Job ID = 11192586 sra ファイルのダウンロード中... Completed: 313613K bytes transferred in 6 seconds (402983K 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 29665763 spots for /home/okishinya/chipatlas/results/rn6/SRX4014806/SRR7085055.sra Written 29665763 spots for /home/okishinya/chipatlas/results/rn6/SRX4014806/SRR7085055.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:32:38 29665763 reads; of these: 29665763 (100.00%) were unpaired; of these: 944254 (3.18%) aligned 0 times 24745281 (83.41%) aligned exactly 1 time 3976228 (13.40%) aligned >1 times 96.82% overall alignment rate Time searching: 00:32:42 Overall time: 00:32:42 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 12 files... [bam_rmdupse_core] 2218213 / 28721509 = 0.0772 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, 15 Sep 2018 11:31:27: # Command line: callpeak -t SRX4014806.bam -f BAM -g 2.15e9 -n SRX4014806.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014806.20 # format = BAM # ChIP-seq file = ['SRX4014806.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 @ Sat, 15 Sep 2018 11:31:27: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:31:27: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:31:27: # Command line: callpeak -t SRX4014806.bam -f BAM -g 2.15e9 -n SRX4014806.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014806.05 # format = BAM # ChIP-seq file = ['SRX4014806.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 @ Sat, 15 Sep 2018 11:31:27: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:31:27: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:31:27: # Command line: callpeak -t SRX4014806.bam -f BAM -g 2.15e9 -n SRX4014806.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014806.10 # format = BAM # ChIP-seq file = ['SRX4014806.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 @ Sat, 15 Sep 2018 11:31:27: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:31:27: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:31:34: 1000000 INFO @ Sat, 15 Sep 2018 11:31:34: 1000000 INFO @ Sat, 15 Sep 2018 11:31:34: 1000000 INFO @ Sat, 15 Sep 2018 11:31:41: 2000000 INFO @ Sat, 15 Sep 2018 11:31:41: 2000000 INFO @ Sat, 15 Sep 2018 11:31:41: 2000000 INFO @ Sat, 15 Sep 2018 11:31:48: 3000000 INFO @ Sat, 15 Sep 2018 11:31:48: 3000000 INFO @ Sat, 15 Sep 2018 11:31:48: 3000000 INFO @ Sat, 15 Sep 2018 11:31:55: 4000000 INFO @ Sat, 15 Sep 2018 11:31:55: 4000000 INFO @ Sat, 15 Sep 2018 11:31:55: 4000000 INFO @ Sat, 15 Sep 2018 11:32:02: 5000000 INFO @ Sat, 15 Sep 2018 11:32:02: 5000000 INFO @ Sat, 15 Sep 2018 11:32:02: 5000000 INFO @ Sat, 15 Sep 2018 11:32:09: 6000000 INFO @ Sat, 15 Sep 2018 11:32:09: 6000000 INFO @ Sat, 15 Sep 2018 11:32:09: 6000000 INFO @ Sat, 15 Sep 2018 11:32:16: 7000000 INFO @ Sat, 15 Sep 2018 11:32:16: 7000000 INFO @ Sat, 15 Sep 2018 11:32:16: 7000000 INFO @ Sat, 15 Sep 2018 11:32:23: 8000000 INFO @ Sat, 15 Sep 2018 11:32:23: 8000000 INFO @ Sat, 15 Sep 2018 11:32:24: 8000000 INFO @ Sat, 15 Sep 2018 11:32:30: 9000000 INFO @ Sat, 15 Sep 2018 11:32:30: 9000000 INFO @ Sat, 15 Sep 2018 11:32:31: 9000000 INFO @ Sat, 15 Sep 2018 11:32:37: 10000000 INFO @ Sat, 15 Sep 2018 11:32:37: 10000000 INFO @ Sat, 15 Sep 2018 11:32:38: 10000000 INFO @ Sat, 15 Sep 2018 11:32:44: 11000000 INFO @ Sat, 15 Sep 2018 11:32:44: 11000000 INFO @ Sat, 15 Sep 2018 11:32:45: 11000000 INFO @ Sat, 15 Sep 2018 11:32:51: 12000000 INFO @ Sat, 15 Sep 2018 11:32:51: 12000000 INFO @ Sat, 15 Sep 2018 11:32:52: 12000000 INFO @ Sat, 15 Sep 2018 11:32:58: 13000000 INFO @ Sat, 15 Sep 