Job ID = 2161346 sra ファイルのダウンロード中... Completed: 1097327K bytes transferred in 11 seconds (769630K bits/sec), in 3 files, 4 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 12759 0 12759 0 0 23751 0 --:--:-- --:--:-- --:--:-- 36769 100 35355 0 35355 0 0 48646 0 --:--:-- --:--:-- --:--:-- 65960 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 14831923 spots for /home/okishinya/chipatlas/results/dm3/SRX020695/SRR060771.sra Written 14831923 spots total Written 15309836 spots for /home/okishinya/chipatlas/results/dm3/SRX020695/SRR060770.sra Written 15309836 spots total Written 15326214 spots for /home/okishinya/chipatlas/results/dm3/SRX020695/SRR060769.sra Written 15326214 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:42 45467973 reads; of these: 45467973 (100.00%) were unpaired; of these: 24875924 (54.71%) aligned 0 times 14269251 (31.38%) aligned exactly 1 time 6322798 (13.91%) aligned >1 times 45.29% overall alignment rate Time searching: 00:10:42 Overall time: 00:10:43 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_sort_core] merging from 8 files... [bam_rmdupse_core] 9150129 / 20592049 = 0.4444 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 12:41:02: # Command line: callpeak -t SRX020695.bam -f BAM -g dm -n SRX020695.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX020695.20 # format = BAM # ChIP-seq file = ['SRX020695.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 12:41:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:41:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:41:02: # Command line: callpeak -t SRX020695.bam -f BAM -g dm -n SRX020695.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX020695.10 # format = BAM # ChIP-seq file = ['SRX020695.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 12:41:02: # Command line: callpeak -t SRX020695.bam -f BAM -g dm -n SRX020695.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX020695.05 # format = BAM # ChIP-seq file = ['SRX020695.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 12:41:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:41:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:41:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:41:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:41:08: 1000000 INFO @ Tue, 21 Apr 2015 12:41:08: 1000000 INFO @ Tue, 21 Apr 2015 12:41:08: 1000000 INFO @ Tue, 21 Apr 2015 12:41:13: 2000000 INFO @ Tue, 21 Apr 2015 12:41:14: 2000000 INFO @ Tue, 21 Apr 2015 12:41:14: 2000000 INFO @ Tue, 21 Apr 2015 12:41:19: 3000000 INFO @ Tue, 21 Apr 2015 12:41:19: 3000000 INFO @ Tue, 21 Apr 2015 12:41:19: 3000000 INFO @ Tue, 21 Apr 2015 12:41:24: 4000000 INFO @ Tue, 21 Apr 2015 12:41:25: 4000000 INFO @ Tue, 21 Apr 2015 12:41:25: 4000000 INFO @ Tue, 21 Apr 2015 12:41:30: 5000000 INFO @ Tue, 21 Apr 2015 12:41:31: 5000000 INFO @ Tue, 21 Apr 2015 12:41:31: 5000000 INFO @ Tue, 21 Apr 2015 12:41:35: 6000000 INFO @ Tue, 21 Apr 2015 12:41:37: 6000000 INFO @ Tue, 21 Apr 2015 12:41:37: 6000000 INFO @ Tue, 21 Apr 2015 12:41:41: 7000000 INFO @ Tue, 21 Apr 2015 12:41:42: 7000000 INFO @ Tue, 21 Apr 2015 12:41:43: 7000000 INFO @ Tue, 21 Apr 2015 12:41:46: 8000000 INFO @ Tue, 21 Apr 2015 12:41:48: 8000000 INFO @ Tue, 21 Apr 2015 12:41:49: 8000000 INFO @ Tue, 21 Apr 2015 12:41:52: 9000000 INFO @ Tue, 21 Apr 2015 12:41:54: 9000000 INFO @ Tue, 21 Apr 2015 12:41:55: 9000000 INFO @ Tue, 21 Apr 2015 12:41:57: 10000000 INFO @ Tue, 21 Apr 2015 12:42:00: 10000000 INFO @ Tue, 21 Apr 2015 12:42:00: 10000000 INFO @ Tue, 21 Apr 2015 12:42:03: 11000000 INFO @ Tue, 21 Apr 2015 12:42:05: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:42:05: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:42:05: #1 total tags in treatment: 11441920 INFO @ Tue, 21 Apr 2015 12:42:05: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:42:05: #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 12:42:06: 11000000 INFO @ Tue, 21 Apr 2015 12:42:06: 11000000 INFO @ Tue, 21 Apr 2015 12:42:08: #1 tags after filtering in treatment: 11436811 INFO @ Tue, 21 Apr 2015 12:42:08: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:42:08: #1 finished! INFO @ Tue, 21 Apr 2015 12:42:08: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:42:09: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:42:09: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:42:09: #1 total tags in treatment: 11441920 INFO @ Tue, 21 Apr 2015 12:42:09: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:42:09: #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 12:42:09: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:42:09: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:42:09: #1 total tags in treatment: 11441920 INFO @ Tue, 21 Apr 2015 12:42:09: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:42:09: #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 12:42:10: #2 number of paired peaks: 1515 INFO @ Tue, 21 Apr 2015 12:42:10: start model_add_line... INFO @ Tue, 21 Apr 2015 12:42:11: #1 tags after filtering in treatment: 11436811 INFO @ Tue, 21 Apr 2015 12:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:42:11: #1 finished! INFO @ Tue, 21 Apr 2015 12:42:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:42:11: #1 tags after filtering in treatment: 11436811 INFO @ Tue, 21 Apr 2015 12:42:11: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:42:11: #1 finished! INFO @ Tue, 21 Apr 2015 12:42:11: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:42:13: #2 number of paired peaks: 1515 INFO @ Tue, 21 Apr 2015 12:42:13: start model_add_line... INFO @ Tue, 21 Apr 2015 12:42:14: #2 number of paired peaks: 1515 INFO @ Tue, 21 Apr 2015 12:42:14: start model_add_line... INFO @ Tue, 21 Apr 2015 12:42:20: start X-correlation... INFO @ Tue, 21 Apr 2015 12:42:20: end of X-cor INFO @ Tue, 21 Apr 2015 12:42:20: #2 finished! INFO @ Tue, 21 Apr 2015 12:42:20: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:42:20: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 21 Apr 2015 12:42:20: #2.2 Generate R script for model : SRX020695.20_model.r WARNING @ Tue, 21 Apr 2015 12:42:20: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:42:20: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 21 Apr 2015 12:42:20: #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 12:42:20: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:42:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:42:23: start X-correlation... INFO @ Tue, 21 Apr 2015 12:42:23: end of X-cor INFO @ Tue, 21 Apr 2015 12:42:23: #2 finished! INFO @ Tue, 21 Apr 2015 12:42:23: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:42:23: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 21 Apr 2015 12:42:23: #2.2 Generate R script for model : SRX020695.05_model.r WARNING @ Tue, 21 Apr 2015 12:42:23: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:42:23: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 21 Apr 2015 12:42:23: #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 12:42:23: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:42:24: start X-correlation... INFO @ Tue, 21 Apr 2015 12:42:24: end of X-cor INFO @ Tue, 21 Apr 2015 12:42:24: #2 finished! INFO @ Tue, 21 Apr 2015 12:42:24: #2 predicted fragment length is 62 bps INFO @ Tue, 21 Apr 2015 12:42:24: #2 alternative fragment length(s) may be 62 bps INFO @ Tue, 21 Apr 2015 12:42:24: #2.2 Generate R script for model : SRX020695.10_model.r WARNING @ Tue, 21 Apr 2015 12:42:24: #2 Since the d (62) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:42:24: #2 You may need to consider one of the other alternative d(s): 62 WARNING @ Tue, 21 Apr 2015 12:42:24: #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 12:42:24: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:42:24: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:43:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:43:22: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:43:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:44:04: #4 Write output xls file... SRX020695.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:44:04: #4 Write peak in narrowPeak format file... SRX020695.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:44:04: #4 Write summits bed file... SRX020695.20_summits.bed INFO @ Tue, 21 Apr 2015 12:44:04: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (3274 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:44:08: #4 Write output xls file... SRX020695.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:44:08: #4 Write peak in narrowPeak format file... SRX020695.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:44:08: #4 Write summits bed file... SRX020695.10_summits.bed INFO @ Tue, 21 Apr 2015 12:44:08: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (7196 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:44:19: #4 Write output xls file... SRX020695.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:44:19: #4 Write peak in narrowPeak format file... SRX020695.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:44:19: #4 Write summits bed file... SRX020695.05_summits.bed INFO @ Tue, 21 Apr 2015 12:44:19: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (14008 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。