Job ID = 10195006 sra ファイルのダウンロード中... Completed: 2957024K bytes transferred in 27 seconds (879379K 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 91787659 spots for /home/okishinya/chipatlas/results/rn6/SRX831356/SRR1743292.sra Written 91787659 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 01:11:56 91787659 reads; of these: 91787659 (100.00%) were unpaired; of these: 2977500 (3.24%) aligned 0 times 66709315 (72.68%) aligned exactly 1 time 22100844 (24.08%) aligned >1 times 96.76% overall alignment rate Time searching: 01:11:58 Overall time: 01:11:58 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 40 files... [bam_rmdupse_core] 48202062 / 88810159 = 0.5428 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 @ Fri, 10 Nov 2017 20:40:28: # Command line: callpeak -t SRX831356.bam -f BAM -g 2.15e9 -n SRX831356.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX831356.20 # format = BAM # ChIP-seq file = ['SRX831356.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 @ Fri, 10 Nov 2017 20:40:28: # Command line: callpeak -t SRX831356.bam -f BAM -g 2.15e9 -n SRX831356.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX831356.10 # format = BAM # ChIP-seq file = ['SRX831356.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 @ Fri, 10 Nov 2017 20:40:28: # Command line: callpeak -t SRX831356.bam -f BAM -g 2.15e9 -n SRX831356.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX831356.05 # format = BAM # ChIP-seq file = ['SRX831356.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 @ Fri, 10 Nov 2017 20:40:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 20:40:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 20:40:28: #1 read tag files... INFO @ Fri, 10 Nov 2017 20:40:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 20:40:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 20:40:28: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 20:40:35: 1000000 INFO @ Fri, 10 Nov 2017 20:40:36: 1000000 INFO @ Fri, 10 Nov 2017 20:40:36: 1000000 INFO @ Fri, 10 Nov 2017 20:40:43: 2000000 INFO @ Fri, 10 Nov 2017 20:40:44: 2000000 INFO @ Fri, 10 Nov 2017 20:40:44: 2000000 INFO @ Fri, 10 Nov 2017 20:40:50: 3000000 INFO @ Fri, 10 Nov 2017 20:40:52: 3000000 INFO @ Fri, 10 Nov 2017 20:40:52: 3000000 INFO @ Fri, 10 Nov 2017 20:40:58: 4000000 INFO @ Fri, 10 Nov 2017 20:41:01: 4000000 INFO @ Fri, 10 Nov 2017 20:41:01: 4000000 INFO @ Fri, 10 Nov 2017 20:41:05: 5000000 INFO @ Fri, 10 Nov 2017 20:41:09: 5000000 INFO @ Fri, 10 Nov 2017 20:41:09: 5000000 INFO @ Fri, 10 Nov 2017 20:41:13: 6000000 INFO @ Fri, 10 Nov 2017 20:41:17: 6000000 INFO @ Fri, 10 Nov 2017 20:41:17: 6000000 INFO @ Fri, 10 Nov 2017 20:41:20: 7000000 INFO @ Fri, 10 Nov 2017 20:41:25: 7000000 INFO @ Fri, 10 Nov 2017 20:41:25: 7000000 INFO @ Fri, 10 Nov 2017 20:41:28: 8000000 INFO @ Fri, 10 Nov 2017 20:41:33: 8000000 INFO @ Fri, 10 Nov 2017 20:41:33: 8000000 INFO @ Fri, 10 Nov 2017 20:41:35: 9000000 INFO @ Fri, 10 Nov 2017 20:41:41: 9000000 INFO @ Fri, 10 Nov 2017 20:41:41: 9000000 INFO @ Fri, 10 Nov 2017 20:41:43: 10000000 INFO @ Fri, 10 Nov 2017 20:41:50: 10000000 INFO @ Fri, 10 Nov 2017 20:41:50: 10000000 INFO @ Fri, 10 Nov 2017 20:41:50: 11000000 INFO @ Fri, 10 Nov 2017 