Job ID = 9029364 sra ファイルのダウンロード中... Completed: 1744216K bytes transferred in 16 seconds (862764K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 12695 0 12695 0 0 1707 0 --:--:-- 0:00:07 --:--:-- 15149 100 44726 0 44726 0 0 5304 0 --:--:-- 0:00:08 --:--:-- 24400 100 72032 0 72032 0 0 8218 0 --:--:-- 0:00:08 --:--:-- 33271 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 31805107 spots for /home/okishinya/chipatlas/results/dm3/SRX1600296/SRR3187800.sra Written 31805107 spots total 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:04 31805107 reads; of these: 31805107 (100.00%) were unpaired; of these: 4999075 (15.72%) aligned 0 times 24175110 (76.01%) aligned exactly 1 time 2630922 (8.27%) aligned >1 times 84.28% overall alignment rate Time searching: 00:11:05 Overall time: 00:11:05 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 14965842 / 26806032 = 0.5583 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, 03 Jun 2017 13:38:31: # Command line: callpeak -t SRX1600296.bam -f BAM -g dm -n SRX1600296.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1600296.20 # format = BAM # ChIP-seq file = ['SRX1600296.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sat, 03 Jun 2017 13:38:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:38:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:38:31: # Command line: callpeak -t SRX1600296.bam -f BAM -g dm -n SRX1600296.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1600296.05 # format = BAM # ChIP-seq file = ['SRX1600296.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sat, 03 Jun 2017 13:38:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:38:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:38:31: # Command line: callpeak -t SRX1600296.bam -f BAM -g dm -n SRX1600296.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1600296.10 # format = BAM # ChIP-seq file = ['SRX1600296.bam'] # control file = None # effective genome size = 1.20e+08 # 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 INFO @ Sat, 03 Jun 2017 13:38:31: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:38:31: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:38:38: 1000000 INFO @ Sat, 03 Jun 2017 13:38:38: 1000000 INFO @ Sat, 03 Jun 2017 13:38:40: 1000000 INFO @ Sat, 03 Jun 2017 13:38:46: 2000000 INFO @ Sat, 03 Jun 2017 13:38:46: 2000000 INFO @ Sat, 03 Jun 2017 13:38:50: 2000000 INFO @ Sat, 03 Jun 2017 13:38:53: 3000000 INFO @ Sat, 03 Jun 2017 13:38:53: 3000000 INFO @ Sat, 03 Jun 2017 13:38:59: 3000000 INFO @ Sat, 03 Jun 2017 13:39:01: 4000000 INFO @ Sat, 03 Jun 2017 13:39:01: 4000000 INFO @ Sat, 03 Jun 2017 13:39:08: 4000000 INFO @ Sat, 03 Jun 2017 13:39:08: 5000000 INFO @ Sat, 03 Jun 2017 13:39:08: 5000000 INFO @ Sat, 03 Jun 2017 13:39:16: 6000000 INFO @ Sat, 03 Jun 2017 13:39:16: 6000000 INFO @ Sat, 03 Jun 2017 13:39:18: 5000000 INFO @ Sat, 03 Jun 2017 13:39:24: 7000000 INFO @ Sat, 03 Jun 2017 13:39:24: 7000000 INFO @ Sat, 03 Jun 2017 13:39:27: 6000000 INFO @ Sat, 03 Jun 2017 13:39:32: 8000000 INFO @ Sat, 03 Jun 2017 13:39:32: 8000000 INFO @ Sat, 03 Jun 2017 13:39:37: 7000000 INFO @ Sat, 03 Jun 2017 13:39:40: 9000000 INFO @ Sat, 03 Jun 2017 13:39:40: 9000000 INFO @ Sat, 03 Jun 2017 13:39:46: 8000000 INFO @ Sat, 03 Jun 2017 13:39:48: 10000000 INFO @ Sat, 03 Jun 2017 13:39:48: 10000000 INFO @ Sat, 03 Jun 2017 13:39:56: 9000000 INFO @ Sat, 03 Jun 2017 13:39:56: 11000000 INFO @ Sat, 03 Jun 2017 13:39:56: 11000000 INFO @ Sat, 03 Jun 2017 13:40:03: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 13:40:03: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 13:40:03: #1 total tags in treatment: 11840190 INFO @ Sat, 03 Jun 2017 13:40:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:40:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:40:03: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 13:40:03: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 13:40:03: #1 total tags in treatment: 11840190 INFO @ Sat, 03 Jun 2017 13:40:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:40:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:40:05: #1 tags after filtering in treatment: 11823644 INFO @ Sat, 03 Jun 2017 13:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:40:05: #1 finished! INFO @ Sat, 03 Jun 2017 13:40:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:40:05: #1 tags after filtering in treatment: 11823644 INFO @ Sat, 03 Jun 2017 13:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:40:05: #1 finished! INFO @ Sat, 03 Jun 2017 13:40:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:40:06: 10000000 INFO @ Sat, 03 Jun 2017 13:40:08: #2 number of paired peaks: 