Job ID = 11192595 sra ファイルのダウンロード中... Completed: 326769K bytes transferred in 31 seconds (85448K 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 31213103 spots for /home/okishinya/chipatlas/results/rn6/SRX4014815/SRR7085064.sra Written 31213103 spots for /home/okishinya/chipatlas/results/rn6/SRX4014815/SRR7085064.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: 00:31:08 31213103 reads; of these: 31213103 (100.00%) were unpaired; of these: 940103 (3.01%) aligned 0 times 27026672 (86.59%) aligned exactly 1 time 3246328 (10.40%) aligned >1 times 96.99% overall alignment rate Time searching: 00:31:10 Overall time: 00:31:10 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] 3140519 / 30273000 = 0.1037 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 11:20:02: # Command line: callpeak -t SRX4014815.bam -f BAM -g 2.15e9 -n SRX4014815.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014815.20 # format = BAM # ChIP-seq file = ['SRX4014815.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 11:20:02: # Command line: callpeak -t SRX4014815.bam -f BAM -g 2.15e9 -n SRX4014815.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014815.05 # format = BAM # ChIP-seq file = ['SRX4014815.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 11:20:02: # Command line: callpeak -t SRX4014815.bam -f BAM -g 2.15e9 -n SRX4014815.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014815.10 # format = BAM # ChIP-seq file = ['SRX4014815.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 11:20:02: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:20:02: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:20:02: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:20:02: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:20:02: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:20:02: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:20:09: 1000000 INFO @ Sat, 15 Sep 2018 11:20:09: 1000000 INFO @ Sat, 15 Sep 2018 11:20:09: 1000000 INFO @ Sat, 15 Sep 2018 11:20:16: 2000000 INFO @ Sat, 15 Sep 2018 11:20:16: 2000000 INFO @ Sat, 15 Sep 2018 11:20:16: 2000000 INFO @ Sat, 15 Sep 2018 11:20:23: 3000000 INFO @ Sat, 15 Sep 2018 11:20:23: 3000000 INFO @ Sat, 15 Sep 2018 11:20:23: 3000000 INFO @ Sat, 15 Sep 2018 11:20:30: 4000000 INFO @ Sat, 15 Sep 2018 11:20:30: 4000000 INFO @ Sat, 15 Sep 2018 11:20:30: 4000000 INFO @ Sat, 15 Sep 2018 11:20:37: 5000000 INFO @ Sat, 15 Sep 2018 11:20:37: 5000000 INFO @ Sat, 15 Sep 2018 11:20:37: 5000000 INFO @ Sat, 15 Sep 2018 11:20:44: 6000000 INFO @ Sat, 15 Sep 2018 11:20:45: 6000000 INFO @ Sat, 15 Sep 2018 11:20:45: 6000000 INFO @ Sat, 15 Sep 2018 11:20:51: 7000000 INFO @ Sat, 15 Sep 2018 11:20:52: 7000000 INFO @ Sat, 15 Sep 2018 11:20:52: 7000000 INFO @ Sat, 15 Sep 2018 11:20:57: 8000000 INFO @ Sat, 15 Sep 2018 11:20:59: 8000000 INFO @ Sat, 15 Sep 2018 11:20:59: 8000000 INFO @ Sat, 15 Sep 2018 11:21:04: 9000000 INFO @ Sat, 15 Sep 2018 11:21:06: 9000000 INFO @ Sat, 15 Sep 2018 11:21:06: 9000000 INFO @ Sat, 15 Sep 2018 11:21:11: 10000000 INFO @ Sat, 15 Sep 2018 11:21:13: 10000000 INFO @ Sat, 15 Sep 2018 11:21:13: 10000000 INFO @ Sat, 15 Sep 2018 11:21:18: 11000000 INFO @ Sat, 15 Sep 2018 11:21:19: 11000000 INFO @ Sat, 15 Sep 2018 11:21:20: 11000000 INFO @ Sat, 15 Sep 2018 11:21:25: 12000000 INFO @ Sat, 15 Sep 2018 11:21:26: 12000000 INFO @ Sat, 15 Sep 2018 11:21:27: 12000000 INFO @ Sat, 15 Sep 2018 11:21:32: 13000000 INFO @ Sat, 15 Sep 2018 11:21:33: 13000000 INFO @ Sat, 15 Sep 2018 11:21:33: 13000000 INFO @ Sat, 15 