Job ID = 11192593 sra ファイルのダウンロード中... Completed: 516690K bytes transferred in 7 seconds (559109K 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 40900601 spots for /home/okishinya/chipatlas/results/rn6/SRX4014813/SRR7085062.sra Written 40900601 spots for /home/okishinya/chipatlas/results/rn6/SRX4014813/SRR7085062.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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:37:45 40900601 reads; of these: 40900601 (100.00%) were unpaired; of these: 1571824 (3.84%) aligned 0 times 34617003 (84.64%) aligned exactly 1 time 4711774 (11.52%) aligned >1 times 96.16% overall alignment rate Time searching: 00:37:51 Overall time: 00:37:51 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 20 files... [bam_rmdupse_core] 5603544 / 39328777 = 0.1425 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 11:30:03: # Command line: callpeak -t SRX4014813.bam -f BAM -g 2.15e9 -n SRX4014813.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014813.05 # format = BAM # ChIP-seq file = ['SRX4014813.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 11:30:03: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:30:03: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:30:03: # Command line: callpeak -t SRX4014813.bam -f BAM -g 2.15e9 -n SRX4014813.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014813.20 # format = BAM # ChIP-seq file = ['SRX4014813.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 11:30:03: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:30:03: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:30:03: # Command line: callpeak -t SRX4014813.bam -f BAM -g 2.15e9 -n SRX4014813.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014813.10 # format = BAM # ChIP-seq file = ['SRX4014813.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 11:30:03: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:30:03: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:30:09: 1000000 INFO @ Sat, 15 Sep 2018 11:30:10: 1000000 INFO @ Sat, 15 Sep 2018 11:30:10: 1000000 INFO @ Sat, 15 Sep 2018 11:30:16: 2000000 INFO @ Sat, 15 Sep 2018 11:30:16: 2000000 INFO @ Sat, 15 Sep 2018 11:30:16: 2000000 INFO @ Sat, 15 Sep 2018 11:30:22: 3000000 INFO @ Sat, 15 Sep 2018 11:30:23: 3000000 INFO @ Sat, 15 Sep 2018 11:30:23: 3000000 INFO @ Sat, 15 Sep 2018 11:30:29: 4000000 INFO @ Sat, 15 Sep 2018 11:30:29: 4000000 INFO @ Sat, 15 Sep 2018 11:30:29: 4000000 INFO @ Sat, 15 Sep 2018 11:30:35: 5000000 INFO @ Sat, 15 Sep 2018 11:30:35: 5000000 INFO @ Sat, 15 Sep 2018 11:30:36: 5000000 INFO @ Sat, 15 Sep 2018 11:30:42: 6000000 INFO @ Sat, 15 Sep 2018 11:30:42: 6000000 INFO @ Sat, 15 Sep 2018 11:30:43: 6000000 INFO @ Sat, 15 Sep 2018 11:30:48: 7000000 INFO @ Sat, 15 Sep 2018 11:30:49: 7000000 INFO @ Sat, 15 Sep 2018 11:30:49: 7000000 INFO @ Sat, 15 Sep 2018 11:30:54: 8000000 INFO @ Sat, 15 Sep 2018 11:30:55: 8000000 INFO @ Sat, 15 Sep 2018 11:30:56: 8000000 INFO @ Sat, 15 Sep 2018 11:31:00: 9000000 INFO @ Sat, 15 Sep 2018 11:31:02: 9000000 INFO @ Sat, 15 Sep 2018 11:31:03: 9000000 INFO @ Sat, 15 Sep 2018 11:31:07: 10000000 INFO @ Sat, 15 Sep 2018 11:31:09: 10000000 INFO @ Sat, 15 Sep 2018 11:31:10: 10000000 INFO @ Sat, 15 Sep 2018 11:31:13: 11000000 INFO @ Sat, 15 Sep 2018 11:31:15: 11000000 INFO @ Sat, 15 Sep 2018 11:31:16: 11000000 INFO @ Sat, 15 Sep 2018 11:31:19: 12000000 INFO @ Sat, 15 Sep 2018 11:31:22: 12000000 INFO @ Sat, 15 Sep 2018 11:31:23: 12000000 INFO @ Sat, 15 Sep 2018 11:31:26: 13000000 INFO @ Sat, 15 Sep 2018 11:31:28: 13000000 INFO @ Sat, 15 Sep 2018 11:31:30: 13000000 INFO @ Sat, 15 Sep 2018 11:31:32: 14000000 INFO @ Sat, 15 Sep 2018 11:31:35: 14000000 INFO @ Sat, 15 Sep 2018 11:31:36: 14000000 INFO @ Sat, 15 Sep 2018 11:31:38: 15000000 INFO @ Sat, 15 Sep 2018 11:31:41: 15000000 INFO @ Sat, 15 Sep 2018 11:31:43: 15000000 