Job ID = 9029330 sra ファイルのダウンロード中... Completed: 308388K bytes transferred in 5 seconds (428615K 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 6903 0 6903 0 0 955 0 --:--:-- 0:00:07 --:--:-- 9777 100 30318 0 30318 0 0 3765 0 --:--:-- 0:00:08 --:--:-- 19725 100 60015 0 60015 0 0 6885 0 --:--:-- 0:00:08 --:--:-- 27279 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 12420637 spots for /home/okishinya/chipatlas/results/dm3/SRX1571734/SRR3162500.sra Written 12420637 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: 00:02:46 12420637 reads; of these: 12420637 (100.00%) were unpaired; of these: 2705129 (21.78%) aligned 0 times 9065418 (72.99%) aligned exactly 1 time 650090 (5.23%) aligned >1 times 78.22% overall alignment rate Time searching: 00:02:46 Overall time: 00:02:46 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] 5006381 / 9715508 = 0.5153 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 13:19:53: # Command line: callpeak -t SRX1571734.bam -f BAM -g dm -n SRX1571734.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1571734.05 # format = BAM # ChIP-seq file = ['SRX1571734.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 13:19:53: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:19:53: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:19:53: # Command line: callpeak -t SRX1571734.bam -f BAM -g dm -n SRX1571734.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1571734.10 # format = BAM # ChIP-seq file = ['SRX1571734.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 13:19:53: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:19:53: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:19:53: # Command line: callpeak -t SRX1571734.bam -f BAM -g dm -n SRX1571734.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1571734.20 # format = BAM # ChIP-seq file = ['SRX1571734.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 13:19:53: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:19:53: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:20:01: 1000000 INFO @ Sat, 03 Jun 2017 13:20:01: 1000000 INFO @ Sat, 03 Jun 2017 13:20:01: 1000000 INFO @ Sat, 03 Jun 2017 13:20:08: 2000000 INFO @ Sat, 03 Jun 2017 13:20:08: 2000000 INFO @ Sat, 03 Jun 2017 13:20:08: 2000000 INFO @ Sat, 03 Jun 2017 13:20:15: 3000000 INFO @ Sat, 03 Jun 2017 13:20:15: 3000000 INFO @ Sat, 03 Jun 2017 13:20:15: 3000000 INFO @ Sat, 03 Jun 2017 13:20:22: 4000000 INFO @ Sat, 03 Jun 2017 13:20:22: 4000000 INFO @ Sat, 03 Jun 2017 13:20:22: 4000000 INFO @ Sat, 03 Jun 2017 13:20:27: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:20:27: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:20:27: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:20:27: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:20:27: #1 total tags in treatment: 4709127 INFO @ Sat, 03 Jun 2017 13:20:27: #1 total tags in treatment: 4709127 INFO @ Sat, 03 Jun 2017 13:20:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:20:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:20:27: #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 13:20:27: #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 13:20:27: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:20:27: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:20:27: #1 total tags in treatment: 4709127 INFO @ Sat, 03 Jun 2017 13:20:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:20:27: #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 13:20:28: #1 tags after filtering in treatment: 4706708 INFO @ Sat, 03 Jun 2017 13:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:20:28: #1 finished! INFO @ Sat, 03 Jun 2017 13:20:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:20:28: #1 tags after filtering in treatment: 4706708 INFO @ Sat, 03 Jun 2017 13:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:20:28: #1 finished! INFO @ Sat, 03 Jun 2017 13:20:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:20:28: #1 tags after filtering in treatment: 4706708 INFO @ Sat, 03 Jun 2017 13:20:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:20:28: #1 finished! INFO @ Sat, 03 Jun 2017 13:20:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:20:30: #2 number of paired peaks: 8623 INFO @ Sat, 03 Jun 2017 13:20:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:20:30: #2 number of paired peaks: 8623 INFO @ Sat, 03 Jun 2017 13:20:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:20:30: #2 number of paired peaks: 8623 INFO @ Sat, 03 Jun 2017 13:20:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:21:13: start X-correlation... INFO @ Sat, 03 Jun 2017 13:21:13: end of X-cor INFO @ Sat, 03 Jun 2017 13:21:13: #2 finished! INFO @ Sat, 03 Jun 2017 13:21:13: #2 predicted fragment length is 351 bps INFO @ Sat, 03 Jun 2017 13:21:13: #2 alternative fragment length(s) may be 351 bps INFO @ Sat, 03 Jun 2017 13:21:13: #2.2 Generate R script for model : SRX1571734.20_model.r INFO @ Sat, 03 Jun 2017 13:21:13: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:21:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:21:14: start X-correlation... INFO @ Sat, 03 Jun 2017 13:21:14: end of X-cor INFO @ Sat, 03 Jun 2017 13:21:14: #2 finished! INFO @ Sat, 03 Jun 2017 13:21:14: #2 predicted fragment length is 351 bps INFO @ Sat, 03 Jun 2017 13:21:14: #2 alternative fragment length(s) may be 351 bps INFO @ Sat, 03 Jun 2017 13:21:14: #2.2 Generate R script for model : SRX1571734.05_model.r INFO @ Sat, 03 Jun 2017 13:21:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:21:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:21:14: start X-correlation... INFO @ Sat, 03 Jun 2017 13:21:14: end of X-cor INFO @ Sat, 03 Jun 2017 13:21:14: #2 finished! INFO @ Sat, 03 Jun 2017 13:21:14: #2 predicted fragment length is 351 bps INFO @ Sat, 03 Jun 2017 13:21:14: #2 alternative fragment length(s) may be 351 bps INFO @ Sat, 03 Jun 2017 13:21:14: #2.2 Generate R script for model : SRX1571734.10_model.r INFO @ Sat, 03 Jun 2017 13:21:14: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:21:14: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 13:21:53: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:21:54: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:21:55: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:22:25: #4 Write output xls file... SRX1571734.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:22:25: #4 Write peak in narrowPeak format file... SRX1571734.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:22:25: #4 Write summits bed file... SRX1571734.20_summits.bed INFO @ Sat, 03 Jun 2017 13:22:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4518 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:22:29: #4 Write output xls file... SRX1571734.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:22:29: #4 Write peak in narrowPeak format file... SRX1571734.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:22:29: #4 Write summits bed file... SRX1571734.10_summits.bed INFO @ Sat, 03 Jun 2017 13:22:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5539 records, 4 fields): 8 millis INFO @ Sat, 03 Jun 2017 13:22:30: #4 Write output xls file... SRX1571734.05_peaks.xls CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:22:30: #4 Write peak in narrowPeak format file... SRX1571734.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:22:30: #4 Write summits bed file... SRX1571734.05_summits.bed INFO @ Sat, 03 Jun 2017 13:22:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6350 records, 4 fields): 10 millis CompletedMACS2peakCalling