Job ID = 9028807 sra ファイルのダウンロード中... Completed: 2534663K bytes transferred in 24 seconds (849207K 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 22317 0 22317 0 0 2913 0 --:--:-- 0:00:07 --:--:-- 17394 100 70317 0 70317 0 0 8124 0 --:--:-- 0:00:08 --:--:-- 30867 100 145k 0 145k 0 0 15467 0 --:--:-- 0:00:09 --:--:-- 45606 100 160k 0 160k 0 0 16744 0 --:--:-- 0:00:09 --:--:-- 47809 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 73597677 spots for /home/okishinya/chipatlas/results/ce10/SRX958294/SRR1917667.sra Written 73597677 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: 00:21:39 73597677 reads; of these: 73597677 (100.00%) were unpaired; of these: 19633768 (26.68%) aligned 0 times 31666826 (43.03%) aligned exactly 1 time 22297083 (30.30%) aligned >1 times 73.32% overall alignment rate Time searching: 00:21:39 Overall time: 00:21:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 24 files... [bam_rmdupse_core] 38323820 / 53963909 = 0.7102 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 12:26:52: # Command line: callpeak -t SRX958294.bam -f BAM -g ce -n SRX958294.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX958294.10 # format = BAM # ChIP-seq file = ['SRX958294.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:26:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:26:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:26:52: # Command line: callpeak -t SRX958294.bam -f BAM -g ce -n SRX958294.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX958294.20 # format = BAM # ChIP-seq file = ['SRX958294.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:26:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:26:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:26:52: # Command line: callpeak -t SRX958294.bam -f BAM -g ce -n SRX958294.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX958294.05 # format = BAM # ChIP-seq file = ['SRX958294.bam'] # control file = None # effective genome size = 9.00e+07 # 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 12:26:52: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:26:52: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:00: 1000000 INFO @ Sat, 03 Jun 2017 12:27:00: 1000000 INFO @ Sat, 03 Jun 2017 12:27:00: 1000000 INFO @ Sat, 03 Jun 2017 12:27:08: 2000000 INFO @ Sat, 03 Jun 2017 12:27:08: 2000000 INFO @ Sat, 03 Jun 2017 12:27:08: 2000000 INFO @ Sat, 03 Jun 2017 12:27:17: 3000000 INFO @ Sat, 03 Jun 2017 12:27:17: 3000000 INFO @ Sat, 03 Jun 2017 12:27:17: 3000000 INFO @ Sat, 03 Jun 2017 12:27:25: 4000000 INFO @ Sat, 03 Jun 2017 12:27:25: 4000000 INFO @ Sat, 03 Jun 2017 12:27:25: 4000000 INFO @ Sat, 03 Jun 2017 12:27:33: 5000000 INFO @ Sat, 03 Jun 2017 12:27:33: 5000000 INFO @ Sat, 03 Jun 2017 12:27:33: 5000000 INFO @ Sat, 03 Jun 2017 12:27:42: 6000000 INFO @ Sat, 03 Jun 2017 12:27:42: 6000000 INFO @ Sat, 03 Jun 2017 12:27:42: 6000000 INFO @ Sat, 03 Jun 2017 12:27:50: 7000000 INFO @ Sat, 03 Jun 2017 12:27:50: 7000000 INFO @ Sat, 03 Jun 2017 12:27:50: 7000000 INFO @ Sat, 03 Jun 2017 12:27:57: 8000000 INFO @ Sat, 03 Jun 2017 12:27:57: 8000000 INFO @ Sat, 03 Jun 2017 12:27:57: 8000000 INFO @ Sat, 03 Jun 2017 12:28:04: 9000000 INFO @ Sat, 03 Jun 2017 12:28:04: 9000000 INFO @ Sat, 03 Jun 2017 12:28:04: 9000000 INFO @ Sat, 03 Jun 2017 12:28:11: 10000000 INFO @ Sat, 03 Jun 2017 12:28:12: 10000000 INFO @ Sat, 03 Jun 2017 12:28:12: 10000000 INFO @ Sat, 03 Jun 2017 12:28:18: 11000000 INFO @ Sat, 03 Jun 2017 12:28:19: 11000000 INFO @ Sat, 03 Jun 2017 12:28:19: 11000000 INFO @ Sat, 03 Jun 2017 12:28:25: 12000000 INFO @ Sat, 03 Jun 2017 12:28:27: 12000000 INFO @ Sat, 03 Jun 2017 12:28:27: 12000000 INFO @ Sat, 03 Jun 2017 12:28:32: 13000000 INFO @ Sat, 03 Jun 2017 12:28:34: 13000000 INFO @ Sat, 03 Jun 2017 12:28:34: 13000000 INFO @ Sat, 03 Jun 2017 12:28:39: 14000000 INFO @ Sat, 03 Jun 2017 12:28:42: 14000000 INFO @ Sat, 03 Jun 2017 12:28:42: 14000000 INFO @ Sat, 03 Jun 2017 12:28:46: 15000000 INFO @ Sat, 03 Jun 2017 12:28:49: 15000000 INFO @ Sat, 03 Jun 2017 12:28:49: 15000000 INFO @ Sat, 03 Jun 2017 12:28:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:28:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:28:51: #1 total tags in treatment: 15640089 INFO @ Sat, 03 Jun 2017 12:28:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:28:51: #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 12:28:54: #1 tags after filtering in treatment: 15632228 INFO @ Sat, 03 Jun 2017 12:28:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:28:54: #1 finished! INFO @ Sat, 