000 INFO @ Sat, 11 Nov 2017 01:08:39: 5000000 INFO @ Sat, 11 Nov 2017 01:08:44: 6000000 INFO @ Sat, 11 Nov 2017 01:08:46: 6000000 INFO @ Sat, 11 Nov 2017 01:08:47: 6000000 INFO @ Sat, 11 Nov 2017 01:08:52: 7000000 INFO @ Sat, 11 Nov 2017 01:08:54: 7000000 INFO @ Sat, 11 Nov 2017 01:08:55: 7000000 INFO @ Sat, 11 Nov 2017 01:09:01: 8000000 INFO @ Sat, 11 Nov 2017 01:09:03: 8000000 INFO @ Sat, 11 Nov 2017 01:09:04: 8000000 INFO @ Sat, 11 Nov 2017 01:09:09: 9000000 INFO @ Sat, 11 Nov 2017 01:09:11: 9000000 INFO @ Sat, 11 Nov 2017 01:09:12: 9000000 INFO @ Sat, 11 Nov 2017 01:09:17: 10000000 INFO @ Sat, 11 Nov 2017 01:09:20: 10000000 INFO @ Sat, 11 Nov 2017 01:09:20: 10000000 INFO @ Sat, 11 Nov 2017 01:09:25: 11000000 INFO @ Sat, 11 Nov 2017 01:09:28: 11000000 INFO @ Sat, 11 Nov 2017 01:09:29: 11000000 INFO @ Sat, 11 Nov 2017 01:09:34: 12000000 INFO @ Sat, 11 Nov 2017 01:09:37: 12000000 INFO @ Sat, 11 Nov 2017 01:09:37: 12000000 INFO @ Sat, 11 Nov 2017 01:09:42: 13000000 INFO @ Sat, 11 Nov 2017 01:09:45: 13000000 INFO @ Sat, 11 Nov 2017 01:09:46: 13000000 INFO @ Sat, 11 Nov 2017 01:09:50: 14000000 INFO @ Sat, 11 Nov 2017 01:09:54: 14000000 INFO @ Sat, 11 Nov 2017 01:09:54: 14000000 INFO @ Sat, 11 Nov 2017 01:09:58: 15000000 INFO @ Sat, 11 Nov 2017 01:10:02: 15000000 INFO @ Sat, 11 Nov 2017 01:10:03: 15000000 INFO @ Sat, 11 Nov 2017 01:10:06: 16000000 INFO @ Sat, 11 Nov 2017 01:10:11: 16000000 INFO @ Sat, 11 Nov 2017 01:10:11: 16000000 INFO @ Sat, 11 Nov 2017 01:10:14: 17000000 INFO @ Sat, 11 Nov 2017 01:10:19: 17000000 INFO @ Sat, 11 Nov 2017 01:10:21: 17000000 INFO @ Sat, 11 Nov 2017 01:10:22: 18000000 INFO @ Sat, 11 Nov 2017 01:10:27: 18000000 INFO @ Sat, 11 Nov 2017 01:10:29: 19000000 INFO @ Sat, 11 Nov 2017 01:10:31: 18000000 INFO @ Sat, 11 Nov 2017 01:10:34: 19000000 INFO @ Sat, 11 Nov 2017 01:10:37: 20000000 INFO @ Sat, 11 Nov 2017 01:10:41: 19000000 INFO @ Sat, 11 Nov 2017 01:10:42: 20000000 INFO @ Sat, 11 Nov 2017 01:10:45: 21000000 INFO @ Sat, 11 Nov 2017 01:10:50: 21000000 INFO @ Sat, 11 Nov 2017 01:10:51: 20000000 INFO @ Sat, 11 Nov 2017 01:10:53: 22000000 INFO @ Sat, 11 Nov 2017 01:10:59: 22000000 INFO @ Sat, 11 Nov 2017 01:11:01: 21000000 INFO @ Sat, 11 Nov 2017 01:11:03: 23000000 INFO @ Sat, 11 Nov 2017 01:11:09: 23000000 INFO @ Sat, 11 Nov 2017 01:11:11: 22000000 INFO @ Sat, 11 Nov 2017 01:11:13: 24000000 INFO @ Sat, 11 Nov 2017 01:11:19: 24000000 INFO @ Sat, 11 Nov 2017 01:11:21: 23000000 INFO @ Sat, 11 Nov 2017 01:11:23: 25000000 INFO @ Sat, 11 Nov 2017 01:11:29: 25000000 INFO @ Sat, 11 Nov 2017 01:11:31: 24000000 INFO @ Sat, 11 Nov 2017 01:11:34: 26000000 INFO @ Sat, 11 Nov 2017 01:11:39: 26000000 INFO @ Sat, 11 Nov 2017 01:11:41: 25000000 INFO @ Sat, 11 Nov 2017 01:11:42: 27000000 INFO @ Sat, 11 Nov 2017 01:11:48: 27000000 INFO @ Sat, 11 Nov 2017 01:11:51: 26000000 INFO @ Sat, 11 Nov 2017 01:11:51: 28000000 INFO @ Sat, 11 Nov 2017 01:11:57: 28000000 INFO @ Sat, 11 Nov 2017 01:11:59: 27000000 INFO @ Sat, 11 Nov 2017 01:12:00: 29000000 INFO @ Sat, 11 Nov 2017 01:12:07: 29000000 INFO @ Sat, 11 Nov 2017 01:12:08: 28000000 INFO @ Sat, 11 Nov 2017 01:12:09: 30000000 INFO @ Sat, 11 Nov 2017 01:12:16: 30000000 INFO @ Sat, 11 Nov 2017 01:12:17: 31000000 INFO @ Sat, 11 Nov 2017 01:12:18: 29000000 INFO @ Sat, 11 Nov 2017 01:12:24: 31000000 INFO @ Sat, 11 Nov 2017 01:12:25: 32000000 INFO @ Sat, 11 Nov 2017 01:12:27: 30000000 INFO @ Sat, 11 Nov 2017 01:12:32: 32000000 INFO @ Sat, 11 Nov 2017 01:12:34: 33000000 INFO @ Sat, 11 Nov 2017 01:12:34: 31000000 INFO @ Sat, 11 Nov 2017 01:12:40: 33000000 INFO @ Sat, 11 Nov 