Job ID = 9031177 sra ファイルのダウンロード中... Completed: 190481K bytes transferred in 5 seconds (304261K bits/sec), in 4 files, 5 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 29874 0 29874 0 0 3720 0 --:--:-- 0:00:08 --:--:-- 18238 100 31745 0 31745 0 0 3952 0 --:--:-- 0:00:08 --:--:-- 19380 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 226496 spots for /home/okishinya/chipatlas/results/dm3/SRX330995/SRR947204.sra Written 226496 spots total Written 1188498 spots for /home/okishinya/chipatlas/results/dm3/SRX330995/SRR947206.sra Written 1188498 spots total Written 3440887 spots for /home/okishinya/chipatlas/results/dm3/SRX330995/SRR947207.sra Written 3440887 spots total Written 6286532 spots for /home/okishinya/chipatlas/results/dm3/SRX330995/SRR947205.sra Written 6286532 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: 00:02:47 11142413 reads; of these: 11142413 (100.00%) were unpaired; of these: 3250380 (29.17%) aligned 0 times 5649258 (50.70%) aligned exactly 1 time 2242775 (20.13%) aligned >1 times 70.83% overall alignment rate Time searching: 00:02:47 Overall time: 00:02:47 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_rmdupse_core] 2176309 / 7892033 = 0.2758 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 18:25:03: # Command line: callpeak -t SRX330995.bam -f BAM -g dm -n SRX330995.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX330995.05 # format = BAM # ChIP-seq file = ['SRX330995.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 18:25:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 18:25:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 18:25:03: # Command line: callpeak -t SRX330995.bam -f BAM -g dm -n SRX330995.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX330995.10 # format = BAM # ChIP-seq file = ['SRX330995.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 18:25:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 18:25:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 18:25:03: # Command line: callpeak -t SRX330995.bam -f BAM -g dm -n SRX330995.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX330995.20 # format = BAM # ChIP-seq file = ['SRX330995.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 18:25:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 18:25:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 18:25:08: 1000000 INFO @ Sat, 03 Jun 2017 18:25:08: 1000000 INFO @ Sat, 03 Jun 2017 18:25:09: 1000000 INFO @ Sat, 03 Jun 2017 18:25:13: 2000000 INFO @ Sat, 03 Jun 2017 18:25:14: 2000000 INFO @ Sat, 03 Jun 2017 18:25:14: 2000000 INFO @ Sat, 03 Jun 2017 18:25:19: 3000000 INFO @ Sat, 03 Jun 2017 18:25:19: 3000000 INFO @ Sat, 03 Jun 2017 18:25:20: 3000000 INFO @ Sat, 03 Jun 2017 18:25:23: 4000000 INFO @ Sat, 03 Jun 2017 18:25:24: 4000000 INFO @ Sat, 03 Jun 2017 18:25:25: 4000000 INFO @ Sat, 03 Jun 2017 18:25:28: 5000000 INFO @ Sat, 03 Jun 2017 18:25:29: 5000000 INFO @ Sat, 03 Jun 2017 18:25:30: 5000000 INFO @ Sat, 03 Jun 2017 18:25:32: #1 tag size is determined as 30 bps INFO @ Sat, 03 Jun 2017 18:25:32: #1 tag size = 30 INFO @ Sat, 03 Jun 2017 18:25:32: #1 total tags in treatment: 5715724 INFO @ Sat, 03 Jun 2017 18:25:32: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 18:25:32: #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 18:25:33: #1 tags after filtering in treatment: 5714505 INFO @ Sat, 03 Jun 2017 18:25:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 18:25:33: #1 finished! INFO @ Sat, 03 Jun 2017 18:25:33: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 18:25:33: #1 tag size is determined as 30 bps INFO @ Sat, 03 Jun 2017 18:25:33: #1 tag size = 30 INFO @ Sat, 03 Jun 2017 18:25:33: #1 total tags in treatment: 5715724 INFO @ Sat, 03 Jun 2017 18:25:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 18:25:33: #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 18:25:34: #1 tag size is determined as 30 bps INFO @ Sat, 03 Jun 2017 18:25:34: #1 tag size = 30 INFO @ Sat, 03 Jun 2017 18:25:34: #1 total tags in treatment: 