20:41:58: 11000000 INFO @ Fri, 10 Nov 2017 20:41:58: 11000000 INFO @ Fri, 10 Nov 2017 20:41:58: 12000000 INFO @ Fri, 10 Nov 2017 20:42:05: 13000000 INFO @ Fri, 10 Nov 2017 20:42:06: 12000000 INFO @ Fri, 10 Nov 2017 20:42:06: 12000000 INFO @ Fri, 10 Nov 2017 20:42:13: 14000000 INFO @ Fri, 10 Nov 2017 20:42:14: 13000000 INFO @ Fri, 10 Nov 2017 20:42:14: 13000000 INFO @ Fri, 10 Nov 2017 20:42:20: 15000000 INFO @ Fri, 10 Nov 2017 20:42:22: 14000000 INFO @ Fri, 10 Nov 2017 20:42:22: 14000000 INFO @ Fri, 10 Nov 2017 20:42:28: 16000000 INFO @ Fri, 10 Nov 2017 20:42:30: 15000000 INFO @ Fri, 10 Nov 2017 20:42:30: 15000000 INFO @ Fri, 10 Nov 2017 20:42:35: 17000000 INFO @ Fri, 10 Nov 2017 20:42:38: 16000000 INFO @ Fri, 10 Nov 2017 20:42:38: 16000000 INFO @ Fri, 10 Nov 2017 20:42:43: 18000000 INFO @ Fri, 10 Nov 2017 20:42:46: 17000000 INFO @ Fri, 10 Nov 2017 20:42:46: 17000000 INFO @ Fri, 10 Nov 2017 20:42:51: 19000000 INFO @ Fri, 10 Nov 2017 20:42:54: 18000000 INFO @ Fri, 10 Nov 2017 20:42:54: 18000000 INFO @ Fri, 10 Nov 2017 20:42:59: 20000000 INFO @ Fri, 10 Nov 2017 20:43:02: 19000000 INFO @ Fri, 10 Nov 2017 20:43:02: 19000000 INFO @ Fri, 10 Nov 2017 20:43:07: 21000000 INFO @ Fri, 10 Nov 2017 20:43:10: 20000000 INFO @ Fri, 10 Nov 2017 20:43:10: 20000000 INFO @ Fri, 10 Nov 2017 20:43:15: 22000000 INFO @ Fri, 10 Nov 2017 20:43:18: 21000000 INFO @ Fri, 10 Nov 2017 20:43:18: 21000000 INFO @ Fri, 10 Nov 2017 20:43:23: 23000000 INFO @ Fri, 10 Nov 2017 20:43:26: 22000000 INFO @ Fri, 10 Nov 2017 20:43:26: 22000000 INFO @ Fri, 10 Nov 2017 20:43:30: 24000000 INFO @ Fri, 10 Nov 2017 20:43:34: 23000000 INFO @ Fri, 10 Nov 2017 20:43:34: 23000000 INFO @ Fri, 10 Nov 2017 20:43:38: 25000000 INFO @ Fri, 10 Nov 2017 20:43:41: 24000000 INFO @ Fri, 10 Nov 2017 20:43:41: 24000000 INFO @ Fri, 10 Nov 2017 20:43:46: 26000000 INFO @ Fri, 10 Nov 2017 20:43:49: 25000000 INFO @ Fri, 10 Nov 2017 20:43:49: 25000000 INFO @ Fri, 10 Nov 2017 20:43:54: 27000000 INFO @ Fri, 10 Nov 2017 20:43:57: 26000000 INFO @ Fri, 10 Nov 2017 20:43:57: 26000000 INFO @ Fri, 10 Nov 2017 20:44:02: 28000000 INFO @ Fri, 10 Nov 2017 20:44:05: 27000000 INFO @ Fri, 10 Nov 2017 20:44:05: 27000000 INFO @ Fri, 10 Nov 2017 20:44:09: 29000000 INFO @ Fri, 10 Nov 2017 20:44:13: 28000000 INFO @ Fri, 10 Nov 2017 20:44:13: 28000000 INFO @ Fri, 10 Nov 2017 20:44:17: 30000000 INFO @ Fri, 10 Nov 2017 20:44:21: 29000000 INFO @ Fri, 10 Nov 2017 20:44:21: 29000000 INFO @ Fri, 10 Nov 2017 20:44:25: 31000000 INFO @ Fri, 10 Nov 2017 20:44:29: 30000000 INFO @ Fri, 10 Nov 2017 20:44:29: 30000000 INFO @ Fri, 10 Nov 2017 20:44:32: 32000000 INFO @ Fri, 10 Nov 2017 20:44:37: 31000000 INFO @ Fri, 10 Nov 2017 20:44:37: 31000000 INFO @ Fri, 10 Nov 2017 20:44:40: 33000000 INFO @ Fri, 10 Nov 2017 20:44:45: 32000000 INFO @ Fri, 10 Nov 2017 20:44:45: 32000000 INFO @ Fri, 10 Nov 2017 20:44:47: 34000000 INFO @ Fri, 10 Nov 2017 20:44:53: 33000000 INFO @ Fri, 10 Nov 2017 20:44:53: 33000000 INFO @ Fri, 10 Nov 2017 20:44:55: 35000000 INFO @ Fri, 10 Nov 2017 20:45:01: 34000000 INFO @ Fri, 10 Nov 2017 20:45:01: 34000000 INFO @ Fri, 10 Nov 2017 20:45:02: 36000000 INFO @ Fri, 10 Nov 2017 20:45:09: 35000000 INFO @ Fri, 10 Nov 2017 20:45:09: 35000000 INFO @ Fri, 10 