Job ID = 11192582 sra ファイルのダウンロード中... Completed: 602857K bytes transferred in 8 seconds (553045K 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 49754274 spots for /home/okishinya/chipatlas/results/rn6/SRX4014803/SRR7085052.sra Written 49754274 spots for /home/okishinya/chipatlas/results/rn6/SRX4014803/SRR7085052.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: 00:40:55 49754274 reads; of these: 49754274 (100.00%) were unpaired; of these: 1491652 (3.00%) aligned 0 times 42485711 (85.39%) aligned exactly 1 time 5776911 (11.61%) aligned >1 times 97.00% overall alignment rate Time searching: 00:40:59 Overall time: 00:40:59 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] 10209619 / 48262622 = 0.2115 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 11:47:23: # Command line: callpeak -t SRX4014803.bam -f BAM -g 2.15e9 -n SRX4014803.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4014803.20 # format = BAM # ChIP-seq file = ['SRX4014803.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 11:47:23: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:47:23: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:47:23: # Command line: callpeak -t SRX4014803.bam -f BAM -g 2.15e9 -n SRX4014803.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4014803.05 # format = BAM # ChIP-seq file = ['SRX4014803.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 11:47:23: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:47:23: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:47:23: # Command line: callpeak -t SRX4014803.bam -f BAM -g 2.15e9 -n SRX4014803.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4014803.10 # format = BAM # ChIP-seq file = ['SRX4014803.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 11:47:23: #1 read tag files... INFO @ Sat, 15 Sep 2018 11:47:23: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 11:47:31: 1000000 INFO @ Sat, 15 Sep 2018 11:47:31: 1000000 INFO @ Sat, 15 Sep 2018 11:47:31: 1000000 INFO @ Sat, 15 Sep 2018 11:47:38: 2000000 INFO @ Sat, 15 Sep 2018 11:47:38: 2000000 INFO @ Sat, 15 Sep 2018 11:47:39: 2000000 INFO @ Sat, 15 Sep 2018 11:47:45: 3000000 INFO @ Sat, 15 Sep 2018 11:47:46: 3000000 INFO @ Sat, 15 Sep 2018 11:47:46: 3000000 INFO @ Sat, 15 Sep 2018 11:47:53: 4000000 INFO @ Sat, 15 Sep 2018 11:47:53: 4000000 INFO @ Sat, 15 Sep 2018 11:47:53: 4000000 INFO @ Sat, 15 Sep 2018 11:48:00: 5000000 INFO @ Sat, 15 Sep 2018 11:48:01: 5000000 INFO @ Sat, 15 Sep 2018 11:48:01: 5000000 INFO @ Sat, 15 Sep 2018 11:48:07: 6000000 INFO @ Sat, 15 Sep 2018 11:48:08: 6000000 INFO @ Sat, 15 Sep 2018 11:48:09: 6000000 INFO @ Sat, 15 Sep 2018 11:48:15: 7000000 INFO @ Sat, 15 Sep 2018 11:48:16: 7000000 INFO @ Sat, 15 Sep 2018 11:48:16: 7000000 INFO @ Sat, 15 Sep 2018 11:48:22: 8000000 INFO @ Sat, 15 Sep 2018 11:48:23: 8000000 INFO @ Sat, 15 Sep 2018 11:48:24: 8000000 INFO @ Sat, 15 Sep 2018 11:48:29: 9000000 INFO @ Sat, 15 Sep 2018 11:48:31: 9000000 INFO @ Sat, 15 Sep 2018 11:48:32: 9000000 INFO @ Sat, 15 Sep 2018 11:48:37: 10000000 INFO @ Sat, 15 Sep 2018 11:48:38: 10000000 INFO @ Sat, 15 Sep 2018 11:48:39: 10000000 INFO @ Sat, 15 Sep 2018 11:48:44: 11000000 INFO @ Sat, 15 Sep 2018 11:48:45: 11000000 INFO @ Sat, 15 Sep 2018 11:48:47: 11000000 INFO @ Sat, 15 Sep 2018 11:48:52: 12000000 INFO @ Sat, 15 Sep 2018 11:48:53: 12000000 INFO @ Sat, 15 Sep 2018 11:48:55: 12000000 INFO @ Sat, 15 Sep 2018 11:48:59: 13000000 INFO @ Sat, 15 Sep 2018 11:49:00: 13000000 INFO @ Sat, 15 Sep 2018 11:49:02: 13000000 INFO @ Sat, 15 Sep 2018 11:49:07: 14000000 INFO @ Sat, 15 Sep 2018 11:49:08: 14000000 INFO @ Sat, 15 Sep 2018 11:49:10: 14000000 INFO @ Sat, 15 Sep 2018 11:49:14: 15000000 INFO @ Sat, 15 Sep 2018 11:49:15: 15000000 INFO @ Sat, 15 Sep 2018 11:49:17: 15000000 INFO @ Sat, 15 Sep 2018 11:49:21: 16000000 INFO @ Sat, 15 Sep 2018 11:49:22: 16000000 INFO @ Sat, 15 Sep 2018 11:49:25: 16000000 INFO @ Sat, 15 Sep 2018 11:49:29: 17000000 INFO @ Sat, 15 Sep 2018 11:49:30: 17000000 INFO @ Sat, 15 Sep 2018 11:49:33: 17000000 