Job ID = 8696827 sra ファイルのダウンロード中... Completed: 950574K bytes transferred in 47 seconds (162809K 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 1051 0 --:--:-- 0:00:07 --:--:-- 9460 100 28367 0 28367 0 0 3475 0 --:--:-- 0:00:08 --:--:-- 16865 100 31488 0 31488 0 0 3777 0 --:--:-- 0:00:08 --:--:-- 16965 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 36933818 spots for /home/okishinya/chipatlas/results/dm3/SRX110765/SRR388347.sra Written 36933818 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: 00:17:41 36933818 reads; of these: 36933818 (100.00%) were unpaired; of these: 11026670 (29.86%) aligned 0 times 24063462 (65.15%) aligned exactly 1 time 1843686 (4.99%) aligned >1 times 70.14% overall alignment rate Time searching: 00:17:41 Overall time: 00:17:41 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 8 files... [bam_rmdupse_core] 8079753 / 25907148 = 0.3119 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 @ Fri, 10 Mar 2017 12:28:43: # Command line: callpeak -t SRX110765.bam -f BAM -g dm -n SRX110765.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110765.05 # format = BAM # ChIP-seq file = ['SRX110765.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 @ Fri, 10 Mar 2017 12:28:43: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:28:43: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:28:43: # Command line: callpeak -t SRX110765.bam -f BAM -g dm -n SRX110765.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110765.20 # format = BAM # ChIP-seq file = ['SRX110765.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 @ Fri, 10 Mar 2017 12:28:43: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:28:43: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:28:43: # Command line: callpeak -t SRX110765.bam -f BAM -g dm -n SRX110765.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110765.10 # format = BAM # ChIP-seq file = ['SRX110765.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 @ Fri, 10 Mar 2017 12:28:43: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:28:43: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:28:57: 1000000 INFO @ Fri, 10 Mar 2017 12:28:57: 1000000 INFO @ Fri, 10 Mar 2017 12:29:12: 2000000 INFO @ Fri, 10 Mar 2017 12:29:12: 2000000 INFO @ Fri, 10 Mar 2017 12:29:16: 1000000 INFO @ Fri, 10 Mar 2017 12:29:22: 3000000 INFO @ Fri, 10 Mar 2017 12:29:22: 3000000 INFO @ Fri, 10 Mar 2017 12:29:30: 2000000 INFO @ Fri, 10 Mar 2017 12:29:32: 4000000 INFO @ Fri, 10 Mar 2017 12:29:32: 4000000 INFO @ Fri, 10 Mar 2017 12:29:42: 5000000 INFO @ Fri, 10 Mar 2017 12:29:42: 5000000 INFO @ Fri, 10 Mar 2017 12:29:44: 3000000 INFO @ Fri, 10 Mar 2017 12:29:51: 6000000 INFO @ Fri, 10 Mar 2017 12:29:51: 6000000 INFO @ Fri, 10 Mar 2017 12:29:58: 4000000 INFO @ Fri, 10 Mar 2017 12:30:01: 7000000 INFO @ Fri, 10 Mar 2017 12:30:01: 7000000 INFO @ Fri, 10 Mar 2017 12:30:10: 8000000 INFO @ Fri, 10 Mar 2017 12:30:10: 8000000 INFO @ Fri, 10 Mar 2017 12:30:13: 5000000 INFO @ Fri, 10 Mar 2017 12:30:19: 9000000 INFO @ Fri, 10 Mar 2017 12:30:19: 9000000 INFO @ Fri, 10 Mar 2017 12:30:27: 6000000 INFO @ Fri, 10 Mar 2017 12:30:29: 10000000 INFO @ Fri, 10 Mar 2017 12:30:29: 10000000 INFO @ Fri, 10 Mar 2017 12:30:39: 11000000 INFO @ Fri, 10 Mar 2017 12:30:39: 11000000 INFO @ Fri, 10 Mar 2017 12:30:41: 7000000 INFO @ Fri, 10 Mar 2017 12:30:53: 12000000 INFO @ Fri, 10 Mar 2017 12:30:53: 12000000 INFO @ Fri, 10 Mar 2017 12:30:54: 8000000 INFO @ Fri, 10 Mar 2017 12:31:01: 13000000 INFO @ Fri, 10 Mar 2017 12:31:01: 13000000 INFO @ Fri, 10 Mar 2017 12:31:07: 9000000 INFO @ Fri, 10 Mar 2017 12:31:09: 14000000 INFO @ Fri, 10 Mar 2017 12:31:09: 14000000 INFO @ Fri, 10 Mar 2017 12:31:16: 15000000 INFO @ Fri, 10 Mar 2017 12:31:16: 15000000 INFO @ Fri, 10 Mar 2017 12:31:20: 10000000 INFO @ Fri, 10 Mar 2017 12:31:23: 16000000 INFO @ Fri, 10 Mar 2017 12:31:23: 16000000 INFO @ Fri, 10 Mar 2017 12:31:30: 17000000 INFO @ Fri, 10 Mar 2017 12:31:30: 17000000 INFO @ Fri, 10 Mar 2017 12:31:32: 11000000 INFO @ Fri, 10 Mar 2017 12:31:37: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:31:37: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:31:37: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:31:37: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:31:37: #1 total tags in treatment: 17827395 INFO @ Fri, 10 Mar 2017 12:31:37: #1 total tags in treatment: 17827395 INFO @ Fri, 10 Mar 2017 12:31:37: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:31:37: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:31:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:31:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:31:40: #1 tags after filtering in treatment: 17823961 INFO @ Fri, 10 Mar 2017 12:31:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:31:40: #1 finished! INFO @ Fri, 10 Mar 2017 12:31:40: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:31:40: #1 tags after filtering in treatment: 17823961 INFO @ Fri, 10 Mar 2017 12:31:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:31:40: #1 finished! INFO @ Fri, 10 Mar 2017 12:31:40: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:31:45: #2 number of paired peaks: 3686 INFO @ Fri, 10 Mar 2017 12:31:45: start model_add_line... INFO @ Fri, 10 Mar 2017 12:31:45: #2 number of paired peaks: 3686 INFO @ Fri, 10 Mar 2017 12:31:45: start model_add_line... INFO @ Fri, 10 Mar 2017 12:31:45: 12000000 INFO @ Fri, 10 Mar 2017 12:31:57: 13000000 INFO @ Fri, 10 Mar 2017 12:32:10: 14000000 INFO @ Fri, 10 Mar 2017 12:32:25: 15000000 INFO @ Fri, 10 Mar 2017 12:32:30: start X-correlation... INFO @ Fri, 10 Mar 2017 12:32:30: end of X-cor INFO @ Fri, 10 Mar 2017 12:32:30: #2 finished! INFO @ Fri, 10 Mar 2017 12:32:30: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:32:30: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:32:30: #2.2 Generate R script for model : SRX110765.05_model.r INFO @ Fri, 10 Mar 2017 12:32:30: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:32:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:32:32: start X-correlation... INFO @ Fri, 10 Mar 2017 12:32:32: end of X-cor INFO @ Fri, 10 Mar 2017 12:32:32: #2 finished! INFO @ Fri, 10 Mar 2017 12:32:32: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:32:32: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:32:32: #2.2 Generate R script for model : SRX110765.20_model.r INFO @ Fri, 10 Mar 2017 12:32:32: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:32:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:32:39: 16000000 INFO @ Fri, 10 Mar 2017 12:32:54: 17000000 INFO @ Fri, 10 Mar 2017 12:33:06: #1 tag size is determined as 40 bps INFO @ Fri, 10 Mar 2017 12:33:06: #1 tag size = 40 INFO @ Fri, 10 Mar 2017 12:33:06: #1 total tags in treatment: 17827395 INFO @ Fri, 10 Mar 2017 12:33:06: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:33:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:33:10: #1 tags after filtering in treatment: 17823961 INFO @ Fri, 10 Mar 2017 12:33:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:33:10: #1 finished! INFO @ Fri, 10 Mar 2017 12:33:10: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:33:15: #2 number of paired peaks: 3686 INFO @ Fri, 10 Mar 2017 12:33:15: start model_add_line... INFO @ Fri, 10 Mar 2017 12:34:01: start X-correlation... INFO @ Fri, 10 Mar 2017 12:34:01: end of X-cor INFO @ Fri, 10 Mar 2017 12:34:01: #2 finished! INFO @ Fri, 10 Mar 2017 12:34:01: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:34:01: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:34:01: #2.2 Generate R script for model : SRX110765.10_model.r INFO @ Fri, 10 Mar 2017 12:34:01: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:34:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:34:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:34:17: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:35:37: #4 Write output xls file... SRX110765.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:35:37: #4 Write peak in narrowPeak format file... SRX110765.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:35:37: #4 Write summits bed file... SRX110765.20_summits.bed INFO @ Fri, 10 Mar 2017 12:35:37: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (6521 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:35:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:35:51: #4 Write output xls file... SRX110765.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:35:52: #4 Write peak in narrowPeak format file... SRX110765.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:35:52: #4 Write summits bed file... SRX110765.05_summits.bed INFO @ Fri, 10 Mar 2017 12:35:52: Done! pass1 - making usageList (13 chroms): 5 millis pass2 - checking and writing primary data (17886 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:37:19: #4 Write output xls file... SRX110765.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:37:19: #4 Write peak in narrowPeak format file... SRX110765.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:37:19: #4 Write summits bed file... SRX110765.10_summits.bed INFO @ Fri, 10 Mar 2017 12:37:19: Done! pass1 - making usageList (13 chroms): 4 millis pass2 - checking and writing primary data (11595 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。