2017 01:12:42: 34000000 INFO @ Sat, 11 Nov 2017 01:12:42: 32000000 INFO @ Sat, 11 Nov 2017 01:12:48: 34000000 INFO @ Sat, 11 Nov 2017 01:12:50: 35000000 INFO @ Sat, 11 Nov 2017 01:12:50: 33000000 INFO @ Sat, 11 Nov 2017 01:12:57: 35000000 INFO @ Sat, 11 Nov 2017 01:12:58: 36000000 INFO @ Sat, 11 Nov 2017 01:12:58: 34000000 INFO @ Sat, 11 Nov 2017 01:13:05: 36000000 INFO @ Sat, 11 Nov 2017 01:13:06: 35000000 INFO @ Sat, 11 Nov 2017 01:13:06: 37000000 INFO @ Sat, 11 Nov 2017 01:13:13: 37000000 INFO @ Sat, 11 Nov 2017 01:13:14: 36000000 INFO @ Sat, 11 Nov 2017 01:13:14: 38000000 INFO @ Sat, 11 Nov 2017 01:13:21: 38000000 INFO @ Sat, 11 Nov 2017 01:13:21: 37000000 INFO @ Sat, 11 Nov 2017 01:13:22: 39000000 INFO @ Sat, 11 Nov 2017 01:13:29: 38000000 INFO @ Sat, 11 Nov 2017 01:13:29: 39000000 INFO @ Sat, 11 Nov 2017 01:13:30: 40000000 INFO @ Sat, 11 Nov 2017 01:13:37: 39000000 INFO @ Sat, 11 Nov 2017 01:13:38: 40000000 INFO @ Sat, 11 Nov 2017 01:13:38: 41000000 INFO @ Sat, 11 Nov 2017 01:13:45: 40000000 INFO @ Sat, 11 Nov 2017 01:13:46: 41000000 INFO @ Sat, 11 Nov 2017 01:13:47: 42000000 INFO @ Sat, 11 Nov 2017 01:13:50: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 01:13:50: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 01:13:50: #1 total tags in treatment: 42404167 INFO @ Sat, 11 Nov 2017 01:13:50: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:13:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:13:52: #1 tags after filtering in treatment: 42404116 INFO @ Sat, 11 Nov 2017 01:13:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:13:52: #1 finished! INFO @ Sat, 11 Nov 2017 01:13:52: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:13:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:13:53: 41000000 INFO @ Sat, 11 Nov 2017 01:13:54: 42000000 INFO @ Sat, 11 Nov 2017 01:13:56: #2 number of paired peaks: 7288 INFO @ Sat, 11 Nov 2017 01:13:56: start model_add_line... INFO @ Sat, 11 Nov 2017 01:13:57: start X-correlation... INFO @ Sat, 11 Nov 2017 01:13:57: end of X-cor INFO @ Sat, 11 Nov 2017 01:13:57: #2 finished! INFO @ Sat, 11 Nov 2017 01:13:57: #2 predicted fragment length is 40 bps INFO @ Sat, 11 Nov 2017 01:13:57: #2 alternative fragment length(s) may be 40,101 bps INFO @ Sat, 11 Nov 2017 01:13:57: #2.2 Generate R script for model : SRX2512949.05_model.r WARNING @ Sat, 11 Nov 2017 01:13:57: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:13:57: #2 You may need to consider one of the other alternative d(s): 40,101 WARNING @ Sat, 11 Nov 2017 01:13:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:13:57: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:13:58: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 01:13:58: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 01:13:58: #1 total tags in treatment: 42404167 INFO @ Sat, 11 Nov 2017 01:13:58: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:13:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:14:00: #1 tags after filtering in treatment: 42404116 INFO @ Sat, 11 Nov 2017 01:14:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:14:00: #1 finished! INFO @ Sat, 11 Nov 2017 01:14:00: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:14:00: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:14:01: 42000000 INFO @ Sat, 11 Nov 2017 01:14:04: #2 number of paired peaks: 7288 INFO @ Sat, 11 Nov 2017 01:14:04: start model_add_line... INFO @ Sat, 11 Nov 2017 01:14:04: #1 tag size is determined as 36 bps INFO @ Sat, 11 Nov 2017 01:14:04: #1 tag size = 36 INFO @ Sat, 11 Nov 2017 01:14:04: #1 total tags in treatment: 