Job ID = 9029234 sra ファイルのダウンロード中... Completed: 525489K bytes transferred in 11 seconds (367693K 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 14324 0 14324 0 0 1924 0 --:--:-- 0:00:07 --:--:-- 14043 100 38318 0 38318 0 0 4631 0 --:--:-- 0:00:08 --:--:-- 20690 100 66526 0 66526 0 0 7583 0 --:--:-- 0:00:08 --:--:-- 28320 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 24051825 spots for /home/okishinya/chipatlas/results/dm3/SRX1433374/SRR2919839.sra Written 24051825 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: 00:09:43 24051825 reads; of these: 24051825 (100.00%) were unpaired; of these: 693017 (2.88%) aligned 0 times 17970122 (74.71%) aligned exactly 1 time 5388686 (22.40%) aligned >1 times 97.12% overall alignment rate Time searching: 00:09:44 Overall time: 00:09:44 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] 3723633 / 23358808 = 0.1594 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 13:08:47: # Command line: callpeak -t SRX1433374.bam -f BAM -g dm -n SRX1433374.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433374.05 # format = BAM # ChIP-seq file = ['SRX1433374.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 13:08:47: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:08:47: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:08:47: # Command line: callpeak -t SRX1433374.bam -f BAM -g dm -n SRX1433374.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433374.20 # format = BAM # ChIP-seq file = ['SRX1433374.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 13:08:47: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:08:47: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:08:47: # Command line: callpeak -t SRX1433374.bam -f BAM -g dm -n SRX1433374.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433374.10 # format = BAM # ChIP-seq file = ['SRX1433374.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 13:08:47: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:08:47: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:08:54: 1000000 INFO @ Sat, 03 Jun 2017 13:08:55: 1000000 INFO @ Sat, 03 Jun 2017 13:08:55: 1000000 INFO @ Sat, 03 Jun 2017 13:09:01: 2000000 INFO @ Sat, 03 Jun 2017 13:09:03: 2000000 INFO @ Sat, 03 Jun 2017 13:09:04: 2000000 INFO @ Sat, 03 Jun 2017 13:09:07: 3000000 INFO @ Sat, 03 Jun 2017 13:09:11: 3000000 INFO @ Sat, 03 Jun 2017 13:09:13: 3000000 INFO @ Sat, 03 Jun 2017 13:09:14: 4000000 INFO @ Sat, 03 Jun 2017 13:09:19: 4000000 INFO @ Sat, 03 Jun 2017 13:09:20: 5000000 INFO @ Sat, 03 Jun 2017 13:09:23: 4000000 INFO @ Sat, 03 Jun 2017 13:09:27: 5000000 INFO @ Sat, 03 Jun 2017 13:09:27: 6000000 INFO @ Sat, 03 Jun 2017 13:09:32: 5000000 INFO @ Sat, 03 Jun 2017 13:09:34: 7000000 INFO @ Sat, 03 Jun 2017 13:09:35: 6000000 INFO @ Sat, 03 Jun 2017 13:09:41: 8000000 INFO @ Sat, 03 Jun 2017 13:09:42: 6000000 INFO @ Sat, 03 Jun 2017 13:09:43: 7000000 INFO @ Sat, 03 Jun 2017 13:09:48: 9000000 INFO @ Sat, 03 Jun 2017 13:09:51: 8000000 INFO @ Sat, 03 Jun 2017 13:09:52: 7000000 INFO @ Sat, 03 Jun 2017 13:09:55: 10000000 INFO @ Sat, 03 Jun 2017 13:09:59: 9000000 INFO @ Sat, 03 Jun 2017 13:10:01: 8000000 INFO @ Sat, 03 Jun 2017 13:10:02: 11000000 INFO @ Sat, 03 Jun 2017 13:10:07: 10000000 INFO @ Sat, 03 Jun 2017 13:10:10: 12000000 INFO @ Sat, 03 Jun 2017 13:10:11: 9000000 INFO @ Sat, 03 Jun 2017 13:10:15: 11000000 INFO @ Sat, 03 Jun 2017 13:10:17: 13000000 INFO @ Sat, 03 Jun 2017 13:10:21: 10000000 INFO @ Sat, 03 Jun 2017 13:10:23: 14000000 INFO @ Sat, 03 Jun 2017 13:10:24: 12000000 INFO @ Sat, 03 Jun 2017 13:10:30: 11000000 INFO @ Sat, 03 Jun 2017 13:10:31: 15000000 INFO @ Sat, 03 Jun 2017 13:10:32: 13000000 INFO @ Sat, 03 Jun 2017 13:10:37: 16000000 INFO @ Sat, 03 Jun 2017 13:10:38: 12000000 INFO @ Sat, 03 Jun 2017 13:10:38: 14000000 INFO @ Sat, 03 Jun 2017 13:10:44: 17000000 INFO @ Sat, 03 Jun 2017 13:10:45: 15000000 INFO @ Sat, 03 Jun 2017 13:10:45: 13000000 INFO @ Sat, 03 Jun 2017 13:10:50: 18000000 INFO @ Sat, 03 Jun 2017 13:10:51: 16000000 INFO @ Sat, 03 Jun 2017 13:10:53: 14000000 INFO @ Sat, 03 Jun 2017 13:10:58: 17000000 INFO @ Sat, 03 Jun 2017 13:10:59: 19000000 INFO @ Sat, 03 Jun 2017 13:11:00: 15000000 INFO @ Sat, 03 Jun 2017 13:11:03: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:03: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:03: #1 total tags in treatment: 19635175 INFO @ Sat, 03 Jun 2017 13:11:03: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:03: #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 13:11:04: 18000000 INFO @ Sat, 03 Jun 2017 13:11:07: #1 tags after filtering in treatment: 19630651 INFO @ Sat, 03 Jun 2017 13:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:07: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:07: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:07: 16000000 INFO @ Sat, 03 Jun 2017 13:11:10: #2 number of paired peaks: 161 WARNING @ Sat, 03 Jun 2017 13:11:10: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:10: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:11: 19000000 INFO @ Sat, 03 Jun 2017 