Job ID = 11170886 sra ファイルのダウンロード中... Completed: 154364K bytes transferred in 13 seconds (90762K bits/sec), in 1 file. Completed: 152613K bytes transferred in 10 seconds (123086K bits/sec), in 1 file. Completed: 150016K bytes transferred in 6 seconds (199545K bits/sec), in 1 file. Completed: 147642K bytes transferred in 5 seconds (235821K bits/sec), in 1 file. 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... Read 6562315 spots for /home/okishinya/chipatlas/results/dm3/SRX1078884/SRR2084563.sra Written 6562315 spots for /home/okishinya/chipatlas/results/dm3/SRX1078884/SRR2084563.sra Read 6684181 spots for /home/okishinya/chipatlas/results/dm3/SRX1078884/SRR2084562.sra Written 6684181 spots for /home/okishinya/chipatlas/results/dm3/SRX1078884/SRR2084562.sra Read 6755928 spots for /home/okishinya/chipatlas/results/dm3/SRX1078884/SRR2084561.sra Written 6755928 spots for /home/okishinya/chipatlas/results/dm3/SRX1078884/SRR2084561.sra Read 6801579 spots for /home/okishinya/chipatlas/results/dm3/SRX1078884/SRR2084560.sra Written 6801579 spots for /home/okishinya/chipatlas/results/dm3/SRX1078884/SRR2084560.sra rm: cannot remove `[DSE]RX*': 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: 00:09:32 26804003 reads; of these: 26804003 (100.00%) were unpaired; of these: 1982866 (7.40%) aligned 0 times 18381640 (68.58%) aligned exactly 1 time 6439497 (24.02%) aligned >1 times 92.60% overall alignment rate Time searching: 00:09:32 Overall time: 00:09:32 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] 6858451 / 24821137 = 0.2763 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, 08 Sep 2018 11:42:11: # Command line: callpeak -t SRX1078884.bam -f BAM -g dm -n SRX1078884.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1078884.05 # format = BAM # ChIP-seq file = ['SRX1078884.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 11:42:11: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:42:11: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:42:11: # Command line: callpeak -t SRX1078884.bam -f BAM -g dm -n SRX1078884.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1078884.10 # format = BAM # ChIP-seq file = ['SRX1078884.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 11:42:11: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:42:11: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:42:11: # Command line: callpeak -t SRX1078884.bam -f BAM -g dm -n SRX1078884.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1078884.20 # format = BAM # ChIP-seq file = ['SRX1078884.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 # Paired-End mode is off INFO @ Sat, 08 Sep 2018 11:42:11: #1 read tag files... INFO @ Sat, 08 Sep 2018 11:42:11: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 11:42:18: 1000000 INFO @ Sat, 08 Sep 2018 11:42:19: 1000000 INFO @ Sat, 08 Sep 2018 11:42:19: 1000000 INFO @ Sat, 08 Sep 2018 11:42:25: 2000000 INFO @ Sat, 08 Sep 2018 11:42:26: 2000000 INFO @ Sat, 08 Sep 2018 11:42:26: 2000000 INFO @ Sat, 08 Sep 2018 11:42:31: 3000000 INFO @ Sat, 08 Sep 2018 11:42:34: 3000000 INFO @ Sat, 08 Sep 2018 11:42:34: 3000000 INFO @ Sat, 08 Sep 2018 11:42:37: 4000000 INFO @ Sat, 08 Sep 2018 11:42:41: 4000000 INFO @ Sat, 08 Sep 2018 11:42:42: 4000000 INFO @ Sat, 08 Sep 2018 11:42:44: 5000000 INFO @ Sat, 08 Sep 2018 11:42:49: 5000000 INFO @ Sat, 08 Sep 2018 11:42:50: 5000000 INFO @ Sat, 08 Sep 2018 11:42:51: 6000000 INFO @ Sat, 08 Sep 2018 11:42:56: 6000000 INFO @ Sat, 08 Sep 2018 11:42:58: 6000000 INFO @ Sat, 08 Sep 2018 11:42:59: 7000000 INFO @ Sat, 08 Sep 2018 11:43:03: 7000000 INFO @ Sat, 08 Sep 2018 11:43:05: 7000000 INFO @ Sat, 08 Sep 2018 11:43:06: 8000000 INFO @ Sat, 08 Sep 2018 11:43:10: 8000000 INFO @ Sat, 08 Sep 2018 11:43:12: 8000000 INFO @ Sat, 08 Sep 2018 11:43:13: 9000000 INFO @ Sat, 08 Sep 2018 11:43:18: 9000000 INFO @ Sat, 08 Sep 2018 11:43:20: 9000000 INFO @ Sat, 08 Sep 2018 11:43:20: 10000000 INFO @ Sat, 08 Sep 2018 11:43:25: 10000000 INFO @ Sat, 08 Sep 2018 11:43:28: 10000000 INFO @ Sat, 08 Sep 2018 11:43:28: 11000000 INFO @ Sat, 08 Sep 2018 11:43:32: 11000000 INFO @ Sat, 08 Sep 2018 11:43:35: 12000000 INFO @ Sat, 08 Sep 2018 11:43:36: 11000000 INFO @ Sat, 08 Sep 2018 11:43:40: 12000000 INFO @ Sat, 08 Sep 2018 11:43:42: 13000000 INFO @ Sat, 08 Sep 2018 11:43:44: 12000000 INFO @ Sat, 08 Sep 2018 11:43:47: 13000000 INFO @ Sat, 08 Sep 2018 11:43:50: 14000000 INFO @ Sat, 08 Sep 2018 11:43:52: 13000000 INFO @ Sat, 08 Sep 2018 11:43:54: 14000000 INFO @ Sat, 08 Sep 2018 11:43:58: 15000000 INFO @ Sat, 08 Sep 2018 11:44:00: 14000000 INFO @ Sat, 08 Sep 2018 11:44:01: 15000000 INFO @ Sat, 08 Sep 2018 11:44:06: 16000000 INFO @ Sat, 08 Sep 2018 11:44:08: 15000000 INFO @ Sat, 08 Sep 2018 11:44:09: 16000000 INFO @ Sat, 08 Sep 2018 11:44:15: 17000000 INFO @ Sat, 08 Sep 2018 11:44:15: 16000000 INFO @ Sat, 08 Sep 2018 11:44:16: 17000000 INFO @ Sat, 08 Sep 2018 11:44:23: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 11:44:23: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 