5715724 INFO @ Sat, 03 Jun 2017 18:25:34: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 18:25:34: #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 18:25:34: #1 tags after filtering in treatment: 5714505 INFO @ Sat, 03 Jun 2017 18:25:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 18:25:34: #1 finished! INFO @ Sat, 03 Jun 2017 18:25:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 18:25:35: #2 number of paired peaks: 4718 INFO @ Sat, 03 Jun 2017 18:25:35: start model_add_line... INFO @ Sat, 03 Jun 2017 18:25:35: #1 tags after filtering in treatment: 5714505 INFO @ Sat, 03 Jun 2017 18:25:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 18:25:35: #1 finished! INFO @ Sat, 03 Jun 2017 18:25:35: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 18:25:36: #2 number of paired peaks: 4718 INFO @ Sat, 03 Jun 2017 18:25:36: start model_add_line... INFO @ Sat, 03 Jun 2017 18:25:36: #2 number of paired peaks: 4718 INFO @ Sat, 03 Jun 2017 18:25:36: start model_add_line... INFO @ Sat, 03 Jun 2017 18:25:55: start X-correlation... INFO @ Sat, 03 Jun 2017 18:25:55: end of X-cor INFO @ Sat, 03 Jun 2017 18:25:55: #2 finished! INFO @ Sat, 03 Jun 2017 18:25:55: #2 predicted fragment length is 79 bps INFO @ Sat, 03 Jun 2017 18:25:55: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 03 Jun 2017 18:25:55: #2.2 Generate R script for model : SRX330995.05_model.r INFO @ Sat, 03 Jun 2017 18:25:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 18:25:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 18:25:55: start X-correlation... INFO @ Sat, 03 Jun 2017 18:25:55: end of X-cor INFO @ Sat, 03 Jun 2017 18:25:55: #2 finished! INFO @ Sat, 03 Jun 2017 18:25:55: #2 predicted fragment length is 79 bps INFO @ Sat, 03 Jun 2017 18:25:55: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 03 Jun 2017 18:25:55: #2.2 Generate R script for model : SRX330995.10_model.r INFO @ Sat, 03 Jun 2017 18:25:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 18:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 18:25:56: start X-correlation... INFO @ Sat, 03 Jun 2017 18:25:56: end of X-cor INFO @ Sat, 03 Jun 2017 18:25:56: #2 finished! INFO @ Sat, 03 Jun 2017 18:25:56: #2 predicted fragment length is 79 bps INFO @ Sat, 03 Jun 2017 18:25:56: #2 alternative fragment length(s) may be 79 bps INFO @ Sat, 03 Jun 2017 18:25:56: #2.2 Generate R script for model : SRX330995.20_model.r INFO @ Sat, 03 Jun 2017 18:25:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 18:25:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 18:26:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 18:26:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 18:26:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 18:26:55: #4 Write output xls file... SRX330995.10_peaks.xls BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 18:26:55: #4 Write peak in narrowPeak format file... SRX330995.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 18:26:55: #4 Write summits bed file... SRX330995.10_summits.bed INFO @ Sat, 03 Jun 2017 18:26:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8130 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 18:26:59: #4 Write output xls file... SRX330995.20_peaks.xls INFO @ Sat, 03 Jun 2017 18:26:59: #4 Write peak in narrowPeak format file... SRX330995.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 18:26:59: #4 Write summits bed file... SRX330995.20_summits.bed INFO @ Sat, 03 Jun 2017 18:26:59: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3916 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 18:27:00: #4 Write output xls file... SRX330995.05_peaks.xls INFO @ Sat, 03 Jun 2017 18:27:00: #4 Write peak in narrowPeak format file... SRX330995.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 18:27:00: #4 Write summits bed file... SRX330995.05_summits.bed INFO @ Sat, 03 Jun 2017 18:27:00: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13201 records, 4 fields): 16 millis CompletedMACS2peakCalling BigWig に変換しました。