Sep 2018 11:21:39: 14000000 INFO @ Sat, 15 Sep 2018 11:21:40: 14000000 INFO @ Sat, 15 Sep 2018 11:21:41: 14000000 INFO @ Sat, 15 Sep 2018 11:21:46: 15000000 INFO @ Sat, 15 Sep 2018 11:21:47: 15000000 INFO @ Sat, 15 Sep 2018 11:21:48: 15000000 INFO @ Sat, 15 Sep 2018 11:21:52: 16000000 INFO @ Sat, 15 Sep 2018 11:21:54: 16000000 INFO @ Sat, 15 Sep 2018 11:21:55: 16000000 INFO @ Sat, 15 Sep 2018 11:21:59: 17000000 INFO @ Sat, 15 Sep 2018 11:22:02: 17000000 INFO @ Sat, 15 Sep 2018 11:22:02: 17000000 INFO @ Sat, 15 Sep 2018 11:22:06: 18000000 INFO @ Sat, 15 Sep 2018 11:22:09: 18000000 INFO @ Sat, 15 Sep 2018 11:22:09: 18000000 INFO @ Sat, 15 Sep 2018 11:22:13: 19000000 INFO @ Sat, 15 Sep 2018 11:22:16: 19000000 INFO @ Sat, 15 Sep 2018 11:22:17: 19000000 INFO @ Sat, 15 Sep 2018 11:22:20: 20000000 INFO @ Sat, 15 Sep 2018 11:22:23: 20000000 INFO @ Sat, 15 Sep 2018 11:22:24: 20000000 INFO @ Sat, 15 Sep 2018 11:22:27: 21000000 INFO @ Sat, 15 Sep 2018 11:22:31: 21000000 INFO @ Sat, 15 Sep 2018 11:22:31: 21000000 INFO @ Sat, 15 Sep 2018 11:22:34: 22000000 INFO @ Sat, 15 Sep 2018 11:22:38: 22000000 INFO @ Sat, 15 Sep 2018 11:22:39: 22000000 INFO @ Sat, 15 Sep 2018 11:22:41: 23000000 INFO @ Sat, 15 Sep 2018 11:22:45: 23000000 INFO @ Sat, 15 Sep 2018 11:22:46: 23000000 INFO @ Sat, 15 Sep 2018 11:22:48: 24000000 INFO @ Sat, 15 Sep 2018 11:22:53: 24000000 INFO @ Sat, 15 Sep 2018 11:22:53: 24000000 INFO @ Sat, 15 Sep 2018 11:22:55: 25000000 INFO @ Sat, 15 Sep 2018 11:23:00: 25000000 INFO @ Sat, 15 Sep 2018 11:23:01: 25000000 INFO @ Sat, 15 Sep 2018 11:23:01: 26000000 INFO @ Sat, 15 Sep 2018 11:23:07: 26000000 INFO @ Sat, 15 Sep 2018 11:23:08: 26000000 INFO @ Sat, 15 Sep 2018 11:23:09: 27000000 INFO @ Sat, 15 Sep 2018 11:23:10: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:23:10: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:23:10: #1 total tags in treatment: 27132481 INFO @ Sat, 15 Sep 2018 11:23:10: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:23:10: #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 11:23:10: #1 tags after filtering in treatment: 27132287 INFO @ Sat, 15 Sep 2018 11:23:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:23:10: #1 finished! INFO @ Sat, 15 Sep 2018 11:23:10: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:23:15: 27000000 INFO @ Sat, 15 Sep 2018 11:23:16: 27000000 INFO @ Sat, 15 Sep 2018 11:23:16: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:23:16: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:23:16: #1 total tags in treatment: 27132481 INFO @ Sat, 15 Sep 2018 11:23:16: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:23:16: #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 11:23:17: #1 tags after filtering in treatment: 27132287 INFO @ Sat, 15 Sep 2018 11:23:17: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:23:17: #1 finished! INFO @ Sat, 15 Sep 2018 11:23:17: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:23:17: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:23:17: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:23:17: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:23:17: #1 total tags in treatment: 27132481 INFO @ Sat, 15 Sep 2018 11:23:17: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:23:17: #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 11:23:18: #1 tags after filtering in treatment: 27132287 INFO @ Sat, 15 Sep 2018 11:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:23:18: #1 finished! INFO @ Sat, 15 Sep 2018 