Job ID = 11632678 sra ファイルのダウンロード中... Completed: 699873K bytes transferred in 19 seconds (291996K 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 40160704 spots for /home/okishinya/chipatlas/results/rn6/SRX3360116/SRR6253222.sra Written 40160704 spots for /home/okishinya/chipatlas/results/rn6/SRX3360116/SRR6253222.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 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:24:37 40160704 reads; of these: 40160704 (100.00%) were unpaired; of these: 7663880 (19.08%) aligned 0 times 24159261 (60.16%) aligned exactly 1 time 8337563 (20.76%) aligned >1 times 80.92% overall alignment rate Time searching: 00:24:39 Overall time: 00:24:39 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 4065029 / 32496824 = 0.1251 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, 15 Feb 2019 06:10:50: # Command line: callpeak -t SRX3360116.bam -f BAM -g 2.15e9 -n SRX3360116.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360116.20 # format = BAM # ChIP-seq file = ['SRX3360116.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 06:10:50: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:10:50: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:10:50: # Command line: callpeak -t SRX3360116.bam -f BAM -g 2.15e9 -n SRX3360116.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360116.05 # format = BAM # ChIP-seq file = ['SRX3360116.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 06:10:50: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:10:50: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:10:50: # Command line: callpeak -t SRX3360116.bam -f BAM -g 2.15e9 -n SRX3360116.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360116.10 # format = BAM # ChIP-seq file = ['SRX3360116.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Fri, 15 Feb 2019 06:10:50: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:10:50: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:10:57: 1000000 INFO @ Fri, 15 Feb 2019 06:10:58: 1000000 INFO @ Fri, 15 Feb 2019 06:10:58: 1000000 INFO @ Fri, 15 Feb 2019 06:11:03: 2000000 INFO @ Fri, 15 Feb 2019 06:11:05: 2000000 INFO @ Fri, 15 Feb 2019 06:11:05: 2000000 INFO @ Fri, 15 Feb 2019 06:11:11: 3000000 INFO @ Fri, 15 Feb 2019 06:11:13: 3000000 INFO @ Fri, 15 Feb 2019 06:11:13: 3000000 INFO @ Fri, 15 Feb 2019 06:11:18: 4000000 INFO @ Fri, 15 Feb 2019 06:11:20: 4000000 INFO @ Fri, 15 Feb 2019 06:11:21: 4000000 INFO @ Fri, 15 Feb 2019 06:11:25: 5000000 INFO @ Fri, 15 Feb 2019 06:11:27: 5000000 INFO @ Fri, 15 Feb 2019 06:11:29: 5000000 INFO @ Fri, 15 Feb 2019 06:11:32: 6000000 INFO @ Fri, 15 Feb 2019 06:11:34: 6000000 INFO @ Fri, 15 Feb 2019 06:11:36: 6000000 INFO @ Fri, 15 Feb 2019 06:11:40: 7000000 INFO @ Fri, 15 Feb 2019 06:11:42: 7000000 INFO @ Fri, 15 Feb 2019 06:11:44: 7000000 INFO @ Fri, 15 Feb 2019 06:11:47: 8000000 INFO @ Fri, 15 Feb 2019 06:11:49: 8000000 INFO @ Fri, 15 Feb 2019 06:11:52: 8000000 INFO @ Fri, 15 Feb 2019 06:11:54: 9000000 INFO @ Fri, 15 Feb 2019 06:11:56: 9000000 INFO @ Fri, 15 Feb 2019 06:12:00: 9000000 INFO @ Fri, 15 Feb 2019 06:12:02: 10000000 INFO @ Fri, 15 Feb 2019 06:12:03: 10000000 INFO @ Fri, 15 Feb 2019 06:12:07: 10000000 INFO @ Fri, 15 Feb 2019 06:12:09: 11000000 INFO @ Fri, 15 Feb 2019 06:12:11: 11000000 INFO @ Fri, 15 Feb 2019 06:12:15: 11000000 INFO @ Fri, 15 Feb 2019 06:12:16: 12000000 INFO @ Fri, 15 Feb 2019 06:12:18: 12000000 INFO @ Fri, 15 Feb 2019 06:12:23: 12000000 INFO @ Fri, 15 Feb 2019 06:12:24: 13000000 INFO @ Fri, 15 Feb 2019 06:12:25: 13000000 INFO @ Fri, 15 Feb 2019 06:12:31: 13000000 INFO @ Fri, 15 Feb 2019 06:12:31: 