2018 11:32:59: 13000000 INFO @ Sat, 15 Sep 2018 11:33:00: 13000000 INFO @ Sat, 15 Sep 2018 11:33:05: 14000000 INFO @ Sat, 15 Sep 2018 11:33:06: 14000000 INFO @ Sat, 15 Sep 2018 11:33:07: 14000000 INFO @ Sat, 15 Sep 2018 11:33:12: 15000000 INFO @ Sat, 15 Sep 2018 11:33:13: 15000000 INFO @ Sat, 15 Sep 2018 11:33:14: 15000000 INFO @ Sat, 15 Sep 2018 11:33:19: 16000000 INFO @ Sat, 15 Sep 2018 11:33:20: 16000000 INFO @ Sat, 15 Sep 2018 11:33:21: 16000000 INFO @ Sat, 15 Sep 2018 11:33:26: 17000000 INFO @ Sat, 15 Sep 2018 11:33:27: 17000000 INFO @ Sat, 15 Sep 2018 11:33:29: 17000000 INFO @ Sat, 15 Sep 2018 11:33:33: 18000000 INFO @ Sat, 15 Sep 2018 11:33:34: 18000000 INFO @ Sat, 15 Sep 2018 11:33:36: 18000000 INFO @ Sat, 15 Sep 2018 11:33:40: 19000000 INFO @ Sat, 15 Sep 2018 11:33:41: 19000000 INFO @ Sat, 15 Sep 2018 11:33:43: 19000000 INFO @ Sat, 15 Sep 2018 11:33:47: 20000000 INFO @ Sat, 15 Sep 2018 11:33:48: 20000000 INFO @ Sat, 15 Sep 2018 11:33:50: 20000000 INFO @ Sat, 15 Sep 2018 11:33:54: 21000000 INFO @ Sat, 15 Sep 2018 11:33:56: 21000000 INFO @ Sat, 15 Sep 2018 11:33:58: 21000000 INFO @ Sat, 15 Sep 2018 11:34:00: 22000000 INFO @ Sat, 15 Sep 2018 11:34:03: 22000000 INFO @ Sat, 15 Sep 2018 11:34:05: 22000000 INFO @ Sat, 15 Sep 2018 11:34:07: 23000000 INFO @ Sat, 15 Sep 2018 11:34:10: 23000000 INFO @ Sat, 15 Sep 2018 11:34:12: 23000000 INFO @ Sat, 15 Sep 2018 11:34:15: 24000000 INFO @ Sat, 15 Sep 2018 11:34:16: 24000000 INFO @ Sat, 15 Sep 2018 11:34:19: 24000000 INFO @ Sat, 15 Sep 2018 11:34:22: 25000000 INFO @ Sat, 15 Sep 2018 11:34:23: 25000000 INFO @ Sat, 15 Sep 2018 11:34:27: 25000000 INFO @ Sat, 15 Sep 2018 11:34:30: 26000000 INFO @ Sat, 15 Sep 2018 11:34:30: 26000000 INFO @ Sat, 15 Sep 2018 11:34:34: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:34:34: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:34:34: #1 total tags in treatment: 26503296 INFO @ Sat, 15 Sep 2018 11:34:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:34:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:34:34: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:34:34: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:34:34: #1 total tags in treatment: 26503296 INFO @ Sat, 15 Sep 2018 11:34:34: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:34:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:34:34: 26000000 INFO @ Sat, 15 Sep 2018 11:34:34: #1 tags after filtering in treatment: 26503116 INFO @ Sat, 15 Sep 2018 11:34:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:34:34: #1 finished! INFO @ Sat, 15 Sep 2018 11:34:34: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:34:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:34:35: #1 tags after filtering in treatment: 26503116 INFO @ Sat, 15 Sep 2018 11:34:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:34:35: #1 finished! INFO @ Sat, 15 Sep 2018 11:34:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:34:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:34:38: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:34:38: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:34:38: #1 total tags in treatment: 26503296 INFO @ Sat, 15 Sep 2018 11:34:38: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:34:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 11:34:39: #1 tags after filtering in treatment: 26503116 INFO @ Sat, 15 Sep 2018 11:34:39: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:34:39: #1 finished! INFO @ Sat, 15 Sep 2018 