Job ID = 10195042 sra ファイルのダウンロード中... Completed: 543275K bytes transferred in 9 seconds (477213K bits/sec), in 1 file. Completed: 898035K bytes transferred in 12 seconds (576831K 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 17208496 spots for /home/okishinya/chipatlas/results/rn6/SRX913511/SRR1870959.sra Written 17208496 spots total Written 24775718 spots for /home/okishinya/chipatlas/results/rn6/SRX913511/SRR1870958.sra Written 24775718 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:43 41984214 reads; of these: 41984214 (100.00%) were unpaired; of these: 9059086 (21.58%) aligned 0 times 24740859 (58.93%) aligned exactly 1 time 8184269 (19.49%) aligned >1 times 78.42% overall alignment rate Time searching: 00:21:46 Overall time: 00:21:46 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 16 files... [bam_rmdupse_core] 11130000 / 32925128 = 0.3380 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 07:53:09: # Command line: callpeak -t SRX913511.bam -f BAM -g 2.15e9 -n SRX913511.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913511.10 # format = BAM # ChIP-seq file = ['SRX913511.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 07:53:09: # Command line: callpeak -t SRX913511.bam -f BAM -g 2.15e9 -n SRX913511.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913511.05 # format = BAM # ChIP-seq file = ['SRX913511.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 07:53:09: # Command line: callpeak -t SRX913511.bam -f BAM -g 2.15e9 -n SRX913511.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913511.20 # format = BAM # ChIP-seq file = ['SRX913511.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 07:53:09: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:53:09: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:53:09: #1 read tag files... INFO @ Sat, 11 Nov 2017 07:53:09: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:53:09: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:53:09: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 07:53:17: 1000000 INFO @ Sat, 11 Nov 2017 07:53:17: 1000000 INFO @ Sat, 11 Nov 2017 07:53:17: 1000000 INFO @ Sat, 11 Nov 2017 07:53:25: 2000000 INFO @ Sat, 11 Nov 2017 07:53:25: 2000000 INFO @ Sat, 11 Nov 2017 07:53:25: 2000000 INFO @ Sat, 11 Nov 2017 07:53:32: 3000000 INFO @ Sat, 11 Nov 2017 07:53:32: 3000000 INFO @ Sat, 11 Nov 2017 07:53:32: 3000000 INFO @ Sat, 11 Nov 2017 07:53:40: 4000000 INFO @ Sat, 11 Nov 2017 07:53:40: 4000000 INFO @ Sat, 11 Nov 2017 07:53:40: 4000000 INFO @ Sat, 11 Nov 2017 07:53:47: 5000000 INFO @ Sat, 11 Nov 2017 07:53:47: 5000000 INFO @ Sat, 11 Nov 2017 07:53:47: 5000000 INFO @ Sat, 11 Nov 2017 07:53:55: 6000000 INFO @ Sat, 11 Nov 2017 07:53:55: 6000000 INFO @ Sat, 11 Nov 2017 07:53:55: 6000000 INFO @ Sat, 11 Nov 2017 07:54:02: 7000000 INFO @ Sat, 11 Nov 2017 07:54:03: 7000000 INFO @ Sat, 11 Nov 2017 07:54:03: 7000000 INFO @ Sat, 11 Nov 2017 07:54:10: 8000000 INFO @ Sat, 11 Nov 2017 07:54:10: 8000000 INFO @ Sat, 11 Nov 2017 07:54:10: 8000000 INFO @ Sat, 11 Nov 2017 07:54:18: 9000000 INFO @ Sat, 11 Nov 2017 07:54:18: 9000000 INFO @ Sat, 11 Nov 2017 07:54:18: 9000000 INFO @ Sat, 11 Nov 2017 07:54:25: 10000000 INFO @ Sat, 11 Nov 2017 07:54:25: 10000000 INFO @ Sat, 11 Nov 2017 07:54:25: 10000000 INFO @ Sat, 11 Nov 2017 07:54:33: 11000000 INFO @ Sat, 11 Nov 2017 07:54:33: 11000000 INFO @ Sat, 11 Nov 2017 07:54:33: 11000000 INFO @ Sat, 11 Nov 2017 07:54:40: 12000000 INFO @ Sat, 11 Nov 2017 07:54:40: 12000000 INFO @ Sat, 11 Nov 2017 07:54:41: 12000000 INFO @ Sat, 11 Nov 2017 07:54:48: 13000000 INFO @ Sat, 11 Nov 2017 07:54:48: 13000000 INFO @ Sat, 11 Nov 2017 07:54:48: 13000000 INFO @ Sat, 11 Nov 2017 07:54:55: 14000000 INFO @ Sat, 11 Nov 2017 07:54:55: 14000000 INFO @ Sat, 11 Nov 2017 07:54:56: 14000000 INFO @ Sat, 11 Nov 2017 07:55:03: 15000000 INFO @ Sat, 11 Nov 2017 07:55:03: 15000000 INFO @ Sat, 11 Nov 2017 07:55:03: 15000000 INFO @ Sat, 11 Nov 2017 07:55:11: 16000000 INFO @ Sat, 11 Nov 2017 07:55:11: 16000000 INFO @ Sat, 11 Nov 2017 07:55:11: 16000000 INFO @ Sat, 11 Nov 2017 07:55:18: 17000000 INFO @ Sat, 11 Nov 2017 07:55:18: 17000000 INFO @ Sat, 11 Nov 2017 07:55:18: 17000000 INFO @ Sat, 11 Nov 2017 07:55:26: 18000000 INFO @ Sat, 11 Nov 2017 07:55:26: 18000000 INFO @ Sat, 11 Nov 2017 07:55:26: 18000000 INFO @ Sat, 11 Nov 2017 07:55:34: 19000000 INFO @ Sat, 11 Nov 2017 07:55:34: 19000000 INFO @ Sat, 11 Nov 2017 07:55:34: 19000000 INFO @ Sat, 11 Nov 2017 07:55:41: 20000000 INFO @ Sat, 11 Nov 2017 07:55:42: 20000000 INFO @ Sat, 11 Nov 2017 07:55:42: 20000000 INFO @ Sat, 11 Nov 2017 07:55:49: 21000000 INFO @ Sat, 11 Nov 2017 07:55:50: 21000000 INFO @ Sat, 11 Nov 2017 07:55:50: 21000000 INFO @ Sat, 11 Nov 2017 07:55:55: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:55:55: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:55:55: #1 total tags in treatment: 21795128 INFO @ Sat, 11 Nov 2017 07:55:55: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:55:55: #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 07:55:55: #1 tags after filtering in treatment: 21795006 INFO @ Sat, 11 Nov 2017 07:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:55:55: #1 finished! INFO @ Sat, 11 Nov 2017 07:55:55: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:55:56: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:55:56: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:55:56: #1 total tags in treatment: 21795128 INFO @ Sat, 11 Nov 2017 07:55:56: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:55:56: #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 07:55:56: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 07:55:56: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 07:55:56: #1 total tags in treatment: 21795128 INFO @ Sat, 11 Nov 2017 07:55:56: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 07:55:56: #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 07:55:57: #1 tags after filtering in treatment: 21795006 INFO @ Sat, 11 Nov 2017 07:55:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:55:57: #1 finished! INFO @ Sat, 11 Nov 2017 07:55:57: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:55:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:55:57: #1 tags after filtering in treatment: 21795006 INFO @ Sat, 11 Nov 2017 07:55:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 07:55:57: #1 finished! INFO @ Sat, 11 Nov 2017 07:55:57: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 07:55:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 07:55:58: #2 number of paired peaks: 14191 INFO @ Sat, 11 Nov 2017 07:55:58: start model_add_line... INFO @ Sat, 11 Nov 2017 07:55:59: start X-correlation... INFO @ Sat, 11 Nov 2017 07:55:59: end of X-cor INFO @ Sat, 11 Nov 2017 07:55:59: #2 finished! INFO @ Sat, 11 Nov 2017 07:55:59: #2 predicted fragment length is 98 bps INFO @ Sat, 11 Nov 2017 07:55:59: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 11 Nov 2017 07:55:59: #2.2 Generate R script for model : SRX913511.20_model.r INFO @ Sat, 11 Nov 2017 07:55:59: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:55:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:55:59: #2 number of paired peaks: 14191 INFO @ Sat, 11 Nov 2017 07:55:59: start model_add_line... INFO @ Sat, 11 Nov 2017 07:55:59: #2 number of paired peaks: 14191 INFO @ Sat, 11 Nov 2017 07:55:59: start model_add_line... INFO @ Sat, 11 Nov 2017 07:56:00: start X-correlation... INFO @ Sat, 11 Nov 2017 07:56:00: end of X-cor INFO @ Sat, 11 Nov 2017 07:56:00: #2 finished! INFO @ Sat, 11 Nov 2017 07:56:00: #2 predicted fragment length is 98 bps INFO @ Sat, 11 Nov 2017 07:56:00: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 11 Nov 2017 07:56:00: #2.2 Generate R script for model : SRX913511.05_model.r INFO @ Sat, 11 Nov 2017 07:56:00: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:56:00: start X-correlation... INFO @ Sat, 11 Nov 2017 07:56:00: end of X-cor INFO @ Sat, 11 Nov 2017 07:56:00: #2 finished! INFO @ Sat, 11 Nov 2017 07:56:00: #2 predicted fragment length is 98 bps INFO @ Sat, 11 Nov 2017 07:56:00: #2 alternative fragment length(s) may be 98 bps INFO @ Sat, 11 Nov 2017 07:56:00: #2.2 Generate R script for model : SRX913511.10_model.r INFO @ Sat, 11 Nov 2017 07:56:00: #3 Call peaks... INFO @ Sat, 11 Nov 2017 07:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 07:56:50: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:56:53: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:56:55: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 07:57:21: #4 Write output xls file... SRX913511.05_peaks.xls INFO @ Sat, 11 Nov 2017 07:57:21: #4 Write peak in narrowPeak format file... SRX913511.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:57:21: #4 Write summits bed file... SRX913511.05_summits.bed INFO @ Sat, 11 Nov 2017 07:57:21: Done! pass1 - making usageList (74 chroms): 1 millis pass2 - checking and writing primary data (957 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:57:22: #4 Write output xls file... SRX913511.20_peaks.xls INFO @ Sat, 11 Nov 2017 07:57:22: #4 Write peak in narrowPeak format file... SRX913511.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:57:22: #4 Write summits bed file... SRX913511.20_summits.bed INFO @ Sat, 11 Nov 2017 07:57:22: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 07:57:28: #4 Write output xls file... SRX913511.10_peaks.xls INFO @ Sat, 11 Nov 2017 07:57:29: #4 Write peak in narrowPeak format file... SRX913511.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 07:57:29: #4 Write summits bed file... SRX913511.10_summits.bed INFO @ Sat, 11 Nov 2017 07:57:29: Done! pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (425 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。