INFO @ Sat, 15 Sep 2018 11:49:36: 18000000 INFO @ Sat, 15 Sep 2018 11:49:37: 18000000 INFO @ Sat, 15 Sep 2018 11:49:40: 18000000 INFO @ Sat, 15 Sep 2018 11:49:43: 19000000 INFO @ Sat, 15 Sep 2018 11:49:44: 19000000 INFO @ Sat, 15 Sep 2018 11:49:48: 19000000 INFO @ Sat, 15 Sep 2018 11:49:51: 20000000 INFO @ Sat, 15 Sep 2018 11:49:52: 20000000 INFO @ Sat, 15 Sep 2018 11:49:56: 20000000 INFO @ Sat, 15 Sep 2018 11:49:59: 21000000 INFO @ Sat, 15 Sep 2018 11:49:59: 21000000 INFO @ Sat, 15 Sep 2018 11:50:04: 21000000 INFO @ Sat, 15 Sep 2018 11:50:06: 22000000 INFO @ Sat, 15 Sep 2018 11:50:07: 22000000 INFO @ Sat, 15 Sep 2018 11:50:12: 22000000 INFO @ Sat, 15 Sep 2018 11:50:14: 23000000 INFO @ Sat, 15 Sep 2018 11:50:14: 23000000 INFO @ Sat, 15 Sep 2018 11:50:20: 23000000 INFO @ Sat, 15 Sep 2018 11:50:21: 24000000 INFO @ Sat, 15 Sep 2018 11:50:22: 24000000 INFO @ Sat, 15 Sep 2018 11:50:27: 24000000 INFO @ Sat, 15 Sep 2018 11:50:29: 25000000 INFO @ Sat, 15 Sep 2018 11:50:29: 25000000 INFO @ Sat, 15 Sep 2018 11:50:35: 25000000 INFO @ Sat, 15 Sep 2018 11:50:37: 26000000 INFO @ Sat, 15 Sep 2018 11:50:37: 26000000 INFO @ Sat, 15 Sep 2018 11:50:43: 26000000 INFO @ Sat, 15 Sep 2018 11:50:44: 27000000 INFO @ Sat, 15 Sep 2018 11:50:44: 27000000 INFO @ Sat, 15 Sep 2018 11:50:51: 27000000 INFO @ Sat, 15 Sep 2018 11:50:52: 28000000 INFO @ Sat, 15 Sep 2018 11:50:52: 28000000 INFO @ Sat, 15 Sep 2018 11:50:59: 28000000 INFO @ Sat, 15 Sep 2018 11:50:59: 29000000 INFO @ Sat, 15 Sep 2018 11:50:59: 29000000 INFO @ Sat, 15 Sep 2018 11:51:06: 30000000 INFO @ Sat, 15 Sep 2018 11:51:07: 29000000 INFO @ Sat, 15 Sep 2018 11:51:07: 30000000 INFO @ Sat, 15 Sep 2018 11:51:14: 31000000 INFO @ Sat, 15 Sep 2018 11:51:15: 30000000 INFO @ Sat, 15 Sep 2018 11:51:15: 31000000 INFO @ Sat, 15 Sep 2018 11:51:21: 32000000 INFO @ Sat, 15 Sep 2018 11:51:22: 32000000 INFO @ Sat, 15 Sep 2018 11:51:22: 31000000 INFO @ Sat, 15 Sep 2018 11:51:29: 33000000 INFO @ Sat, 15 Sep 2018 11:51:30: 33000000 INFO @ Sat, 15 Sep 2018 11:51:30: 32000000 INFO @ Sat, 15 Sep 2018 11:51:36: 34000000 INFO @ Sat, 15 Sep 2018 11:51:38: 34000000 INFO @ Sat, 15 Sep 2018 11:51:38: 33000000 INFO @ Sat, 15 Sep 2018 11:51:43: 35000000 INFO @ Sat, 15 Sep 2018 11:51:45: 35000000 INFO @ Sat, 15 Sep 2018 11:51:46: 34000000 INFO @ Sat, 15 Sep 2018 11:51:51: 36000000 INFO @ Sat, 15 Sep 2018 11:51:53: 36000000 INFO @ Sat, 15 Sep 2018 11:51:54: 35000000 INFO @ Sat, 15 Sep 2018 11:51:58: 37000000 INFO @ Sat, 15 Sep 2018 11:52:00: 37000000 INFO @ Sat, 15 Sep 2018 11:52:02: 36000000 INFO @ Sat, 15 Sep 2018 11:52:06: 38000000 INFO @ Sat, 15 Sep 2018 11:52:06: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:52:06: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:52:06: #1 total tags in treatment: 38053003 INFO @ Sat, 15 Sep 2018 11:52:06: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:52:06: #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 11:52:07: #1 tags after filtering in treatment: 38052832 INFO @ Sat, 15 Sep 2018 11:52:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:52:07: #1 finished! INFO @ Sat, 15 Sep 2018 11:52:07: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:52:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:52:08: 38000000 INFO @ Sat, 15 Sep 2018 11:52:09: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:52:09: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:52:09: #1 total tags in treatment: 38053003 INFO @ Sat, 15 Sep 2018 11:52:09: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:52:09: #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 11:52:09: 37000000 INFO @ Sat, 15 Sep 2018 11:52:10: #1 tags after filtering in treatment: 38052832 INFO @ Sat, 15 Sep 2018 11:52:10: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:52:10: #1 finished! INFO @ Sat, 15 Sep 2018 11:52:10: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:52:10: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:52:17: 38000000 INFO @ Sat, 15 Sep 2018 11:52:17: #2 number of paired peaks: 137492 