Job ID = 10175254 sra ファイルのダウンロード中... Completed: 626330K bytes transferred in 15 seconds (321449K 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... Written 35966536 spots for /home/okishinya/chipatlas/results/dm3/SRX2804232/SRR5534660.sra Written 35966536 spots total 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 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: 00:13:50 35966536 reads; of these: 35966536 (100.00%) were unpaired; of these: 2202233 (6.12%) aligned 0 times 25524390 (70.97%) aligned exactly 1 time 8239913 (22.91%) aligned >1 times 93.88% overall alignment rate Time searching: 00:13:50 Overall time: 00:13:50 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 16 files... [bam_rmdupse_core] 12476703 / 33764303 = 0.3695 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 @ Mon, 06 Nov 2017 12:24:48: # Command line: callpeak -t SRX2804232.bam -f BAM -g dm -n SRX2804232.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2804232.05 # format = BAM # ChIP-seq file = ['SRX2804232.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 @ Mon, 06 Nov 2017 12:24:48: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:24:48: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:24:48: # Command line: callpeak -t SRX2804232.bam -f BAM -g dm -n SRX2804232.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2804232.10 # format = BAM # ChIP-seq file = ['SRX2804232.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 @ Mon, 06 Nov 2017 12:24:48: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:24:48: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:24:48: # Command line: callpeak -t SRX2804232.bam -f BAM -g dm -n SRX2804232.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2804232.20 # format = BAM # ChIP-seq file = ['SRX2804232.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 @ Mon, 06 Nov 2017 12:24:48: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:24:48: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:24:54: 1000000 INFO @ Mon, 06 Nov 2017 12:24:54: 1000000 INFO @ Mon, 06 Nov 2017 12:24:55: 1000000 INFO @ Mon, 06 Nov 2017 12:25:01: 2000000 INFO @ Mon, 06 Nov 2017 12:25:01: 2000000 INFO @ Mon, 06 Nov 2017 12:25:01: 2000000 INFO @ Mon, 06 Nov 2017 12:25:08: 3000000 INFO @ Mon, 06 Nov 2017 12:25:08: 3000000 INFO @ Mon, 06 Nov 2017 12:25:08: 3000000 INFO @ Mon, 06 Nov 2017 12:25:14: 4000000 INFO @ Mon, 06 Nov 2017 12:25:14: 4000000 INFO @ Mon, 06 Nov 2017 12:25:15: 4000000 INFO @ Mon, 06 Nov 2017 12:25:21: 5000000 INFO @ Mon, 06 Nov 2017 12:25:21: 5000000 INFO @ Mon, 06 Nov 2017 12:25:22: 5000000 INFO @ Mon, 06 Nov 2017 12:25:27: 6000000 INFO @ Mon, 06 Nov 2017 12:25:27: 6000000 INFO @ Mon, 06 Nov 2017 12:25:29: 6000000 INFO @ Mon, 06 Nov 2017 12:25:34: 7000000 INFO @ Mon, 06 Nov 2017 12:25:34: 7000000 INFO @ Mon, 06 Nov 2017 12:25:36: 7000000 INFO @ Mon, 06 Nov 2017 12:25:40: 8000000 INFO @ Mon, 06 Nov 2017 12:25:40: 8000000 INFO @ Mon, 06 Nov 2017 12:25:43: 8000000 INFO @ Mon, 06 Nov 2017 12:25:47: 9000000 INFO @ Mon, 06 Nov 2017 12:25:47: 9000000 INFO @ Mon, 06 Nov 2017 12:25:50: 9000000 INFO @ Mon, 06 Nov 2017 12:25:54: 10000000 INFO @ Mon, 06 Nov 2017 12:25:54: 10000000 INFO @ Mon, 06 Nov 2017 12:25:57: 10000000 INFO @ Mon, 06 Nov 2017 12:26:01: 11000000 INFO @ Mon, 06 Nov 2017 12:26:01: 11000000 INFO @ Mon, 06 Nov 2017 12:26:04: 11000000 INFO @ Mon, 06 Nov 2017 12:26:08: 12000000 INFO @ Mon, 06 Nov 2017 12:26:08: 12000000 INFO @ Mon, 06 Nov 2017 12:26:11: 12000000 INFO @ Mon, 06 Nov 2017 12:26:14: 13000000 INFO @ Mon, 06 Nov 2017 12:26:15: 13000000 INFO @ Mon, 06 Nov 2017 12:26:18: 13000000 INFO @ Mon, 06 Nov 2017 12:26:22: 14000000 INFO @ Mon, 06 Nov 2017 12:26:22: 14000000 INFO @ Mon, 06 Nov 2017 12:26:27: 14000000 INFO @ Mon, 06 Nov 2017 12:26:29: 15000000 INFO @ Mon, 06 Nov 2017 12:26:29: 15000000 INFO @ Mon, 06 Nov 2017 12:26:35: 15000000 INFO @ Mon, 06 Nov 2017 12:26:37: 16000000 INFO @ Mon, 06 Nov 2017 12:26:37: 16000000 INFO @ Mon, 06 Nov 2017 12:26:43: 16000000 INFO @ Mon, 06 Nov 2017 12:26:44: 17000000 INFO @ Mon, 06 Nov 2017 12:26:45: 17000000 INFO @ Mon, 06 Nov 2017 12:26:51: 18000000 INFO @ Mon, 06 Nov 2017 12:26:51: 17000000 INFO @ Mon, 06 Nov 2017 12:26:52: 18000000 INFO @ Mon, 06 Nov 2017 12:26:59: 19000000 INFO @ Mon, 06 Nov 2017 12:27:00: 18000000 INFO @ Mon, 06 Nov 2017 12:27:00: 19000000 INFO @ Mon, 06 Nov 2017 12:27:06: 20000000 INFO @ Mon, 06 Nov 2017 12:27:07: 19000000 INFO @ Mon, 06 Nov 2017 12:27:07: 20000000 INFO @ Mon, 06 Nov 2017 12:27:12: 21000000 INFO @ Mon, 06 Nov 2017 12:27:13: 21000000 INFO @ Mon, 06 Nov 2017 12:27:14: 20000000 INFO @ Mon, 06 Nov 2017 12:27:14: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:27:14: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:27:14: #1 total tags in treatment: 21287600 INFO @ Mon, 06 Nov 2017 