Job ID = 2161925 sra ファイルのダウンロード中... Completed: 1047644K bytes transferred in 12 seconds (697958K bits/sec), in 2 files, 3 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 44056 0 44056 0 0 46071 0 --:--:-- --:--:-- --:--:-- 57589 100 45601 0 45601 0 0 47643 0 --:--:-- --:--:-- --:--:-- 59531 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 21115027 spots for /home/okishinya/chipatlas/results/dm3/SRX041388/SRR099119.sra Written 21115027 spots total Written 24780472 spots for /home/okishinya/chipatlas/results/dm3/SRX041388/SRR099118.sra Written 24780472 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: 00:13:34 45895499 reads; of these: 45895499 (100.00%) were unpaired; of these: 6086058 (13.26%) aligned 0 times 31247956 (68.09%) aligned exactly 1 time 8561485 (18.65%) aligned >1 times 86.74% overall alignment rate Time searching: 00:13:34 Overall time: 00:13:34 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 12 files... [bam_rmdupse_core] 33112479 / 39809441 = 0.8318 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 13:37:02: # Command line: callpeak -t SRX041388.bam -f BAM -g dm -n SRX041388.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX041388.20 # format = BAM # ChIP-seq file = ['SRX041388.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 13:37:02: # Command line: callpeak -t SRX041388.bam -f BAM -g dm -n SRX041388.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX041388.10 # format = BAM # ChIP-seq file = ['SRX041388.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 13:37:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:37:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:37:02: # Command line: callpeak -t SRX041388.bam -f BAM -g dm -n SRX041388.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX041388.05 # format = BAM # ChIP-seq file = ['SRX041388.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 13:37:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:37:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:37:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:37:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:37:08: 1000000 INFO @ Tue, 21 Apr 2015 13:37:08: 1000000 INFO @ Tue, 21 Apr 2015 13:37:08: 1000000 INFO @ Tue, 21 Apr 2015 13:37:13: 2000000 INFO @ Tue, 21 Apr 2015 13:37:13: 2000000 INFO @ Tue, 21 Apr 2015 13:37:13: 2000000 INFO @ Tue, 21 Apr 2015 13:37:18: 3000000 INFO @ Tue, 21 Apr 2015 13:37:19: 3000000 INFO @ Tue, 21 Apr 2015 13:37:19: 3000000 INFO @ Tue, 21 Apr 2015 13:37:24: 4000000 INFO @ Tue, 21 Apr 2015 13:37:24: 4000000 INFO @ Tue, 21 Apr 2015 13:37:25: 4000000 INFO @ Tue, 21 Apr 2015 13:37:30: 5000000 INFO @ Tue, 21 Apr 2015 13:37:30: 5000000 INFO @ Tue, 21 Apr 2015 13:37:31: 5000000 INFO @ Tue, 21 Apr 2015 13:37:35: 6000000 INFO @ Tue, 21 Apr 2015 13:37:35: 6000000 INFO @ Tue, 21 Apr 2015 13:37:37: 6000000 INFO @ Tue, 21 Apr 2015 13:37:39: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:37:39: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:37:39: #1 total tags in treatment: 6696962 INFO @ Tue, 21 Apr 2015 13:37:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:37:39: #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 13:37:39: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:37:39: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:37:39: #1 total tags in treatment: 6696962 INFO @ Tue, 21 Apr 2015 13:37:39: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:37:39: #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 13:37:40: #1 tags after filtering in treatment: 6695330 INFO @ Tue, 21 Apr 2015 13:37:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:37:40: #1 finished! INFO @ Tue, 21 Apr 2015 13:37:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:37:40: #1 tags after filtering in treatment: 6695330 INFO @ Tue, 21 Apr 2015 13:37:40: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:37:40: #1 finished! INFO @ Tue, 21 Apr 2015 13:37:40: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:37:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:37:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:37:41: #1 total tags in treatment: 6696962 INFO @ Tue, 21 Apr 2015 13:37:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:37:41: #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 13:37:42: #1 tags after filtering in treatment: 6695330 INFO @ Tue, 21 Apr 2015 13:37:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:37:42: #1 finished! INFO @ Tue, 21 Apr 2015 13:37:42: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:37:42: #2 number of paired peaks: 3288 INFO @ Tue, 21 Apr 2015 13:37:42: start model_add_line... INFO @ Tue, 21 Apr 2015 13:37:42: #2 number of paired peaks: 3288 INFO @ Tue, 21 Apr 2015 13:37:42: start model_add_line... INFO @ Tue, 21 Apr 2015 13:37:44: #2 number of paired peaks: 3288 INFO @ Tue, 21 Apr 2015 13:37:44: start model_add_line... INFO @ Tue, 21 Apr 2015 13:37:55: start X-correlation... INFO @ Tue, 21 Apr 2015 13:37:55: end of X-cor INFO @ Tue, 21 Apr 2015 13:37:55: #2 finished! INFO @ Tue, 21 Apr 2015 13:37:55: #2 predicted fragment length is 166 bps INFO @ Tue, 21 Apr 2015 13:37:55: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 21 Apr 2015 13:37:55: #2.2 Generate R script for model : SRX041388.05_model.r INFO @ Tue, 21 Apr 2015 13:37:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:37:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:37:55: start X-correlation... INFO @ Tue, 21 Apr 2015 13:37:55: end of X-cor INFO @ Tue, 21 Apr 2015 13:37:55: #2 finished! INFO @ Tue, 21 Apr 2015 13:37:55: #2 predicted fragment length is 166 bps INFO @ Tue, 21 Apr 2015 13:37:55: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 21 Apr 2015 13:37:55: #2.2 Generate R script for model : SRX041388.20_model.r INFO @ Tue, 21 Apr 2015 13:37:55: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:37:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:37:57: start X-correlation... INFO @ Tue, 21 Apr 2015 13:37:57: end of X-cor INFO @ Tue, 21 Apr 2015 13:37:57: #2 finished! INFO @ Tue, 21 Apr 2015 13:37:57: #2 predicted fragment length is 166 bps INFO @ Tue, 21 Apr 2015 13:37:57: #2 alternative fragment length(s) may be 166 bps INFO @ Tue, 21 Apr 2015 13:37:57: #2.2 Generate R script for model : SRX041388.10_model.r INFO @ Tue, 21 Apr 2015 13:37:57: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:37:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:38:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:38:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:38:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:39:07: #4 Write output xls file... SRX041388.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:39:07: #4 Write peak in narrowPeak format file... SRX041388.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:39:07: #4 Write summits bed file... SRX041388.20_summits.bed INFO @ Tue, 21 Apr 2015 13:39:07: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3855 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:39:16: #4 Write output xls file... SRX041388.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:39:16: #4 Write output xls file... SRX041388.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:39:16: #4 Write peak in narrowPeak format file... SRX041388.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:39:16: #4 Write peak in narrowPeak format file... SRX041388.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:39:16: #4 Write summits bed file... SRX041388.05_summits.bed INFO @ Tue, 21 Apr 2015 13:39:16: #4 Write summits bed file... SRX041388.10_summits.bed INFO @ Tue, 21 Apr 2015 13:39:16: Done! INFO @ Tue, 21 Apr 2015 13:39:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7534 records, 4 fields): 11 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (11126 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。