Nov 2017 20:45:10: 37000000 INFO @ Fri, 10 Nov 2017 20:45:17: 36000000 INFO @ Fri, 10 Nov 2017 20:45:17: 36000000 INFO @ Fri, 10 Nov 2017 20:45:18: 38000000 INFO @ Fri, 10 Nov 2017 20:45:25: 37000000 INFO @ Fri, 10 Nov 2017 20:45:25: 37000000 INFO @ Fri, 10 Nov 2017 20:45:26: 39000000 INFO @ Fri, 10 Nov 2017 20:45:33: 40000000 INFO @ Fri, 10 Nov 2017 20:45:34: 38000000 INFO @ Fri, 10 Nov 2017 20:45:34: 38000000 INFO @ Fri, 10 Nov 2017 20:45:38: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 20:45:38: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 20:45:38: #1 total tags in treatment: 40608097 INFO @ Fri, 10 Nov 2017 20:45:38: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 20:45:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 20:45:39: #1 tags after filtering in treatment: 40608043 INFO @ Fri, 10 Nov 2017 20:45:39: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 20:45:39: #1 finished! INFO @ Fri, 10 Nov 2017 20:45:39: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 20:45:39: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 20:45:42: 39000000 INFO @ Fri, 10 Nov 2017 20:45:42: 39000000 INFO @ Fri, 10 Nov 2017 20:45:43: #2 number of paired peaks: 6553 INFO @ Fri, 10 Nov 2017 20:45:43: start model_add_line... INFO @ Fri, 10 Nov 2017 20:45:44: start X-correlation... INFO @ Fri, 10 Nov 2017 20:45:44: end of X-cor INFO @ Fri, 10 Nov 2017 20:45:44: #2 finished! INFO @ Fri, 10 Nov 2017 20:45:44: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 20:45:44: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Nov 2017 20:45:44: #2.2 Generate R script for model : SRX831356.05_model.r WARNING @ Fri, 10 Nov 2017 20:45:44: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 20:45:44: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Nov 2017 20:45:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 20:45:44: #3 Call peaks... INFO @ Fri, 10 Nov 2017 20:45:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 20:45:50: 40000000 INFO @ Fri, 10 Nov 2017 20:45:50: 40000000 INFO @ Fri, 10 Nov 2017 20:45:55: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 20:45:55: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 20:45:55: #1 total tags in treatment: 40608097 INFO @ Fri, 10 Nov 2017 20:45:55: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 20:45:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 20:45:55: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 20:45:55: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 20:45:55: #1 total tags in treatment: 40608097 INFO @ Fri, 10 Nov 2017 20:45:55: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 20:45:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 20:45:56: #1 tags after filtering in treatment: 40608043 INFO @ Fri, 10 Nov 2017 20:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 20:45:56: #1 finished! INFO @ Fri, 10 Nov 2017 20:45:56: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 20:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 20:45:56: #1 tags after filtering in treatment: 40608043 INFO @ Fri, 10 Nov 2017 20:45:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 20:45:56: #1 finished! INFO @ Fri, 10 Nov 2017 