11:23:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:23:19: #2 number of paired peaks: 155155 INFO @ Sat, 15 Sep 2018 11:23:19: start model_add_line... INFO @ Sat, 15 Sep 2018 11:23:19: start X-correlation... INFO @ Sat, 15 Sep 2018 11:23:19: end of X-cor INFO @ Sat, 15 Sep 2018 11:23:19: #2 finished! INFO @ Sat, 15 Sep 2018 11:23:19: #2 predicted fragment length is 243 bps INFO @ Sat, 15 Sep 2018 11:23:19: #2 alternative fragment length(s) may be 4,243 bps INFO @ Sat, 15 Sep 2018 11:23:19: #2.2 Generate R script for model : SRX4014815.10_model.r INFO @ Sat, 15 Sep 2018 11:23:19: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:23:25: #2 number of paired peaks: 155155 INFO @ Sat, 15 Sep 2018 11:23:25: start model_add_line... INFO @ Sat, 15 Sep 2018 11:23:26: start X-correlation... INFO @ Sat, 15 Sep 2018 11:23:26: end of X-cor INFO @ Sat, 15 Sep 2018 11:23:26: #2 finished! INFO @ Sat, 15 Sep 2018 11:23:26: #2 predicted fragment length is 243 bps INFO @ Sat, 15 Sep 2018 11:23:26: #2 alternative fragment length(s) may be 4,243 bps INFO @ Sat, 15 Sep 2018 11:23:26: #2.2 Generate R script for model : SRX4014815.20_model.r INFO @ Sat, 15 Sep 2018 11:23:26: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:23:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:23:26: #2 number of paired peaks: 155155 INFO @ Sat, 15 Sep 2018 11:23:26: start model_add_line... INFO @ Sat, 15 Sep 2018 11:23:27: start X-correlation... INFO @ Sat, 15 Sep 2018 11:23:27: end of X-cor INFO @ Sat, 15 Sep 2018 11:23:27: #2 finished! INFO @ Sat, 15 Sep 2018 11:23:27: #2 predicted fragment length is 243 bps INFO @ Sat, 15 Sep 2018 11:23:27: #2 alternative fragment length(s) may be 4,243 bps INFO @ Sat, 15 Sep 2018 11:23:27: #2.2 Generate R script for model : SRX4014815.05_model.r INFO @ Sat, 15 Sep 2018 11:23:27: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:23:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:24:34: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:24:37: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:24:44: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:25:17: #4 Write output xls file... SRX4014815.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:25:17: #4 Write peak in narrowPeak format file... SRX4014815.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:25:17: #4 Write summits bed file... SRX4014815.10_summits.bed INFO @ Sat, 15 Sep 2018 11:25:17: Done! pass1 - making usageList (76 chroms): 1 millis pass2 - checking and writing primary data (5441 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:25:20: #4 Write output xls file... SRX4014815.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:25:20: #4 Write peak in narrowPeak format file... SRX4014815.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:25:20: #4 Write summits bed file... SRX4014815.20_summits.bed INFO @ Sat, 15 Sep 2018 11:25:20: Done! pass1 - making usageList (49 chroms): 1 millis pass2 - checking and writing primary data (1141 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:25:26: #4 Write output xls file... SRX4014815.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:25:26: #4 Write peak in narrowPeak format file... SRX4014815.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:25:26: #4 Write summits bed file... SRX4014815.05_summits.bed INFO @ Sat, 15 Sep 2018 11:25:27: Done! pass1 - making usageList (120 chroms): 4 millis pass2 - checking and writing primary data (17745 records, 4 fields): 25 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。