11:44:23: #1 total tags in treatment: 17962686 INFO @ Sat, 08 Sep 2018 11:44:23: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:44:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:44:23: 17000000 INFO @ Sat, 08 Sep 2018 11:44:23: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 11:44:23: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 11:44:23: #1 total tags in treatment: 17962686 INFO @ Sat, 08 Sep 2018 11:44:23: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:44:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:44:23: #1 tags after filtering in treatment: 17962686 INFO @ Sat, 08 Sep 2018 11:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:44:23: #1 finished! INFO @ Sat, 08 Sep 2018 11:44:23: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:44:23: #1 tags after filtering in treatment: 17962686 INFO @ Sat, 08 Sep 2018 11:44:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:44:23: #1 finished! INFO @ Sat, 08 Sep 2018 11:44:23: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:44:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:44:25: #2 number of paired peaks: 4560 INFO @ Sat, 08 Sep 2018 11:44:25: start model_add_line... INFO @ Sat, 08 Sep 2018 11:44:25: #2 number of paired peaks: 4560 INFO @ Sat, 08 Sep 2018 11:44:25: start model_add_line... INFO @ Sat, 08 Sep 2018 11:44:25: start X-correlation... INFO @ Sat, 08 Sep 2018 11:44:25: end of X-cor INFO @ Sat, 08 Sep 2018 11:44:25: #2 finished! INFO @ Sat, 08 Sep 2018 11:44:25: #2 predicted fragment length is 180 bps INFO @ Sat, 08 Sep 2018 11:44:25: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 08 Sep 2018 11:44:25: #2.2 Generate R script for model : SRX1078884.05_model.r INFO @ Sat, 08 Sep 2018 11:44:25: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:44:25: start X-correlation... INFO @ Sat, 08 Sep 2018 11:44:25: end of X-cor INFO @ Sat, 08 Sep 2018 11:44:25: #2 finished! INFO @ Sat, 08 Sep 2018 11:44:25: #2 predicted fragment length is 180 bps INFO @ Sat, 08 Sep 2018 11:44:25: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 08 Sep 2018 11:44:25: #2.2 Generate R script for model : SRX1078884.10_model.r INFO @ Sat, 08 Sep 2018 11:44:25: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:44:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:44:30: #1 tag size is determined as 50 bps INFO @ Sat, 08 Sep 2018 11:44:30: #1 tag size = 50 INFO @ Sat, 08 Sep 2018 11:44:30: #1 total tags in treatment: 17962686 INFO @ Sat, 08 Sep 2018 11:44:30: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 11:44:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 11:44:31: #1 tags after filtering in treatment: 17962686 INFO @ Sat, 08 Sep 2018 11:44:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 11:44:31: #1 finished! INFO @ Sat, 08 Sep 2018 11:44:31: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 11:44:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 11:44:32: #2 number of paired peaks: 4560 INFO @ Sat, 08 Sep 2018 11:44:32: start model_add_line... INFO @ Sat, 08 Sep 2018 11:44:33: start X-correlation... INFO @ Sat, 08 Sep 2018 11:44:33: end of X-cor INFO @ Sat, 08 Sep 2018 11:44:33: #2 finished! INFO @ Sat, 08 Sep 2018 11:44:33: #2 predicted fragment length is 180 bps INFO @ Sat, 08 Sep 2018 11:44:33: #2 alternative fragment length(s) may be 180 bps INFO @ Sat, 08 Sep 2018 11:44:33: #2.2 Generate R script for model : SRX1078884.20_model.r INFO @ Sat, 08 Sep 2018 11:44:33: #3 Call peaks... INFO @ Sat, 08 Sep 2018 11:44:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 11:45:20: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:45:21: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:45:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 11:45:44: #4 Write output xls file... SRX1078884.05_peaks.xls INFO @ Sat, 08 Sep 2018 11:45:44: #4 Write peak in narrowPeak format file... SRX1078884.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:45:44: #4 Write summits bed file... SRX1078884.05_summits.bed INFO @ Sat, 08 Sep 2018 11:45:45: Done! INFO @ Sat, 08 Sep 2018 11:45:45: #4 Write output xls file... SRX1078884.10_peaks.xls INFO @ Sat, 08 Sep 2018 11:45:45: #4 Write peak in narrowPeak format file... SRX1078884.10_peaks.narrowPeak pass1 - making usageList (15 chroms): 3 millis INFO @ Sat, 08 Sep 2018 11:45:45: #4 Write summits bed file... SRX1078884.10_summits.bed pass2 - checking and writing primary data (10432 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:45:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8482 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 11:45:49: #4 Write output xls file... SRX1078884.20_peaks.xls INFO @ Sat, 08 Sep 2018 11:45:49: #4 Write peak in narrowPeak format file... SRX1078884.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 11:45:49: #4 Write summits bed file... SRX1078884.20_summits.bed INFO @ Sat, 08 Sep 2018 11:45:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6408 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。