INFO @ Sat, 15 Sep 2018 11:31:45: 16000000 INFO @ Sat, 15 Sep 2018 11:31:48: 16000000 INFO @ Sat, 15 Sep 2018 11:31:50: 16000000 INFO @ Sat, 15 Sep 2018 11:31:51: 17000000 INFO @ Sat, 15 Sep 2018 11:31:54: 17000000 INFO @ Sat, 15 Sep 2018 11:31:56: 17000000 INFO @ Sat, 15 Sep 2018 11:31:57: 18000000 INFO @ Sat, 15 Sep 2018 11:32:01: 18000000 INFO @ Sat, 15 Sep 2018 11:32:03: 18000000 INFO @ Sat, 15 Sep 2018 11:32:03: 19000000 INFO @ Sat, 15 Sep 2018 11:32:07: 19000000 INFO @ Sat, 15 Sep 2018 11:32:09: 19000000 INFO @ Sat, 15 Sep 2018 11:32:09: 20000000 INFO @ Sat, 15 Sep 2018 11:32:14: 20000000 INFO @ Sat, 15 Sep 2018 11:32:16: 21000000 INFO @ Sat, 15 Sep 2018 11:32:16: 20000000 INFO @ Sat, 15 Sep 2018 11:32:20: 21000000 INFO @ Sat, 15 Sep 2018 11:32:22: 22000000 INFO @ Sat, 15 Sep 2018 11:32:23: 21000000 INFO @ Sat, 15 Sep 2018 11:32:27: 22000000 INFO @ Sat, 15 Sep 2018 11:32:28: 23000000 INFO @ Sat, 15 Sep 2018 11:32:29: 22000000 INFO @ Sat, 15 Sep 2018 11:32:33: 23000000 INFO @ Sat, 15 Sep 2018 11:32:34: 24000000 INFO @ Sat, 15 Sep 2018 11:32:36: 23000000 INFO @ Sat, 15 Sep 2018 11:32:40: 24000000 INFO @ Sat, 15 Sep 2018 11:32:40: 25000000 INFO @ Sat, 15 Sep 2018 11:32:42: 24000000 INFO @ Sat, 15 Sep 2018 11:32:46: 25000000 INFO @ Sat, 15 Sep 2018 11:32:47: 26000000 INFO @ Sat, 15 Sep 2018 11:32:49: 25000000 INFO @ Sat, 15 Sep 2018 11:32:53: 27000000 INFO @ Sat, 15 Sep 2018 11:32:53: 26000000 INFO @ Sat, 15 Sep 2018 11:32:56: 26000000 INFO @ Sat, 15 Sep 2018 11:32:59: 28000000 INFO @ Sat, 15 Sep 2018 11:33:00: 27000000 INFO @ Sat, 15 Sep 2018 11:33:02: 27000000 INFO @ Sat, 15 Sep 2018 11:33:06: 29000000 INFO @ Sat, 15 Sep 2018 11:33:06: 28000000 INFO @ Sat, 15 Sep 2018 11:33:09: 28000000 INFO @ Sat, 15 Sep 2018 11:33:12: 30000000 INFO @ Sat, 15 Sep 2018 11:33:13: 29000000 INFO @ Sat, 15 Sep 2018 11:33:15: 29000000 INFO @ Sat, 15 Sep 2018 11:33:19: 31000000 INFO @ Sat, 15 Sep 2018 11:33:20: 30000000 INFO @ Sat, 15 Sep 2018 11:33:21: 30000000 INFO @ Sat, 15 Sep 2018 11:33:25: 32000000 INFO @ Sat, 15 Sep 2018 11:33:27: 31000000 INFO @ Sat, 15 Sep 2018 11:33:28: 31000000 INFO @ Sat, 15 Sep 2018 11:33:32: 33000000 INFO @ Sat, 15 Sep 2018 11:33:34: 32000000 INFO @ Sat, 15 Sep 2018 11:33:34: 32000000 INFO @ Sat, 15 Sep 2018 11:33:37: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:33:37: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:33:37: #1 total tags in treatment: 33725233 INFO @ Sat, 15 Sep 2018 11:33:37: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:33:37: #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 11:33:38: #1 tags after filtering in treatment: 33725045 INFO @ Sat, 15 Sep 2018 11:33:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:33:38: #1 finished! INFO @ Sat, 15 Sep 2018 11:33:38: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:33:40: 33000000 INFO @ Sat, 15 Sep 2018 11:33:40: 33000000 INFO @ Sat, 15 Sep 2018 11:33:45: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:33:45: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:33:45: #1 total tags in treatment: 33725233 INFO @ Sat, 15 Sep 2018 11:33:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:33:45: #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 11:33:45: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:33:45: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:33:45: #1 total tags in treatment: 33725233 INFO @ Sat, 15 Sep 2018 11:33:45: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:33:45: #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 11:33:46: #1 tags after filtering in treatment: 33725045 INFO @ Sat, 15 Sep 2018 11:33:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:33:46: #1 finished! INFO @ Sat, 15 Sep 2018 11:33:46: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:33:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:33:46: #1 tags after filtering in treatment: 33725045 INFO @ Sat, 15 Sep 2018 11:33:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:33:46: #1 finished! INFO @ Sat, 15 Sep 2018 11:33:46: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:33:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:33:47: #2 number of paired peaks: 127238 INFO @ Sat, 15 Sep 2018 11:33:47: start model_add_line... INFO @ Sat, 15 Sep 2018 11:33:48: start X-correlation... INFO @ Sat, 15 Sep 2018 11:33:48: end of X-cor INFO @ Sat, 15 Sep 2018 11:33:48: #2 finished! INFO @ Sat, 15 Sep 2018 11:33:48: #2 predicted fragment length is 272 bps INFO @ Sat, 15 Sep 2018 11:33:48: #2 alternative fragment length(s) may be 4,272 bps INFO @ Sat, 15 Sep 2018 11:33:48: #2.2 Generate R script for model : SRX4014813.05_model.r INFO @ Sat, 15 Sep 2018 11:33:48: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:33:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:33:55: #2 number of paired peaks: 127238 INFO @ Sat, 15 Sep 2018 11:33:55: start model_add_line... INFO @ Sat, 15 Sep 2018 11:33:55: #2 number of paired peaks: 127238 INFO @ Sat, 15 Sep 2018 11:33:55: start model_add_line... INFO @ Sat, 15 Sep 2018 11:33:56: start X-correlation... INFO @ Sat, 15 Sep 2018 11:33:56: end of X-cor INFO @ Sat, 15 Sep 2018 11:33:56: #2 finished! INFO @ Sat, 15 Sep 2018 11:33:56: #2 predicted fragment length is 272 bps INFO @ Sat, 15 Sep 2018 11:33:56: #2 alternative fragment length(s) may be 4,272 bps INFO @ Sat, 15 Sep 2018 11:33:56: #2.2 Generate R script for model : SRX4014813.10_model.r INFO @ Sat, 15 Sep 2018 11:33:56: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:33:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:33:56: start X-correlation... INFO @ Sat, 15 Sep 2018 11:33:56: end of X-cor INFO @ Sat, 15 Sep 2018 11:33:56: #2 finished! INFO @ Sat, 15 Sep 2018 11:33:56: #2 predicted fragment length is 272 bps INFO @ Sat, 15 Sep 2018 11:33:56: #2 alternative fragment length(s) may be 4,272 bps INFO @ Sat, 15 Sep 2018 11:33:56: #2.2 Generate R script for model : SRX4014813.20_model.r INFO @ Sat, 15 Sep 2018 11:33:56: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:33:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:35:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:35:38: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:35:41: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:36:23: #4 Write output xls file... SRX4014813.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:36:24: #4 Write peak in narrowPeak format file... SRX4014813.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:36:24: #4 Write summits bed file... SRX4014813.05_summits.bed INFO @ Sat, 15 Sep 2018 11:36:24: Done! pass1 - making usageList (120 chroms): 6 millis pass2 - checking and writing primary data (30726 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:36:41: #4 Write output xls file... SRX4014813.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:36:41: #4 Write peak in narrowPeak format file... SRX4014813.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:36:41: #4 Write summits bed file... SRX4014813.10_summits.bed INFO @ Sat, 15 Sep 2018 11:36:42: Done! pass1 - making usageList (92 chroms): 5 millis pass2 - checking and writing primary data (20086 records, 4 fields): 27 millis INFO @ Sat, 15 Sep 2018 11:36:42: #4 Write output xls file... SRX4014813.20_peaks.xls CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:36:42: #4 Write peak in narrowPeak format file... SRX4014813.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:36:42: #4 Write summits bed file... SRX4014813.20_summits.bed INFO @ Sat, 15 Sep 2018 11:36:42: Done! pass1 - making usageList (67 chroms): 2 millis pass2 - checking and writing primary data (11130 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。