Job ID = 2161343 sra ファイルのダウンロード中... Completed: 954298K bytes transferred in 10 seconds (771853K bits/sec), in 2 files, 3 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 101 5467 0 5467 0 0 9627 0 --:--:-- --:--:-- --:--:-- 14462 100 35360 0 35360 0 0 46683 0 --:--:-- --:--:-- --:--:-- 62363 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 14971135 spots for /home/okishinya/chipatlas/results/dm3/SRX020692/SRR060798.sra Written 14971135 spots total Written 15843784 spots for /home/okishinya/chipatlas/results/dm3/SRX020692/SRR060799.sra Written 15843784 spots total 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: 00:00:00 Multiseed full-index search: 00:05:42 30814919 reads; of these: 30814919 (100.00%) were unpaired; of these: 15366298 (49.87%) aligned 0 times 12548280 (40.72%) aligned exactly 1 time 2900341 (9.41%) aligned >1 times 50.13% overall alignment rate Time searching: 00:05:43 Overall time: 00:05:43 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_rmdupse_core] 4425671 / 15448621 = 0.2865 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 @ Tue, 21 Apr 2015 12:34:37: # Command line: callpeak -t SRX020692.bam -f BAM -g dm -n SRX020692.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX020692.20 # format = BAM # ChIP-seq file = ['SRX020692.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 @ Tue, 21 Apr 2015 12:34:37: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:34:37: # Command line: callpeak -t SRX020692.bam -f BAM -g dm -n SRX020692.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX020692.10 # format = BAM # ChIP-seq file = ['SRX020692.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 @ Tue, 21 Apr 2015 12:34:37: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:34:37: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:34:37: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:34:37: # Command line: callpeak -t SRX020692.bam -f BAM -g dm -n SRX020692.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX020692.05 # format = BAM # ChIP-seq file = ['SRX020692.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 @ Tue, 21 Apr 2015 12:34:37: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:34:37: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:34:43: 1000000 INFO @ Tue, 21 Apr 2015 12:34:44: 1000000 INFO @ Tue, 21 Apr 2015 12:34:44: 1000000 INFO @ Tue, 21 Apr 2015 12:34:49: 2000000 INFO @ Tue, 21 Apr 2015 12:34:50: 2000000 INFO @ Tue, 21 Apr 2015 12:34:50: 2000000 INFO @ Tue, 21 Apr 2015 12:34:55: 3000000 INFO @ Tue, 21 Apr 2015 12:34:56: 3000000 INFO @ Tue, 21 Apr 2015 12:34:56: 3000000 INFO @ Tue, 21 Apr 2015 12:35:01: 4000000 INFO @ Tue, 21 Apr 2015 12:35:02: 4000000 INFO @ Tue, 21 Apr 2015 12:35:02: 4000000 INFO @ Tue, 21 Apr 2015 12:35:07: 5000000 INFO @ Tue, 21 Apr 2015 12:35:08: 5000000 INFO @ Tue, 21 Apr 2015 12:35:08: 5000000 INFO @ Tue, 21 Apr 2015 12:35:13: 6000000 INFO @ Tue, 21 Apr 2015 12:35:15: 6000000 INFO @ Tue, 21 Apr 2015 12:35:15: 6000000 INFO @ Tue, 21 Apr 2015 12:35:19: 7000000 INFO @ Tue, 21 Apr 2015 12:35:21: 7000000 INFO @ Tue, 21 Apr 2015 12:35:21: 7000000 INFO @ Tue, 21 Apr 2015 12:35:25: 8000000 INFO @ Tue, 21 Apr 2015 12:35:27: 8000000 INFO @ Tue, 21 Apr 2015 12:35:27: 8000000 INFO @ Tue, 21 Apr 2015 12:35:31: 9000000 INFO @ Tue, 21 Apr 2015 12:35:33: 9000000 INFO @ Tue, 21 Apr 2015 12:35:33: 9000000 INFO @ Tue, 21 Apr 2015 12:35:37: 10000000 INFO @ Tue, 21 Apr 2015 12:35:39: 10000000 INFO @ Tue, 21 Apr 2015 12:35:39: 10000000 INFO @ Tue, 21 Apr 2015 12:35:43: 11000000 INFO @ Tue, 21 Apr 2015 12:35:43: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:35:43: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:35:43: #1 total tags in treatment: 11022950 INFO @ Tue, 21 Apr 2015 12:35:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:35:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:35:45: #1 tags after filtering in treatment: 11019879 INFO @ Tue, 21 Apr 2015 12:35:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:35:45: #1 finished! INFO @ Tue, 21 Apr 2015 12:35:45: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:35:45: 11000000 INFO @ Tue, 21 Apr 2015 12:35:45: 11000000 INFO @ Tue, 21 Apr 2015 12:35:46: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:35:46: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:35:46: #1 total tags in treatment: 11022950 INFO @ Tue, 21 Apr 2015 12:35:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:35:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:35:46: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:35:46: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:35:46: #1 total tags in treatment: 11022950 INFO @ Tue, 21 Apr 2015 12:35:46: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:35:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:35:47: #2 number of paired peaks: 2347 INFO @ Tue, 21 Apr 2015 12:35:47: start model_add_line... INFO @ Tue, 21 Apr 2015 12:35:48: #1 tags after filtering in treatment: 11019879 INFO @ Tue, 21 Apr 2015 12:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:35:48: #1 finished! INFO @ Tue, 21 Apr 2015 12:35:48: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:35:48: #1 tags after filtering in treatment: 11019879 INFO @ Tue, 21 Apr 2015 12:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:35:48: #1 finished! INFO @ Tue, 21 Apr 2015 12:35:48: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:35:50: #2 number of paired peaks: 2347 INFO @ Tue, 21 Apr 2015 12:35:50: start model_add_line... INFO @ Tue, 21 Apr 2015 12:35:50: #2 number of paired peaks: 2347 INFO @ Tue, 21 Apr 2015 12:35:50: start model_add_line... INFO @ Tue, 21 Apr 2015 12:36:03: start X-correlation... INFO @ Tue, 21 Apr 2015 12:36:03: end of X-cor INFO @ Tue, 21 Apr 2015 12:36:03: #2 finished! INFO @ Tue, 21 Apr 2015 12:36:03: #2 predicted fragment length is 71 bps INFO @ Tue, 21 Apr 2015 12:36:03: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 21 Apr 2015 12:36:03: #2.2 Generate R script for model : SRX020692.20_model.r WARNING @ Tue, 21 Apr 2015 12:36:03: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:36:03: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 21 Apr 2015 12:36:03: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:36:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:36:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:36:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:36:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:36:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:36:05: #2 predicted fragment length is 71 bps INFO @ Tue, 21 Apr 2015 12:36:05: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 21 Apr 2015 12:36:05: #2.2 Generate R script for model : SRX020692.10_model.r WARNING @ Tue, 21 Apr 2015 12:36:05: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:36:05: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 21 Apr 2015 12:36:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:36:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:36:05: start X-correlation... INFO @ Tue, 21 Apr 2015 12:36:05: end of X-cor INFO @ Tue, 21 Apr 2015 12:36:05: #2 finished! INFO @ Tue, 21 Apr 2015 12:36:05: #2 predicted fragment length is 71 bps INFO @ Tue, 21 Apr 2015 12:36:05: #2 alternative fragment length(s) may be 71 bps INFO @ Tue, 21 Apr 2015 12:36:05: #2.2 Generate R script for model : SRX020692.05_model.r WARNING @ Tue, 21 Apr 2015 12:36:05: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:36:05: #2 You may need to consider one of the other alternative d(s): 71 WARNING @ Tue, 21 Apr 2015 12:36:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:36:05: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:36:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:37:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:37:02: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:37:04: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:37:44: #4 Write output xls file... SRX020692.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:37:44: #4 Write peak in narrowPeak format file... SRX020692.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:37:44: #4 Write summits bed file... SRX020692.20_summits.bed INFO @ Tue, 21 Apr 2015 12:37:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3390 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:37:50: #4 Write output xls file... SRX020692.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:37:50: #4 Write peak in narrowPeak format file... SRX020692.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:37:50: #4 Write summits bed file... SRX020692.10_summits.bed INFO @ Tue, 21 Apr 2015 12:37:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8592 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:37:58: #4 Write output xls file... SRX020692.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:37:58: #4 Write peak in narrowPeak format file... SRX020692.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:37:58: #4 Write summits bed file... SRX020692.05_summits.bed INFO @ Tue, 21 Apr 2015 12:37:58: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13836 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。