Job ID = 9029768 sra ファイルのダウンロード中... Completed: 582015K bytes transferred in 8 seconds (562023K 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 20110 0 20110 0 0 2622 0 --:--:-- 0:00:07 --:--:-- 16204 100 30907 0 30907 0 0 3862 0 --:--:-- 0:00:08 --:--:-- 19648 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 21035775 spots for /home/okishinya/chipatlas/results/dm3/SRX2055951/SRR4069183.sra Written 21035775 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: 00:09:04 21035775 reads; of these: 21035775 (100.00%) were unpaired; of these: 2702401 (12.85%) aligned 0 times 11662615 (55.44%) aligned exactly 1 time 6670759 (31.71%) aligned >1 times 87.15% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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 8 files... [bam_rmdupse_core] 4165722 / 18333374 = 0.2272 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 15:21:58: # Command line: callpeak -t SRX2055951.bam -f BAM -g dm -n SRX2055951.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2055951.05 # format = BAM # ChIP-seq file = ['SRX2055951.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 15:21:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:21:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:21:58: # Command line: callpeak -t SRX2055951.bam -f BAM -g dm -n SRX2055951.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2055951.20 # format = BAM # ChIP-seq file = ['SRX2055951.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 15:21:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:21:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:21:58: # Command line: callpeak -t SRX2055951.bam -f BAM -g dm -n SRX2055951.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2055951.10 # format = BAM # ChIP-seq file = ['SRX2055951.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 15:21:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:21:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:22:05: 1000000 INFO @ Sat, 03 Jun 2017 15:22:05: 1000000 INFO @ Sat, 03 Jun 2017 15:22:05: 1000000 INFO @ Sat, 03 Jun 2017 15:22:11: 2000000 INFO @ Sat, 03 Jun 2017 15:22:12: 2000000 INFO @ Sat, 03 Jun 2017 15:22:12: 2000000 INFO @ Sat, 03 Jun 2017 15:22:17: 3000000 INFO @ Sat, 03 Jun 2017 15:22:19: 3000000 INFO @ Sat, 03 Jun 2017 15:22:19: 3000000 INFO @ Sat, 03 Jun 2017 15:22:24: 4000000 INFO @ Sat, 03 Jun 2017 15:22:26: 4000000 INFO @ Sat, 03 Jun 2017 15:22:26: 4000000 INFO @ Sat, 03 Jun 2017 15:22:30: 5000000 INFO @ Sat, 03 Jun 2017 15:22:33: 5000000 INFO @ Sat, 03 Jun 2017 15:22:33: 5000000 INFO @ Sat, 03 Jun 2017 15:22:36: 6000000 INFO @ Sat, 03 Jun 2017 15:22:39: 6000000 INFO @ Sat, 03 Jun 2017 15:22:39: 6000000 INFO @ Sat, 03 Jun 2017 15:22:43: 7000000 INFO @ Sat, 03 Jun 2017 15:22:47: 7000000 INFO @ Sat, 03 Jun 2017 15:22:47: 7000000 INFO @ Sat, 03 Jun 2017 15:22:50: 8000000 INFO @ Sat, 03 Jun 2017 15:22:54: 8000000 INFO @ Sat, 03 Jun 2017 15:22:54: 8000000 INFO @ Sat, 03 Jun 2017 15:22:56: 9000000 INFO @ Sat, 03 Jun 2017 15:23:01: 9000000 INFO @ Sat, 03 Jun 2017 15:23:01: 9000000 INFO @ Sat, 03 Jun 2017 15:23:04: 10000000 INFO @ Sat, 03 Jun 2017 15:23:08: 10000000 INFO @ Sat, 03 Jun 2017 15:23:08: 10000000 INFO @ Sat, 03 Jun 2017 15:23:10: 11000000 INFO @ Sat, 03 Jun 2017 15:23:15: 11000000 INFO @ Sat, 03 Jun 2017 15:23:15: 11000000 INFO @ Sat, 03 Jun 2017 15:23:17: 12000000 INFO @ Sat, 03 Jun 2017 15:23:22: 12000000 INFO @ Sat, 03 Jun 2017 15:23:22: 12000000 INFO @ Sat, 03 Jun 2017 15:23:23: 13000000 INFO @ Sat, 03 Jun 2017 15:23:29: 13000000 INFO @ Sat, 03 Jun 2017 15:23:29: 13000000 INFO @ Sat, 03 Jun 2017 15:23:30: 14000000 INFO @ Sat, 03 Jun 2017 15:23:31: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:23:31: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:23:31: #1 total tags in treatment: 14167652 INFO @ Sat, 03 Jun 2017 15:23:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:23:31: #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 15:23:34: #1 tags after filtering in treatment: 14164278 INFO @ Sat, 03 Jun 2017 15:23:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:23:34: #1 finished! INFO @ Sat, 03 Jun 2017 15:23:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:23:36: 14000000 INFO @ Sat, 03 Jun 2017 15:23:36: 14000000 INFO @ Sat, 03 Jun 2017 15:23:37: #2 number of paired peaks: 1211 INFO @ Sat, 03 Jun 2017 15:23:37: start model_add_line... INFO @ Sat, 03 Jun 2017 15:23:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:23:37: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:23:37: #1 total tags in treatment: 14167652 INFO @ Sat, 03 Jun 2017 15:23:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:23:37: #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 15:23:37: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 15:23:37: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 15:23:37: #1 total tags in treatment: 14167652 INFO @ Sat, 03 Jun 2017 15:23:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:23:37: #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 15:23:39: #1 tags after filtering in treatment: 14164278 INFO @ Sat, 03 Jun 2017 15:23:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:23:39: #1 finished! INFO @ Sat, 03 Jun 2017 15:23:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:23:39: #1 tags after filtering in treatment: 14164278 INFO @ Sat, 03 Jun 2017 15:23:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:23:39: #1 finished! INFO @ Sat, 03 Jun 2017 15:23:39: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:23:42: #2 number of paired peaks: 1211 INFO @ Sat, 03 Jun 2017 15:23:42: start model_add_line... INFO @ Sat, 03 Jun 2017 15:23:42: #2 number of paired peaks: 1211 INFO @ Sat, 03 Jun 2017 15:23:42: start model_add_line... INFO @ Sat, 03 Jun 2017 15:23:47: start X-correlation... INFO @ Sat, 03 Jun 2017 15:23:47: end of X-cor INFO @ Sat, 03 Jun 2017 15:23:47: #2 finished! INFO @ Sat, 03 Jun 2017 15:23:47: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Jun 2017 15:23:47: #2 alternative fragment length(s) may be 61 bps INFO @ Sat, 03 Jun 2017 15:23:47: #2.2 Generate R script for model : SRX2055951.10_model.r WARNING @ Sat, 03 Jun 2017 15:23:47: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:23:47: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sat, 03 Jun 2017 15:23:47: #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 15:23:47: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:23:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:23:53: start X-correlation... INFO @ Sat, 03 Jun 2017 15:23:53: end of X-cor INFO @ Sat, 03 Jun 2017 15:23:53: #2 finished! INFO @ Sat, 03 Jun 2017 15:23:53: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Jun 2017 15:23:53: #2 alternative fragment length(s) may be 61 bps INFO @ Sat, 03 Jun 2017 15:23:53: #2.2 Generate R script for model : SRX2055951.20_model.r WARNING @ Sat, 03 Jun 2017 15:23:53: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:23:53: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sat, 03 Jun 2017 15:23:53: #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 15:23:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:23:53: start X-correlation... INFO @ Sat, 03 Jun 2017 15:23:53: end of X-cor INFO @ Sat, 03 Jun 2017 15:23:53: #2 finished! INFO @ Sat, 03 Jun 2017 15:23:53: #2 predicted fragment length is 61 bps INFO @ Sat, 03 Jun 2017 15:23:53: #2 alternative fragment length(s) may be 61 bps INFO @ Sat, 03 Jun 2017 15:23:53: #2.2 Generate R script for model : SRX2055951.05_model.r WARNING @ Sat, 03 Jun 2017 15:23:53: #2 Since the d (61) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 15:23:53: #2 You may need to consider one of the other alternative d(s): 61 WARNING @ Sat, 03 Jun 2017 15:23:53: #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 15:23:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:25:02: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:25:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:25:06: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:26:01: #4 Write output xls file... SRX2055951.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:26:01: #4 Write peak in narrowPeak format file... SRX2055951.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:26:01: #4 Write summits bed file... SRX2055951.10_summits.bed INFO @ Sat, 03 Jun 2017 15:26:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3016 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:26:01: #4 Write output xls file... SRX2055951.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:26:01: #4 Write peak in narrowPeak format file... SRX2055951.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:26:01: #4 Write summits bed file... SRX2055951.20_summits.bed INFO @ Sat, 03 Jun 2017 15:26:01: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1634 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:26:02: #4 Write output xls file... SRX2055951.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:26:02: #4 Write peak in narrowPeak format file... SRX2055951.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:26:02: #4 Write summits bed file... SRX2055951.05_summits.bed INFO @ Sat, 03 Jun 2017 15:26:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4905 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。