13:11:13: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:13: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:13: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:13: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Jun 2017 13:11:13: #2 alternative fragment length(s) may be 60 bps INFO @ Sat, 03 Jun 2017 13:11:13: #2.2 Generate R script for model : SRX1433374.10_model.r WARNING @ Sat, 03 Jun 2017 13:11:13: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:13: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sat, 03 Jun 2017 13:11:13: #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 13:11:13: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:15: 17000000 INFO @ Sat, 03 Jun 2017 13:11:15: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:15: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:15: #1 total tags in treatment: 19635175 INFO @ Sat, 03 Jun 2017 13:11:15: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:15: #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 13:11:18: #1 tags after filtering in treatment: 19630651 INFO @ Sat, 03 Jun 2017 13:11:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:18: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:21: 18000000 INFO @ Sat, 03 Jun 2017 13:11:22: #2 number of paired peaks: 161 WARNING @ Sat, 03 Jun 2017 13:11:22: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:22: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:25: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:25: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:25: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:25: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Jun 2017 13:11:25: #2 alternative fragment length(s) may be 60 bps INFO @ Sat, 03 Jun 2017 13:11:25: #2.2 Generate R script for model : SRX1433374.20_model.r WARNING @ Sat, 03 Jun 2017 13:11:25: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:25: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sat, 03 Jun 2017 13:11:25: #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 13:11:25: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:11:27: 19000000 INFO @ Sat, 03 Jun 2017 13:11:31: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 13:11:31: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 13:11:31: #1 total tags in treatment: 19635175 INFO @ Sat, 03 Jun 2017 13:11:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:11:31: #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 13:11:34: #1 tags after filtering in treatment: 19630651 INFO @ Sat, 03 Jun 2017 13:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:11:34: #1 finished! INFO @ Sat, 03 Jun 2017 13:11:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:11:38: #2 number of paired peaks: 161 WARNING @ Sat, 03 Jun 2017 13:11:38: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Sat, 03 Jun 2017 13:11:38: start model_add_line... INFO @ Sat, 03 Jun 2017 13:11:41: start X-correlation... INFO @ Sat, 03 Jun 2017 13:11:41: end of X-cor INFO @ Sat, 03 Jun 2017 13:11:41: #2 finished! INFO @ Sat, 03 Jun 2017 13:11:41: #2 predicted fragment length is 60 bps INFO @ Sat, 03 Jun 2017 13:11:41: #2 alternative fragment length(s) may be 60 bps INFO @ Sat, 03 Jun 2017 13:11:41: #2.2 Generate R script for model : SRX1433374.05_model.r WARNING @ Sat, 03 Jun 2017 13:11:41: #2 Since the d (60) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 13:11:41: #2 You may need to consider one of the other alternative d(s): 60 WARNING @ Sat, 03 Jun 2017 13:11:41: #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 13:11:41: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:11:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:12:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:13:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:06: #4 Write output xls file... SRX1433374.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:06: #4 Write peak in narrowPeak format file... SRX1433374.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:06: #4 Write summits bed file... SRX1433374.10_summits.bed INFO @ Sat, 03 Jun 2017 13:14:06: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1358 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:14:20: #4 Write output xls file... SRX1433374.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:20: #4 Write peak in narrowPeak format file... SRX1433374.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:20: #4 Write summits bed file... SRX1433374.20_summits.bed INFO @ Sat, 03 Jun 2017 13:14:20: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (812 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:14:49: #4 Write output xls file... SRX1433374.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:49: #4 Write peak in narrowPeak format file... SRX1433374.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:49: #4 Write summits bed file... SRX1433374.05_summits.bed INFO @ Sat, 03 Jun 2017 13:14:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2126 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。