12:27:14: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:27:14: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:27:15: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:27:15: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:27:15: #1 total tags in treatment: 21287600 INFO @ Mon, 06 Nov 2017 12:27:15: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:27:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:27:15: #1 tags after filtering in treatment: 21287600 INFO @ Mon, 06 Nov 2017 12:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:27:15: #1 finished! INFO @ Mon, 06 Nov 2017 12:27:15: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:27:15: #1 tags after filtering in treatment: 21287600 INFO @ Mon, 06 Nov 2017 12:27:15: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:27:15: #1 finished! INFO @ Mon, 06 Nov 2017 12:27:15: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:27:15: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:27:17: #2 number of paired peaks: 5194 INFO @ Mon, 06 Nov 2017 12:27:17: start model_add_line... INFO @ Mon, 06 Nov 2017 12:27:17: start X-correlation... INFO @ Mon, 06 Nov 2017 12:27:17: end of X-cor INFO @ Mon, 06 Nov 2017 12:27:17: #2 finished! INFO @ Mon, 06 Nov 2017 12:27:17: #2 predicted fragment length is 185 bps INFO @ Mon, 06 Nov 2017 12:27:17: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 06 Nov 2017 12:27:17: #2.2 Generate R script for model : SRX2804232.10_model.r INFO @ Mon, 06 Nov 2017 12:27:17: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:27:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:27:17: #2 number of paired peaks: 5194 INFO @ Mon, 06 Nov 2017 12:27:17: start model_add_line... INFO @ Mon, 06 Nov 2017 12:27:18: start X-correlation... INFO @ Mon, 06 Nov 2017 12:27:18: end of X-cor INFO @ Mon, 06 Nov 2017 12:27:18: #2 finished! INFO @ Mon, 06 Nov 2017 12:27:18: #2 predicted fragment length is 185 bps INFO @ Mon, 06 Nov 2017 12:27:18: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 06 Nov 2017 12:27:18: #2.2 Generate R script for model : SRX2804232.20_model.r INFO @ Mon, 06 Nov 2017 12:27:18: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:27:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:27:20: 21000000 INFO @ Mon, 06 Nov 2017 12:27:22: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:27:22: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:27:22: #1 total tags in treatment: 21287600 INFO @ Mon, 06 Nov 2017 12:27:22: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:27:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:27:22: #1 tags after filtering in treatment: 21287600 INFO @ Mon, 06 Nov 2017 12:27:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:27:22: #1 finished! INFO @ Mon, 06 Nov 2017 12:27:22: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:27:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:27:24: #2 number of paired peaks: 5194 INFO @ Mon, 06 Nov 2017 12:27:24: start model_add_line... INFO @ Mon, 06 Nov 2017 12:27:25: start X-correlation... INFO @ Mon, 06 Nov 2017 12:27:25: end of X-cor INFO @ Mon, 06 Nov 2017 12:27:25: #2 finished! INFO @ Mon, 06 Nov 2017 12:27:25: #2 predicted fragment length is 185 bps INFO @ Mon, 06 Nov 2017 12:27:25: #2 alternative fragment length(s) may be 185 bps INFO @ Mon, 06 Nov 2017 12:27:25: #2.2 Generate R script for model : SRX2804232.05_model.r INFO @ Mon, 06 Nov 2017 12:27:25: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:27:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:28:28: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:28:28: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:28:37: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:28:55: #4 Write output xls file... SRX2804232.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:28:55: #4 Write peak in narrowPeak format file... SRX2804232.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:28:55: #4 Write summits bed file... SRX2804232.20_summits.bed INFO @ Mon, 06 Nov 2017 12:28:55: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5694 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:28:58: #4 Write output xls file... SRX2804232.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:28:58: #4 Write peak in narrowPeak format file... SRX2804232.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:28:58: #4 Write summits bed file... SRX2804232.10_summits.bed INFO @ Mon, 06 Nov 2017 12:28:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7539 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:29:06: #4 Write output xls file... SRX2804232.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:29:06: #4 Write peak in narrowPeak format file... SRX2804232.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:29:06: #4 Write summits bed file... SRX2804232.05_summits.bed INFO @ Mon, 06 Nov 2017 12:29:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9123 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。