20:45:56: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 20:45:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 20:46:00: #2 number of paired peaks: 6553 INFO @ Fri, 10 Nov 2017 20:46:00: start model_add_line... INFO @ Fri, 10 Nov 2017 20:46:00: #2 number of paired peaks: 6553 INFO @ Fri, 10 Nov 2017 20:46:00: start model_add_line... INFO @ Fri, 10 Nov 2017 20:46:01: start X-correlation... INFO @ Fri, 10 Nov 2017 20:46:01: end of X-cor INFO @ Fri, 10 Nov 2017 20:46:01: #2 finished! INFO @ Fri, 10 Nov 2017 20:46:01: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 20:46:01: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Nov 2017 20:46:01: #2.2 Generate R script for model : SRX831356.20_model.r WARNING @ Fri, 10 Nov 2017 20:46:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 20:46:01: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Nov 2017 20:46:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 20:46:01: #3 Call peaks... INFO @ Fri, 10 Nov 2017 20:46:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 20:46:01: start X-correlation... INFO @ Fri, 10 Nov 2017 20:46:01: end of X-cor INFO @ Fri, 10 Nov 2017 20:46:01: #2 finished! INFO @ Fri, 10 Nov 2017 20:46:01: #2 predicted fragment length is 50 bps INFO @ Fri, 10 Nov 2017 20:46:01: #2 alternative fragment length(s) may be 50 bps INFO @ Fri, 10 Nov 2017 20:46:01: #2.2 Generate R script for model : SRX831356.10_model.r WARNING @ Fri, 10 Nov 2017 20:46:01: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Nov 2017 20:46:01: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Fri, 10 Nov 2017 20:46:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Nov 2017 20:46:01: #3 Call peaks... INFO @ Fri, 10 Nov 2017 20:46:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 20:47:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 20:47:33: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 20:47:41: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 20:48:12: #4 Write output xls file... SRX831356.05_peaks.xls INFO @ Fri, 10 Nov 2017 20:48:12: #4 Write peak in narrowPeak format file... SRX831356.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 20:48:12: #4 Write summits bed file... SRX831356.05_summits.bed INFO @ Fri, 10 Nov 2017 20:48:12: Done! pass1 - making usageList (67 chroms): 1 millis pass2 - checking and writing primary data (2543 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 20:48:28: #4 Write output xls file... SRX831356.20_peaks.xls INFO @ Fri, 10 Nov 2017 20:48:28: #4 Write peak in narrowPeak format file... SRX831356.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 20:48:28: #4 Write summits bed file... SRX831356.20_summits.bed INFO @ Fri, 10 Nov 2017 20:48:28: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (676 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 20:48:34: #4 Write output xls file... SRX831356.10_peaks.xls INFO @ Fri, 10 Nov 2017 20:48:34: #4 Write peak in narrowPeak format file... SRX831356.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 20:48:34: #4 Write summits bed file... SRX831356.10_summits.bed INFO @ Fri, 10 Nov 2017 20:48:34: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (1372 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。