42404167 INFO @ Sat, 11 Nov 2017 01:14:04: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:14:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 01:14:05: start X-correlation... INFO @ Sat, 11 Nov 2017 01:14:05: end of X-cor INFO @ Sat, 11 Nov 2017 01:14:05: #2 finished! INFO @ Sat, 11 Nov 2017 01:14:05: #2 predicted fragment length is 40 bps INFO @ Sat, 11 Nov 2017 01:14:05: #2 alternative fragment length(s) may be 40,101 bps INFO @ Sat, 11 Nov 2017 01:14:05: #2.2 Generate R script for model : SRX2512949.10_model.r WARNING @ Sat, 11 Nov 2017 01:14:05: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:14:05: #2 You may need to consider one of the other alternative d(s): 40,101 WARNING @ Sat, 11 Nov 2017 01:14:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:14:05: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:14:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:14:06: #1 tags after filtering in treatment: 42404116 INFO @ Sat, 11 Nov 2017 01:14:06: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:14:06: #1 finished! INFO @ Sat, 11 Nov 2017 01:14:06: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:14:06: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:14:10: #2 number of paired peaks: 7288 INFO @ Sat, 11 Nov 2017 01:14:10: start model_add_line... INFO @ Sat, 11 Nov 2017 01:14:11: start X-correlation... INFO @ Sat, 11 Nov 2017 01:14:11: end of X-cor INFO @ Sat, 11 Nov 2017 01:14:11: #2 finished! INFO @ Sat, 11 Nov 2017 01:14:11: #2 predicted fragment length is 40 bps INFO @ Sat, 11 Nov 2017 01:14:11: #2 alternative fragment length(s) may be 40,101 bps INFO @ Sat, 11 Nov 2017 01:14:11: #2.2 Generate R script for model : SRX2512949.20_model.r WARNING @ Sat, 11 Nov 2017 01:14:11: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 11 Nov 2017 01:14:11: #2 You may need to consider one of the other alternative d(s): 40,101 WARNING @ Sat, 11 Nov 2017 01:14:11: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 11 Nov 2017 01:14:11: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:14:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:15:58: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:16:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:16:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:17:07: #4 Write output xls file... SRX2512949.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:17:08: #4 Write peak in narrowPeak format file... SRX2512949.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:17:08: #4 Write summits bed file... SRX2512949.05_summits.bed INFO @ Sat, 11 Nov 2017 01:17:08: Done! pass1 - making usageList (102 chroms): 2 millis pass2 - checking and writing primary data (4981 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:17:13: #4 Write output xls file... SRX2512949.20_peaks.xls INFO @ Sat, 11 Nov 2017 01:17:13: #4 Write peak in narrowPeak format file... SRX2512949.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:17:13: #4 Write summits bed file... SRX2512949.20_summits.bed INFO @ Sat, 11 Nov 2017 01:17:13: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (988 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:17:15: #4 Write output xls file... SRX2512949.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:17:15: #4 Write peak in narrowPeak format file... SRX2512949.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:17:15: #4 Write summits bed file... SRX2512949.10_summits.bed INFO @ Sat, 11 Nov 2017 01:17:15: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (2292 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。