Job ID = 9029326 sra ファイルのダウンロード中... Completed: 286730K bytes transferred in 5 seconds (409764K 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 7663 0 7663 0 0 1054 0 --:--:-- 0:00:07 --:--:-- 10931 100 30318 0 30318 0 0 3669 0 --:--:-- 0:00:08 --:--:-- 17865 100 54318 0 54318 0 0 5974 0 --:--:-- 0:00:09 --:--:-- 21495 100 71670 0 71670 0 0 7741 0 --:--:-- 0:00:09 --:--:-- 26603 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 9795504 spots for /home/okishinya/chipatlas/results/dm3/SRX1561067/SRR3145070.sra Written 9795504 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: 00:02:59 9795504 reads; of these: 9795504 (100.00%) were unpaired; of these: 3083249 (31.48%) aligned 0 times 5885656 (60.09%) aligned exactly 1 time 826599 (8.44%) aligned >1 times 68.52% overall alignment rate Time searching: 00:02:59 Overall time: 00:02:59 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] 925319 / 6712255 = 0.1379 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 13:17:50: # Command line: callpeak -t SRX1561067.bam -f BAM -g dm -n SRX1561067.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1561067.05 # format = BAM # ChIP-seq file = ['SRX1561067.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 13:17:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:50: # Command line: callpeak -t SRX1561067.bam -f BAM -g dm -n SRX1561067.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1561067.10 # format = BAM # ChIP-seq file = ['SRX1561067.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 13:17:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:50: # Command line: callpeak -t SRX1561067.bam -f BAM -g dm -n SRX1561067.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1561067.20 # format = BAM # ChIP-seq file = ['SRX1561067.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 13:17:50: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:50: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:57: 1000000 INFO @ Sat, 03 Jun 2017 13:17:57: 1000000 INFO @ Sat, 03 Jun 2017 13:17:57: 1000000 INFO @ Sat, 03 Jun 2017 13:18:03: 2000000 INFO @ Sat, 03 Jun 2017 13:18:04: 2000000 INFO @ Sat, 03 Jun 2017 13:18:04: 2000000 INFO @ Sat, 03 Jun 2017 13:18:09: 3000000 INFO @ Sat, 03 Jun 2017 13:18:11: 3000000 INFO @ Sat, 03 Jun 2017 13:18:12: 3000000 INFO @ Sat, 03 Jun 2017 13:18:16: 4000000 INFO @ Sat, 03 Jun 2017 13:18:18: 4000000 INFO @ Sat, 03 Jun 2017 13:18:20: 4000000 INFO @ Sat, 03 Jun 2017 13:18:22: 5000000 INFO @ Sat, 03 Jun 2017 13:18:25: 5000000 INFO @ Sat, 03 Jun 2017 13:18:27: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:18:27: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:18:27: #1 total tags in treatment: 5786936 INFO @ Sat, 03 Jun 2017 13:18:27: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:18:27: #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 13:18:28: 5000000 INFO @ Sat, 03 Jun 2017 13:18:28: #1 tags after filtering in treatment: 5784964 INFO @ Sat, 03 Jun 2017 13:18:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:18:28: #1 finished! INFO @ Sat, 03 Jun 2017 13:18:28: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:18:30: #2 number of paired peaks: 4500 INFO @ Sat, 03 Jun 2017 13:18:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:18:31: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:18:31: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:18:31: #1 total tags in treatment: 5786936 INFO @ Sat, 03 Jun 2017 13:18:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:18:31: #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 13:18:32: #1 tags after filtering in treatment: 5784964 INFO @ Sat, 03 Jun 2017 13:18:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:18:32: #1 finished! INFO @ Sat, 03 Jun 2017 13:18:32: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:18:33: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:18:33: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:18:33: #1 total tags in treatment: 5786936 INFO @ Sat, 03 Jun 2017 13:18:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:18:33: #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 13:18:33: #2 number of paired peaks: 4500 INFO @ Sat, 03 Jun 2017 13:18:33: start model_add_line... INFO @ Sat, 03 Jun 2017 13:18:34: #1 tags after filtering in treatment: 5784964 INFO @ Sat, 03 Jun 2017 13:18:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:18:34: #1 finished! INFO @ Sat, 03 Jun 2017 13:18:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:18:36: #2 number of paired peaks: 4500 INFO @ Sat, 03 Jun 2017 13:18:36: start model_add_line... INFO @ Sat, 03 Jun 2017 13:18:49: start X-correlation... INFO @ Sat, 03 Jun 2017 13:18:49: end of X-cor INFO @ Sat, 03 Jun 2017 13:18:49: #2 finished! INFO @ Sat, 03 Jun 2017 13:18:49: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Jun 2017 13:18:49: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Jun 2017 13:18:49: #2.2 Generate R script for model : SRX1561067.05_model.r INFO @ Sat, 03 Jun 2017 13:18:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:18:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:18:52: start X-correlation... INFO @ Sat, 03 Jun 2017 13:18:52: end of X-cor INFO @ Sat, 03 Jun 2017 13:18:52: #2 finished! INFO @ Sat, 03 Jun 2017 13:18:52: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Jun 2017 13:18:52: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Jun 2017 13:18:52: #2.2 Generate R script for model : SRX1561067.10_model.r INFO @ Sat, 03 Jun 2017 13:18:52: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:18:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:18:55: start X-correlation... INFO @ Sat, 03 Jun 2017 13:18:55: end of X-cor INFO @ Sat, 03 Jun 2017 13:18:55: #2 finished! INFO @ Sat, 03 Jun 2017 13:18:55: #2 predicted fragment length is 128 bps INFO @ Sat, 03 Jun 2017 13:18:55: #2 alternative fragment length(s) may be 128 bps INFO @ Sat, 03 Jun 2017 13:18:55: #2.2 Generate R script for model : SRX1561067.20_model.r INFO @ Sat, 03 Jun 2017 13:18:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:18:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:19:24: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:19:27: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:19:30: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:19:58: #4 Write output xls file... SRX1561067.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:59: #4 Write peak in narrowPeak format file... SRX1561067.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:59: #4 Write summits bed file... SRX1561067.05_summits.bed INFO @ Sat, 03 Jun 2017 13:19:59: #4 Write output xls file... SRX1561067.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:19:59: Done! INFO @ Sat, 03 Jun 2017 13:19:59: #4 Write peak in narrowPeak format file... SRX1561067.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:19:59: #4 Write summits bed file... SRX1561067.10_summits.bed INFO @ Sat, 03 Jun 2017 13:19:59: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9987 records, 4 fields): 14 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6730 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:20:00: #4 Write output xls file... SRX1561067.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:20:00: #4 Write peak in narrowPeak format file... SRX1561067.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:20:00: #4 Write summits bed file... SRX1561067.20_summits.bed INFO @ Sat, 03 Jun 2017 13:20:00: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3726 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。