03 Jun 2017 12:28:54: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:28:54: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:28:54: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:28:54: #1 total tags in treatment: 15640089 INFO @ Sat, 03 Jun 2017 12:28:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:28:54: #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 12:28:54: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 12:28:54: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 12:28:54: #1 total tags in treatment: 15640089 INFO @ Sat, 03 Jun 2017 12:28:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:28:54: #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 12:28:57: #1 tags after filtering in treatment: 15632228 INFO @ Sat, 03 Jun 2017 12:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:28:57: #1 finished! INFO @ Sat, 03 Jun 2017 12:28:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:28:57: #1 tags after filtering in treatment: 15632228 INFO @ Sat, 03 Jun 2017 12:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:28:57: #1 finished! INFO @ Sat, 03 Jun 2017 12:28:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:28:57: #2 number of paired peaks: 2720 INFO @ Sat, 03 Jun 2017 12:28:57: start model_add_line... INFO @ Sat, 03 Jun 2017 12:29:00: #2 number of paired peaks: 2720 INFO @ Sat, 03 Jun 2017 12:29:00: start model_add_line... INFO @ Sat, 03 Jun 2017 12:29:00: #2 number of paired peaks: 2720 INFO @ Sat, 03 Jun 2017 12:29:00: start model_add_line... INFO @ Sat, 03 Jun 2017 12:29:36: start X-correlation... INFO @ Sat, 03 Jun 2017 12:29:36: end of X-cor INFO @ Sat, 03 Jun 2017 12:29:36: #2 finished! INFO @ Sat, 03 Jun 2017 12:29:36: #2 predicted fragment length is 149 bps INFO @ Sat, 03 Jun 2017 12:29:36: #2 alternative fragment length(s) may be 4,149 bps INFO @ Sat, 03 Jun 2017 12:29:36: #2.2 Generate R script for model : SRX958294.05_model.r INFO @ Sat, 03 Jun 2017 12:29:36: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:29:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:29:38: start X-correlation... INFO @ Sat, 03 Jun 2017 12:29:38: end of X-cor INFO @ Sat, 03 Jun 2017 12:29:38: #2 finished! INFO @ Sat, 03 Jun 2017 12:29:38: #2 predicted fragment length is 149 bps INFO @ Sat, 03 Jun 2017 12:29:38: #2 alternative fragment length(s) may be 4,149 bps INFO @ Sat, 03 Jun 2017 12:29:38: #2.2 Generate R script for model : SRX958294.10_model.r INFO @ Sat, 03 Jun 2017 12:29:38: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:29:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:29:39: start X-correlation... INFO @ Sat, 03 Jun 2017 12:29:39: end of X-cor INFO @ Sat, 03 Jun 2017 12:29:39: #2 finished! INFO @ Sat, 03 Jun 2017 12:29:39: #2 predicted fragment length is 149 bps INFO @ Sat, 03 Jun 2017 12:29:39: #2 alternative fragment length(s) may be 4,149 bps INFO @ Sat, 03 Jun 2017 12:29:39: #2.2 Generate R script for model : SRX958294.20_model.r INFO @ Sat, 03 Jun 2017 12:29:39: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:29:39: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:31:04: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:31:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:31:13: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:32:10: #4 Write output xls file... SRX958294.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:32:10: #4 Write peak in narrowPeak format file... SRX958294.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:32:10: #4 Write summits bed file... SRX958294.10_summits.bed INFO @ Sat, 03 Jun 2017 12:32:10: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6859 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:32:13: #4 Write output xls file... SRX958294.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:32:13: #4 Write peak in narrowPeak format file... SRX958294.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:32:13: #4 Write summits bed file... SRX958294.20_summits.bed INFO @ Sat, 03 Jun 2017 12:32:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4006 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:32:27: #4 Write output xls file... SRX958294.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:32:27: #4 Write peak in narrowPeak format file... SRX958294.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:32:27: #4 Write summits bed file... SRX958294.05_summits.bed INFO @ Sat, 03 Jun 2017 12:32:28: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9562 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。