11:34:39: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:34:39: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:34:42: #2 number of paired peaks: 142711 INFO @ Sat, 15 Sep 2018 11:34:42: start model_add_line... INFO @ Sat, 15 Sep 2018 11:34:42: #2 number of paired peaks: 142711 INFO @ Sat, 15 Sep 2018 11:34:42: start model_add_line... INFO @ Sat, 15 Sep 2018 11:34:42: start X-correlation... INFO @ Sat, 15 Sep 2018 11:34:42: end of X-cor INFO @ Sat, 15 Sep 2018 11:34:42: #2 finished! INFO @ Sat, 15 Sep 2018 11:34:42: #2 predicted fragment length is 270 bps INFO @ Sat, 15 Sep 2018 11:34:42: #2 alternative fragment length(s) may be 4,270 bps INFO @ Sat, 15 Sep 2018 11:34:42: #2.2 Generate R script for model : SRX4014806.20_model.r INFO @ Sat, 15 Sep 2018 11:34:42: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:34:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:34:43: start X-correlation... INFO @ Sat, 15 Sep 2018 11:34:43: end of X-cor INFO @ Sat, 15 Sep 2018 11:34:43: #2 finished! INFO @ Sat, 15 Sep 2018 11:34:43: #2 predicted fragment length is 270 bps INFO @ Sat, 15 Sep 2018 11:34:43: #2 alternative fragment length(s) may be 4,270 bps INFO @ Sat, 15 Sep 2018 11:34:43: #2.2 Generate R script for model : SRX4014806.10_model.r INFO @ Sat, 15 Sep 2018 11:34:43: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:34:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:34:46: #2 number of paired peaks: 142711 INFO @ Sat, 15 Sep 2018 11:34:46: start model_add_line... INFO @ Sat, 15 Sep 2018 11:34:47: start X-correlation... INFO @ Sat, 15 Sep 2018 11:34:47: end of X-cor INFO @ Sat, 15 Sep 2018 11:34:47: #2 finished! INFO @ Sat, 15 Sep 2018 11:34:47: #2 predicted fragment length is 270 bps INFO @ Sat, 15 Sep 2018 11:34:47: #2 alternative fragment length(s) may be 4,270 bps INFO @ Sat, 15 Sep 2018 11:34:47: #2.2 Generate R script for model : SRX4014806.05_model.r INFO @ Sat, 15 Sep 2018 11:34:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:34:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:35:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:35:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:35:57: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:36:26: #4 Write output xls file... SRX4014806.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:36:26: #4 Write peak in narrowPeak format file... SRX4014806.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:36:26: #4 Write summits bed file... SRX4014806.20_summits.bed INFO @ Sat, 15 Sep 2018 11:36:26: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (529 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:36:29: #4 Write output xls file... SRX4014806.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:36:29: #4 Write peak in narrowPeak format file... SRX4014806.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:36:29: #4 Write summits bed file... SRX4014806.10_summits.bed INFO @ Sat, 15 Sep 2018 11:36:29: Done! pass1 - making usageList (63 chroms): 1 millis pass2 - checking and writing primary data (4605 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:36:37: #4 Write output xls file... SRX4014806.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:36:38: #4 Write peak in narrowPeak format file... SRX4014806.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:36:38: #4 Write summits bed file... SRX4014806.05_summits.bed INFO @ Sat, 15 Sep 2018 11:36:38: Done! pass1 - making usageList (115 chroms): 4 millis pass2 - checking and writing primary data (19765 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。