Job ID = 9029763 sra ファイルのダウンロード中... Completed: 1098136K bytes transferred in 13 seconds (668717K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1893 0 --:--:-- 0:00:07 --:--:-- 12732 100 31049 0 31049 0 0 3849 0 --:--:-- 0:00:08 --:--:-- 19118 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 22695222 spots for /home/okishinya/chipatlas/results/dm3/SRX2055947/SRR4069179.sra Written 22695222 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: 00:00:00 Multiseed full-index search: 00:10:56 22695222 reads; of these: 22695222 (100.00%) were unpaired; of these: 2922817 (12.88%) aligned 0 times 11711829 (51.60%) aligned exactly 1 time 8060576 (35.52%) aligned >1 times 87.12% overall alignment rate Time searching: 00:10:56 Overall time: 00:10:56 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] 3599065 / 19772405 = 0.1820 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 15:22:30: # Command line: callpeak -t SRX2055947.bam -f BAM -g dm -n SRX2055947.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055947.10 # format = BAM # ChIP-seq file = ['SRX2055947.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 15:22:30: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:22:30: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:22:30: # Command line: callpeak -t SRX2055947.bam -f BAM -g dm -n SRX2055947.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055947.05 # format = BAM # ChIP-seq file = ['SRX2055947.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 15:22:30: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:22:30: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:22:30: # Command line: callpeak -t SRX2055947.bam -f BAM -g dm -n SRX2055947.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055947.20 # format = BAM # ChIP-seq file = ['SRX2055947.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 15:22:30: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:22:30: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:22:36: 1000000 INFO @ Sat, 03 Jun 2017 15:22:36: 1000000 INFO @ Sat, 03 Jun 2017 15:22:36: 1000000 INFO @ Sat, 03 Jun 2017 15:22:42: 2000000 INFO @ Sat, 03 Jun 2017 15:22:42: 2000000 INFO @ Sat, 03 Jun 2017 15:22:42: 2000000 INFO @ Sat, 03 Jun 2017 15:22:48: 3000000 INFO @ Sat, 03 Jun 2017 15:22:48: 3000000 INFO @ Sat, 03 Jun 2017 15:22:49: 3000000 INFO @ Sat, 03 Jun 2017 15:22:53: 4000000 INFO @ Sat, 03 Jun 2017 15:22:54: 4000000 INFO @ Sat, 03 Jun 2017 15:22:56: 4000000 INFO @ Sat, 03 Jun 2017 15:22:59: 5000000 INFO @ Sat, 03 Jun 2017 15:23:00: 5000000 INFO @ Sat, 03 Jun 2017 15:23:03: 5000000 INFO @ Sat, 03 Jun 2017 15:23:05: 6000000 INFO @ Sat, 03 Jun 2017 15:23:07: 6000000 INFO @ Sat, 03 Jun 2017 15:23:10: 6000000 INFO @ Sat, 03 Jun 2017 15:23:10: 7000000 INFO @ Sat, 03 Jun 2017 15:23:13: 7000000 INFO @ Sat, 03 Jun 2017 15:23:16: 8000000 INFO @ Sat, 03 Jun 2017 15:23:17: 7000000 INFO @ Sat, 03 Jun 2017 15:23:20: 8000000 INFO @ Sat, 03 Jun 2017 15:23:22: 9000000 INFO @ Sat, 03 Jun 2017 15:23:24: 8000000 INFO @ Sat, 03 Jun 2017 15:23:26: 9000000 INFO @ Sat, 03 Jun 2017 15:23:27: 10000000 INFO @ Sat, 03 Jun 2017 15:23:31: 9000000 INFO @ Sat, 03 Jun 2017 15:23:32: 10000000 INFO @ Sat, 03 Jun 2017 15:23:33: 11000000 INFO @ Sat, 03 Jun 2017 15:23:38: 10000000 INFO @ Sat, 03 Jun 2017 15:23:39: 11000000 INFO @ Sat, 03 Jun 2017 15:23:39: 12000000 INFO @ Sat, 03 Jun 2017 15:23:44: 13000000 INFO @ Sat, 03 Jun 2017 15:23:44: 11000000 INFO @ Sat, 03 Jun 2017 15:23:45: 12000000 INFO @ Sat, 03 Jun 2017 15:23:50: 14000000 INFO @ Sat, 03 Jun 2017 15:23:51: 13000000 INFO @ Sat, 03 Jun 2017 15:23:51: 12000000 INFO @ Sat, 03 Jun 2017 15:23:55: 15000000 INFO @ Sat, 03 Jun 2017 15:23:57: 14000000 INFO @ Sat, 03 Jun 2017 15:23:58: 13000000 INFO @ Sat, 03 Jun 2017 15:24:01: 16000000 INFO @ Sat, 03 Jun 2017 15:24:02: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:24:02: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:24:02: #1 total tags in treatment: 16173340 INFO @ Sat, 03 Jun 2017 15:24:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:24:02: #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 15:24:04: 15000000 INFO @ Sat, 03 Jun 2017 15:24:05: 14000000 INFO @ Sat, 03 Jun 2017 15:24:05: #1 tags after filtering in treatment: 16169254 INFO @ Sat, 03 Jun 2017 15:24:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:24:05: #1 finished! INFO @ Sat, 03 Jun 2017 15:24:05: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:24:08: #2 number of paired peaks: 1082 INFO @ Sat, 03 Jun 2017 15:24:08: start model_add_line... INFO @ Sat, 03 Jun 2017 15:24:10: 16000000 INFO @ Sat, 03 Jun 2017 15:24:11: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:24:11: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:24:11: #1 total tags in treatment: 16173340 INFO @ Sat, 03 Jun 2017 15:24:11: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:24:11: #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 15:24:12: 15000000 INFO @ Sat, 03 Jun 2017 15:24:14: #1 tags after filtering in treatment: 16169254 INFO @ Sat, 03 Jun 2017 15:24:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:24:14: #1 finished! INFO @ Sat, 03 Jun 2017 15:24:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:24:17: #2 number of paired peaks: 1082 INFO @ Sat, 03 Jun 2017 15:24:17: start model_add_line... INFO @ Sat, 03 Jun 2017 15:24:18: 16000000 INFO @ Sat, 03 Jun 2017 15:24:19: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:24:19: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:24:19: #1 total tags in treatment: 16173340 INFO @ Sat, 03 Jun 2017 15:24:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:24:19: #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 15:24:20: start X-correlation... INFO @ Sat, 03 Jun 2017 15:24:20: end of X-cor INFO @ Sat, 03 Jun 2017 15:24:20: #2 finished! INFO @ Sat, 03 Jun 2017 15:24:20: #2 predicted fragment length is 77 bps INFO @ Sat, 03 Jun 2017 15:24:20: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 03 Jun 2017 15:24:20: #2.2 Generate R script for model : SRX2055947.20_model.r WARNING @ Sat, 03 Jun 2017 15:24:20: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:24:20: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 03 Jun 2017 15:24:20: #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 15:24:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:24:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:24:22: #1 tags after filtering in treatment: 16169254 INFO @ Sat, 03 Jun 2017 15:24:22: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:24:22: #1 finished! INFO @ Sat, 03 Jun 2017 15:24:22: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:24:25: #2 number of paired peaks: 1082 INFO @ Sat, 03 Jun 2017 15:24:25: start model_add_line... INFO @ Sat, 03 Jun 2017 15:24:29: start X-correlation... INFO @ Sat, 03 Jun 2017 15:24:29: end of X-cor INFO @ Sat, 03 Jun 2017 15:24:29: #2 finished! INFO @ Sat, 03 Jun 2017 15:24:29: #2 predicted fragment length is 77 bps INFO @ Sat, 03 Jun 2017 15:24:29: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 03 Jun 2017 15:24:29: #2.2 Generate R script for model : SRX2055947.05_model.r WARNING @ Sat, 03 Jun 2017 15:24:29: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:24:29: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 03 Jun 2017 15:24:29: #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 15:24:29: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:24:37: start X-correlation... INFO @ Sat, 03 Jun 2017 15:24:37: end of X-cor INFO @ Sat, 03 Jun 2017 15:24:37: #2 finished! INFO @ Sat, 03 Jun 2017 15:24:37: #2 predicted fragment length is 77 bps INFO @ Sat, 03 Jun 2017 15:24:37: #2 alternative fragment length(s) may be 77 bps INFO @ Sat, 03 Jun 2017 15:24:37: #2.2 Generate R script for model : SRX2055947.10_model.r WARNING @ Sat, 03 Jun 2017 15:24:37: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:24:37: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Sat, 03 Jun 2017 15:24:37: #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 15:24:37: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:24:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:25:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:25:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:25:59: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:26:57: #4 Write output xls file... SRX2055947.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:26:57: #4 Write peak in narrowPeak format file... SRX2055947.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:26:57: #4 Write summits bed file... SRX2055947.20_summits.bed INFO @ Sat, 03 Jun 2017 15:26:57: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1764 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:27:02: #4 Write output xls file... SRX2055947.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:27:02: #4 Write peak in narrowPeak format file... SRX2055947.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:27:03: #4 Write summits bed file... SRX2055947.05_summits.bed INFO @ Sat, 03 Jun 2017 15:27:03: Done! INFO @ Sat, 03 Jun 2017 15:27:03: #4 Write output xls file... SRX2055947.10_peaks.xls pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6178 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:27:03: #4 Write peak in narrowPeak format file... SRX2055947.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:27:03: #4 Write summits bed file... SRX2055947.10_summits.bed INFO @ Sat, 03 Jun 2017 15:27:03: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3325 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。