INFO @ Sat, 15 Sep 2018 11:52:17: start model_add_line... INFO @ Sat, 15 Sep 2018 11:52:17: #1 tag size is determined as 75 bps INFO @ Sat, 15 Sep 2018 11:52:17: #1 tag size = 75 INFO @ Sat, 15 Sep 2018 11:52:17: #1 total tags in treatment: 38053003 INFO @ Sat, 15 Sep 2018 11:52:17: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 11:52:17: #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 11:52:18: start X-correlation... INFO @ Sat, 15 Sep 2018 11:52:18: end of X-cor INFO @ Sat, 15 Sep 2018 11:52:18: #2 finished! INFO @ Sat, 15 Sep 2018 11:52:18: #2 predicted fragment length is 249 bps INFO @ Sat, 15 Sep 2018 11:52:18: #2 alternative fragment length(s) may be 249 bps INFO @ Sat, 15 Sep 2018 11:52:18: #2.2 Generate R script for model : SRX4014803.10_model.r INFO @ Sat, 15 Sep 2018 11:52:18: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:52:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:52:18: #1 tags after filtering in treatment: 38052832 INFO @ Sat, 15 Sep 2018 11:52:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 11:52:18: #1 finished! INFO @ Sat, 15 Sep 2018 11:52:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 11:52:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 11:52:20: #2 number of paired peaks: 137492 INFO @ Sat, 15 Sep 2018 11:52:20: start model_add_line... INFO @ Sat, 15 Sep 2018 11:52:21: start X-correlation... INFO @ Sat, 15 Sep 2018 11:52:21: end of X-cor INFO @ Sat, 15 Sep 2018 11:52:21: #2 finished! INFO @ Sat, 15 Sep 2018 11:52:21: #2 predicted fragment length is 249 bps INFO @ Sat, 15 Sep 2018 11:52:21: #2 alternative fragment length(s) may be 249 bps INFO @ Sat, 15 Sep 2018 11:52:21: #2.2 Generate R script for model : SRX4014803.05_model.r INFO @ Sat, 15 Sep 2018 11:52:21: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:52:28: #2 number of paired peaks: 137492 INFO @ Sat, 15 Sep 2018 11:52:28: start model_add_line... INFO @ Sat, 15 Sep 2018 11:52:29: start X-correlation... INFO @ Sat, 15 Sep 2018 11:52:29: end of X-cor INFO @ Sat, 15 Sep 2018 11:52:29: #2 finished! INFO @ Sat, 15 Sep 2018 11:52:29: #2 predicted fragment length is 249 bps INFO @ Sat, 15 Sep 2018 11:52:29: #2 alternative fragment length(s) may be 249 bps INFO @ Sat, 15 Sep 2018 11:52:29: #2.2 Generate R script for model : SRX4014803.20_model.r INFO @ Sat, 15 Sep 2018 11:52:29: #3 Call peaks... INFO @ Sat, 15 Sep 2018 11:52:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 11:54:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:54:13: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:54:14: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 11:55:10: #4 Write output xls file... SRX4014803.10_peaks.xls INFO @ Sat, 15 Sep 2018 11:55:10: #4 Write peak in narrowPeak format file... SRX4014803.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:55:10: #4 Write summits bed file... SRX4014803.10_summits.bed INFO @ Sat, 15 Sep 2018 11:55:10: Done! pass1 - making usageList (107 chroms): 14 millis pass2 - checking and writing primary data (18869 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:55:18: #4 Write output xls file... SRX4014803.05_peaks.xls INFO @ Sat, 15 Sep 2018 11:55:18: #4 Write peak in narrowPeak format file... SRX4014803.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:55:18: #4 Write summits bed file... SRX4014803.05_summits.bed INFO @ Sat, 15 Sep 2018 11:55:18: Done! pass1 - making usageList (134 chroms): 6 millis pass2 - checking and writing primary data (29599 records, 4 fields): 39 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 11:55:19: #4 Write output xls file... SRX4014803.20_peaks.xls INFO @ Sat, 15 Sep 2018 11:55:19: #4 Write peak in narrowPeak format file... SRX4014803.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 11:55:20: #4 Write summits bed file... SRX4014803.20_summits.bed INFO @ Sat, 15 Sep 2018 11:55:20: Done! pass1 - making usageList (78 chroms): 3 millis pass2 - checking and writing primary data (10951 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。