Job ID = 9033048 sra ファイルのダウンロード中... Completed: 609425K bytes transferred in 8 seconds (589231K 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 1703 0 --:--:-- 0:00:07 --:--:-- 14882 100 47622 0 47622 0 0 5638 0 --:--:-- 0:00:08 --:--:-- 25769 100 63873 0 63873 0 0 7416 0 --:--:-- 0:00:08 --:--:-- 31730 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 19021504 spots for /home/okishinya/chipatlas/results/dm3/SRX886167/SRR1813781.sra Written 19021504 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: 00:06:42 19021504 reads; of these: 19021504 (100.00%) were unpaired; of these: 778675 (4.09%) aligned 0 times 12546020 (65.96%) aligned exactly 1 time 5696809 (29.95%) aligned >1 times 95.91% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 7266642 / 18242829 = 0.3983 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 @ Sun, 04 Jun 2017 00:12:58: # Command line: callpeak -t SRX886167.bam -f BAM -g dm -n SRX886167.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX886167.10 # format = BAM # ChIP-seq file = ['SRX886167.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 @ Sun, 04 Jun 2017 00:12:58: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:12:58: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:12:58: # Command line: callpeak -t SRX886167.bam -f BAM -g dm -n SRX886167.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX886167.05 # format = BAM # ChIP-seq file = ['SRX886167.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 @ Sun, 04 Jun 2017 00:12:58: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:12:58: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:12:58: # Command line: callpeak -t SRX886167.bam -f BAM -g dm -n SRX886167.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX886167.20 # format = BAM # ChIP-seq file = ['SRX886167.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 @ Sun, 04 Jun 2017 00:12:58: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:12:58: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:13:04: 1000000 INFO @ Sun, 04 Jun 2017 00:13:05: 1000000 INFO @ Sun, 04 Jun 2017 00:13:05: 1000000 INFO @ Sun, 04 Jun 2017 00:13:11: 2000000 INFO @ Sun, 04 Jun 2017 00:13:11: 2000000 INFO @ Sun, 04 Jun 2017 00:13:11: 2000000 INFO @ Sun, 04 Jun 2017 00:13:17: 3000000 INFO @ Sun, 04 Jun 2017 00:13:18: 3000000 INFO @ Sun, 04 Jun 2017 00:13:18: 3000000 INFO @ Sun, 04 Jun 2017 00:13:23: 4000000 INFO @ Sun, 04 Jun 2017 00:13:24: 4000000 INFO @ Sun, 04 Jun 2017 00:13:24: 4000000 INFO @ Sun, 04 Jun 2017 00:13:29: 5000000 INFO @ Sun, 04 Jun 2017 00:13:31: 5000000 INFO @ Sun, 04 Jun 2017 00:13:31: 5000000 INFO @ Sun, 04 Jun 2017 00:13:35: 6000000 INFO @ Sun, 04 Jun 2017 00:13:37: 6000000 INFO @ Sun, 04 Jun 2017 00:13:37: 6000000 INFO @ Sun, 04 Jun 2017 00:13:41: 7000000 INFO @ Sun, 04 Jun 2017 00:13:44: 7000000 INFO @ Sun, 04 Jun 2017 00:13:44: 7000000 INFO @ Sun, 04 Jun 2017 00:13:47: 8000000 INFO @ Sun, 04 Jun 2017 00:13:50: 8000000 INFO @ Sun, 04 Jun 2017 00:13:50: 8000000 INFO @ Sun, 04 Jun 2017 00:13:54: 9000000 INFO @ Sun, 04 Jun 2017 00:13:57: 9000000 INFO @ Sun, 04 Jun 2017 00:13:57: 9000000 INFO @ Sun, 04 Jun 2017 00:14:00: 10000000 INFO @ Sun, 04 Jun 2017 00:14:03: 10000000 INFO @ Sun, 04 Jun 2017 00:14:03: 10000000 INFO @ Sun, 04 Jun 2017 00:14:06: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:14:06: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:14:06: #1 total tags in treatment: 10976187 INFO @ Sun, 04 Jun 2017 00:14:06: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:14:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:14:08: #1 tags after filtering in treatment: 10973717 INFO @ Sun, 04 Jun 2017 00:14:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:14:08: #1 finished! INFO @ Sun, 04 Jun 2017 00:14:08: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:14:10: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:14:10: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:14:10: #1 total tags in treatment: 10976187 INFO @ Sun, 04 Jun 2017 00:14:10: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:14:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:14:10: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:14:10: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:14:10: #1 total tags in treatment: 10976187 INFO @ Sun, 04 Jun 2017 00:14:10: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:14:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:14:11: #2 number of paired peaks: 2090 INFO @ Sun, 04 Jun 2017 00:14:11: start model_add_line... INFO @ Sun, 04 Jun 2017 00:14:12: #1 tags after filtering in treatment: 10973717 INFO @ Sun, 04 Jun 2017 00:14:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:14:12: #1 finished! INFO @ Sun, 04 Jun 2017 00:14:12: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:14:12: #1 tags after filtering in treatment: 10973717 INFO @ Sun, 04 Jun 2017 00:14:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:14:12: #1 finished! INFO @ Sun, 04 Jun 2017 00:14:12: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:14:14: #2 number of paired peaks: 2090 INFO @ Sun, 04 Jun 2017 00:14:14: start model_add_line... INFO @ Sun, 04 Jun 2017 00:14:14: #2 number of paired peaks: 2090 INFO @ Sun, 04 Jun 2017 00:14:14: start model_add_line... INFO @ Sun, 04 Jun 2017 00:14:29: start X-correlation... INFO @ Sun, 04 Jun 2017 00:14:29: end of X-cor INFO @ Sun, 04 Jun 2017 00:14:29: #2 finished! INFO @ Sun, 04 Jun 2017 00:14:29: #2 predicted fragment length is 53 bps INFO @ Sun, 04 Jun 2017 00:14:29: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 04 Jun 2017 00:14:29: #2.2 Generate R script for model : SRX886167.20_model.r WARNING @ Sun, 04 Jun 2017 00:14:29: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:14:29: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 04 Jun 2017 00:14:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:14:29: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:14:32: start X-correlation... INFO @ Sun, 04 Jun 2017 00:14:32: end of X-cor INFO @ Sun, 04 Jun 2017 00:14:32: #2 finished! INFO @ Sun, 04 Jun 2017 00:14:32: #2 predicted fragment length is 53 bps INFO @ Sun, 04 Jun 2017 00:14:32: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 04 Jun 2017 00:14:32: #2.2 Generate R script for model : SRX886167.10_model.r WARNING @ Sun, 04 Jun 2017 00:14:32: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:14:32: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 04 Jun 2017 00:14:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:14:32: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:14:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:14:32: start X-correlation... INFO @ Sun, 04 Jun 2017 00:14:32: end of X-cor INFO @ Sun, 04 Jun 2017 00:14:32: #2 finished! INFO @ Sun, 04 Jun 2017 00:14:32: #2 predicted fragment length is 53 bps INFO @ Sun, 04 Jun 2017 00:14:32: #2 alternative fragment length(s) may be 3,53 bps INFO @ Sun, 04 Jun 2017 00:14:32: #2.2 Generate R script for model : SRX886167.05_model.r WARNING @ Sun, 04 Jun 2017 00:14:32: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Jun 2017 00:14:32: #2 You may need to consider one of the other alternative d(s): 3,53 WARNING @ Sun, 04 Jun 2017 00:14:32: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Jun 2017 00:14:32: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:14:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:15:30: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:15:31: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:15:33: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:16:13: #4 Write output xls file... SRX886167.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:16:13: #4 Write peak in narrowPeak format file... SRX886167.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:16:13: #4 Write summits bed file... SRX886167.10_summits.bed INFO @ Sun, 04 Jun 2017 00:16:13: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2777 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:16:16: #4 Write output xls file... SRX886167.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:16:16: #4 Write peak in narrowPeak format file... SRX886167.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:16:16: #4 Write summits bed file... SRX886167.20_summits.bed INFO @ Sun, 04 Jun 2017 00:16:16: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1623 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:16:17: #4 Write output xls file... SRX886167.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:16:17: #4 Write peak in narrowPeak format file... SRX886167.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:16:17: #4 Write summits bed file... SRX886167.05_summits.bed INFO @ Sun, 04 Jun 2017 00:16:17: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4003 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。