14000000 INFO @ Fri, 15 Feb 2019 06:12:32: 14000000 INFO @ Fri, 15 Feb 2019 06:12:38: 15000000 INFO @ Fri, 15 Feb 2019 06:12:38: 14000000 INFO @ Fri, 15 Feb 2019 06:12:39: 15000000 INFO @ Fri, 15 Feb 2019 06:12:45: 16000000 INFO @ Fri, 15 Feb 2019 06:12:46: 15000000 INFO @ Fri, 15 Feb 2019 06:12:47: 16000000 INFO @ Fri, 15 Feb 2019 06:12:52: 17000000 INFO @ Fri, 15 Feb 2019 06:12:54: 16000000 INFO @ Fri, 15 Feb 2019 06:12:54: 17000000 INFO @ Fri, 15 Feb 2019 06:13:00: 18000000 INFO @ Fri, 15 Feb 2019 06:13:01: 18000000 INFO @ Fri, 15 Feb 2019 06:13:02: 17000000 INFO @ Fri, 15 Feb 2019 06:13:07: 19000000 INFO @ Fri, 15 Feb 2019 06:13:08: 19000000 INFO @ Fri, 15 Feb 2019 06:13:09: 18000000 INFO @ Fri, 15 Feb 2019 06:13:14: 20000000 INFO @ Fri, 15 Feb 2019 06:13:15: 20000000 INFO @ Fri, 15 Feb 2019 06:13:17: 19000000 INFO @ Fri, 15 Feb 2019 06:13:21: 21000000 INFO @ Fri, 15 Feb 2019 06:13:23: 21000000 INFO @ Fri, 15 Feb 2019 06:13:25: 20000000 INFO @ Fri, 15 Feb 2019 06:13:29: 22000000 INFO @ Fri, 15 Feb 2019 06:13:30: 22000000 INFO @ Fri, 15 Feb 2019 06:13:33: 21000000 INFO @ Fri, 15 Feb 2019 06:13:36: 23000000 INFO @ Fri, 15 Feb 2019 06:13:37: 23000000 INFO @ Fri, 15 Feb 2019 06:13:40: 22000000 INFO @ Fri, 15 Feb 2019 06:13:43: 24000000 INFO @ Fri, 15 Feb 2019 06:13:44: 24000000 INFO @ Fri, 15 Feb 2019 06:13:48: 23000000 INFO @ Fri, 15 Feb 2019 06:13:51: 25000000 INFO @ Fri, 15 Feb 2019 06:13:52: 25000000 INFO @ Fri, 15 Feb 2019 06:13:56: 24000000 INFO @ Fri, 15 Feb 2019 06:13:58: 26000000 INFO @ Fri, 15 Feb 2019 06:13:59: 26000000 INFO @ Fri, 15 Feb 2019 06:14:04: 25000000 INFO @ Fri, 15 Feb 2019 06:14:05: 27000000 INFO @ Fri, 15 Feb 2019 06:14:06: 27000000 INFO @ Fri, 15 Feb 2019 06:14:11: 26000000 INFO @ Fri, 15 Feb 2019 06:14:13: 28000000 INFO @ Fri, 15 Feb 2019 06:14:14: 28000000 INFO @ Fri, 15 Feb 2019 06:14:16: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:14:16: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:14:16: #1 total tags in treatment: 28431795 INFO @ Fri, 15 Feb 2019 06:14:16: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:14:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:14:17: #1 tags after filtering in treatment: 28431684 INFO @ Fri, 15 Feb 2019 06:14:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:14:17: #1 finished! INFO @ Fri, 15 Feb 2019 06:14:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:14:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:14:17: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:14:17: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:14:17: #1 total tags in treatment: 28431795 INFO @ Fri, 15 Feb 2019 06:14:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:14:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:14:18: #1 tags after filtering in treatment: 28431684 INFO @ Fri, 15 Feb 2019 06:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:14:18: #1 finished! INFO @ Fri, 15 Feb 2019 06:14:18: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:14:19: 27000000 INFO @ Fri, 15 Feb 2019 06:14:21: #2 number of paired peaks: 42521 INFO @ Fri, 15 Feb 2019 06:14:21: start model_add_line... INFO @ Fri, 15 Feb 2019 06:14:22: start X-correlation... INFO @ Fri, 15 Feb 2019 06:14:22: end of X-cor INFO @ Fri, 15 Feb 2019 06:14:22: #2 finished! INFO @ Fri, 15 Feb 2019 06:14:22: #2 predicted fragment length is 168 bps INFO @ Fri, 15 Feb 2019 06:14:22: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 15 Feb 2019 06:14:22: #2.2 Generate R script for model : SRX3360116.20_model.r INFO @ Fri, 15 Feb 2019 06:14:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:14:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:14:22: #2 number of paired peaks: 42521 INFO @ Fri, 15 Feb 2019 06:14:22: start model_add_line... INFO @ Fri, 15 Feb 2019 06:14:23: start X-correlation... INFO @ Fri, 15 Feb 2019 06:14:23: end of X-cor INFO @ Fri, 15 Feb 2019 06:14:23: #2 finished! INFO @ Fri, 15 Feb 2019 06:14:23: #2 predicted fragment length is 168 bps INFO @ Fri, 15 Feb 2019 06:14:23: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 15 Feb 2019 06:14:23: #2.2 Generate R script for model : SRX3360116.10_model.r INFO @ Fri, 15 Feb 2019 06:14:23: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:14:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:14:26: 28000000 INFO @ Fri, 15 Feb 2019 06:14:29: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:14:29: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:14:29: #1 total tags in treatment: 28431795 INFO @ Fri, 15 Feb 2019 06:14:29: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:14:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 06:14:30: #1 tags after filtering in treatment: 28431684 INFO @ Fri, 15 Feb 2019 06:14:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:14:30: #1 finished! INFO @ Fri, 15 Feb 2019 06:14:30: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:14:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:14:34: #2 number of paired peaks: 42521 INFO @ Fri, 15 Feb 2019 06:14:34: start model_add_line... INFO @ Fri, 15 Feb 2019 06:14:35: start X-correlation... INFO @ Fri, 15 Feb 2019 06:14:35: end of X-cor INFO @ Fri, 15 Feb 2019 06:14:35: #2 finished! INFO @ Fri, 15 Feb 2019 06:14:35: #2 predicted fragment length is 168 bps INFO @ Fri, 15 Feb 2019 06:14:35: #2 alternative fragment length(s) may be 168 bps INFO @ Fri, 15 Feb 2019 06:14:35: #2.2 Generate R script for model : SRX3360116.05_model.r INFO @ Fri, 15 Feb 2019 06:14:35: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:14:35: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:15:36: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:15:38: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:15:53: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:16:18: #4 Write output xls file... SRX3360116.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:16:18: #4 Write peak in narrowPeak format file... SRX3360116.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:16:18: #4 Write summits bed file... SRX3360116.10_summits.bed INFO @ Fri, 15 Feb 2019 06:16:18: Done! pass1 - making usageList (100 chroms): 7 millis pass2 - checking and writing primary data (18305 records, 4 fields): 29 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:16:25: #4 Write output xls file... SRX3360116.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:16:25: #4 Write peak in narrowPeak format file... SRX3360116.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:16:25: #4 Write summits bed file... SRX3360116.20_summits.bed INFO @ Fri, 15 Feb 2019 06:16:25: Done! pass1 - making usageList (76 chroms): 8 millis pass2 - checking and writing primary data (12314 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:16:35: #4 Write output xls file... SRX3360116.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:16:35: #4 Write peak in narrowPeak format file... SRX3360116.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:16:35: #4 Write summits bed file... SRX3360116.05_summits.bed INFO @ Fri, 15 Feb 2019 06:16:35: Done! pass1 - making usageList (127 chroms): 9 millis pass2 - checking and writing primary data (22867 records, 4 fields): 35 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。