5161 INFO @ Sat, 03 Jun 2017 13:40:08: start model_add_line... INFO @ Sat, 03 Jun 2017 13:40:08: #2 number of paired peaks: 5161 INFO @ Sat, 03 Jun 2017 13:40:08: start model_add_line... INFO @ Sat, 03 Jun 2017 13:40:15: 11000000 INFO @ Sat, 03 Jun 2017 13:40:24: #1 tag size is determined as 76 bps INFO @ Sat, 03 Jun 2017 13:40:24: #1 tag size = 76 INFO @ Sat, 03 Jun 2017 13:40:24: #1 total tags in treatment: 11840190 INFO @ Sat, 03 Jun 2017 13:40:24: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:40:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:40:26: #1 tags after filtering in treatment: 11823644 INFO @ Sat, 03 Jun 2017 13:40:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:40:26: #1 finished! INFO @ Sat, 03 Jun 2017 13:40:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:40:29: #2 number of paired peaks: 5161 INFO @ Sat, 03 Jun 2017 13:40:29: start model_add_line... INFO @ Sat, 03 Jun 2017 13:40:41: start X-correlation... INFO @ Sat, 03 Jun 2017 13:40:41: end of X-cor INFO @ Sat, 03 Jun 2017 13:40:41: #2 finished! INFO @ Sat, 03 Jun 2017 13:40:41: #2 predicted fragment length is 126 bps INFO @ Sat, 03 Jun 2017 13:40:41: #2 alternative fragment length(s) may be 4,126 bps INFO @ Sat, 03 Jun 2017 13:40:41: #2.2 Generate R script for model : SRX1600296.05_model.r WARNING @ Sat, 03 Jun 2017 13:40:41: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:40:41: #2 You may need to consider one of the other alternative d(s): 4,126 WARNING @ Sat, 03 Jun 2017 13:40:41: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:40:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:40:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:40:42: start X-correlation... INFO @ Sat, 03 Jun 2017 13:40:42: end of X-cor INFO @ Sat, 03 Jun 2017 13:40:42: #2 finished! INFO @ Sat, 03 Jun 2017 13:40:42: #2 predicted fragment length is 126 bps INFO @ Sat, 03 Jun 2017 13:40:42: #2 alternative fragment length(s) may be 4,126 bps INFO @ Sat, 03 Jun 2017 13:40:42: #2.2 Generate R script for model : SRX1600296.20_model.r WARNING @ Sat, 03 Jun 2017 13:40:42: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:40:42: #2 You may need to consider one of the other alternative d(s): 4,126 WARNING @ Sat, 03 Jun 2017 13:40:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:40:42: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:40:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:41:03: start X-correlation... INFO @ Sat, 03 Jun 2017 13:41:03: end of X-cor INFO @ Sat, 03 Jun 2017 13:41:03: #2 finished! INFO @ Sat, 03 Jun 2017 13:41:03: #2 predicted fragment length is 126 bps INFO @ Sat, 03 Jun 2017 13:41:03: #2 alternative fragment length(s) may be 4,126 bps INFO @ Sat, 03 Jun 2017 13:41:03: #2.2 Generate R script for model : SRX1600296.10_model.r WARNING @ Sat, 03 Jun 2017 13:41:03: #2 Since the d (126) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:41:03: #2 You may need to consider one of the other alternative d(s): 4,126 WARNING @ Sat, 03 Jun 2017 13:41:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 13:41:03: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:41:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:41:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:41:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:42:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:42:46: #4 Write output xls file... SRX1600296.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:42:46: #4 Write peak in narrowPeak format file... SRX1600296.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:42:46: #4 Write summits bed file... SRX1600296.20_summits.bed INFO @ Sat, 03 Jun 2017 13:42:46: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4838 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:42:48: #4 Write output xls file... SRX1600296.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:42:49: #4 Write peak in narrowPeak format file... SRX1600296.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:42:49: #4 Write summits bed file... SRX1600296.05_summits.bed INFO @ Sat, 03 Jun 2017 13:42:49: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (10395 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:43:06: #4 Write output xls file... SRX1600296.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:43:06: #4 Write peak in narrowPeak format file... SRX1600296.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:43:06: #4 Write summits bed file... SRX1600296.10_summits.bed INFO @ Sat, 03 Jun 2017 13:43:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8303 records, 4 fields): 11 millis CompletedMACS2peakCalling BigWig に変換しました。