Job ID = 10487603 sra ファイルのダウンロード中... Completed: 994639K bytes transferred in 25 seconds (316352K 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... Written 35888444 spots for /home/okishinya/chipatlas/results/rn6/SRX3087683/SRR5927319.sra Written 35888444 spots total 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:44:37 35888444 reads; of these: 35888444 (100.00%) were unpaired; of these: 1733788 (4.83%) aligned 0 times 28071554 (78.22%) aligned exactly 1 time 6083102 (16.95%) aligned >1 times 95.17% overall alignment rate Time searching: 00:44:40 Overall time: 00:44:40 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] 5491373 / 34154656 = 0.1608 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 @ Sun, 18 Mar 2018 10:45:59: # Command line: callpeak -t SRX3087683.bam -f BAM -g 2.15e9 -n SRX3087683.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087683.10 # format = BAM # ChIP-seq file = ['SRX3087683.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 @ Sun, 18 Mar 2018 10:45:59: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:45:59: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:45:59: # Command line: callpeak -t SRX3087683.bam -f BAM -g 2.15e9 -n SRX3087683.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087683.20 # format = BAM # ChIP-seq file = ['SRX3087683.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 @ Sun, 18 Mar 2018 10:45:59: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:45:59: # Command line: callpeak -t SRX3087683.bam -f BAM -g 2.15e9 -n SRX3087683.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087683.05 # format = BAM # ChIP-seq file = ['SRX3087683.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 @ Sun, 18 Mar 2018 10:45:59: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:45:59: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:45:59: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:46:06: 1000000 INFO @ Sun, 18 Mar 2018 10:46:06: 1000000 INFO @ Sun, 18 Mar 2018 10:46:07: 1000000 INFO @ Sun, 18 Mar 2018 10:46:13: 2000000 INFO @ Sun, 18 Mar 2018 10:46:14: 2000000 INFO @ Sun, 18 Mar 2018 10:46:15: 2000000 INFO @ Sun, 18 Mar 2018 10:46:20: 3000000 INFO @ Sun, 18 Mar 2018 10:46:21: 3000000 INFO @ Sun, 18 Mar 2018 10:46:23: 3000000 INFO @ Sun, 18 Mar 2018 10:46:27: 4000000 INFO @ Sun, 18 Mar 2018 10:46:28: 4000000 INFO @ Sun, 18 Mar 2018 10:46:31: 4000000 INFO @ Sun, 18 Mar 2018 10:46:34: 5000000 INFO @ Sun, 18 Mar 2018 10:46:36: 5000000 INFO @ Sun, 18 Mar 2018 10:46:39: 5000000 INFO @ Sun, 18 Mar 2018 10:46:41: 6000000 INFO @ Sun, 18 Mar 2018 10:46:43: 6000000 INFO @ Sun, 18 Mar 2018 10:46:47: 6000000 INFO @ Sun, 18 Mar 2018 10:46:48: 7000000 INFO @ Sun, 18 Mar 2018 10:46:50: 7000000 INFO @ Sun, 18 Mar 2018 10:46:55: 7000000 INFO @ Sun, 18 Mar 2018 10:46:55: 8000000 INFO @ Sun, 18 Mar 2018 10:46:57: 8000000 INFO @ Sun, 18 Mar 2018 10:47:02: 9000000 INFO @ Sun, 18 Mar 2018 10:47:02: 8000000 INFO @ Sun, 18 Mar 2018 10:47:04: 9000000 INFO @ Sun, 18 Mar 2018 10:47:09: 10000000 INFO @ Sun, 18 Mar 2018 10:47:10: 9000000 INFO @ Sun, 18 Mar 2018 10:47:11: 10000000 INFO @ Sun, 18 Mar 2018 10:47:17: 11000000 INFO @ Sun, 18 Mar 2018 10:47:17: 10000000 INFO @ Sun, 18 Mar 2018 10:47:18: 11000000 INFO @ Sun, 18 Mar 2018 10:47:24: 12000000 INFO @ Sun, 18 Mar 2018 10:47:25: 11000000 INFO @ Sun, 18 Mar 2018 10:47:25: 12000000 INFO @ Sun, 18 Mar 2018 10:47:31: 13000000 INFO @ Sun, 18 Mar 2018 10:47:32: 12000000 INFO @ Sun, 18 Mar 2018 10:47:32: 13000000 INFO @ Sun, 18 Mar 2018 10:47:39: 14000000 INFO @ Sun, 18 Mar 2018 10:47:39: 14000000 INFO @ Sun, 18 Mar 2018 10:47:40: 13000000 INFO @ Sun, 18 Mar 2018 10:47:46: 15000000 INFO @ Sun, 18 Mar 2018 10:47:46: 15000000 INFO @ Sun, 18 Mar 2018 10:47:47: 14000000 INFO @ Sun, 18 Mar 2018 10:47:53: 16000000 INFO @ Sun, 18 Mar 2018 10:47:53: 16000000 INFO @ Sun, 18 Mar 2018 10:47:55: 15000000 INFO @ Sun, 18 Mar 2018 10:48:00: 17000000 INFO @ Sun, 18 Mar 2018 10:48:01: 17000000 INFO @ Sun, 18 Mar 2018 10:48:02: 16000000 INFO @ Sun, 18 Mar 2018 10:48:07: 18000000 INFO @ Sun, 18 Mar 2018 10:48:08: 18000000 INFO @ Sun, 18 Mar 2018 10:48:10: 17000000 INFO @ Sun, 18 Mar 2018 10:48:14: 19000000 INFO @ Sun, 18 Mar 2018 10:48:15: 19000000 INFO @ Sun, 18 Mar 2018 10:48:17: 18000000 INFO @ Sun, 18 Mar 2018 10:48:21: 20000000 INFO @ Sun, 18 Mar 2018 10:48:23: 20000000 INFO @ Sun, 18 Mar 2018 10:48:25: 19000000 INFO @ Sun, 18 Mar 2018 10:48:28: 21000000 INFO @ Sun, 18 Mar 2018 10:48:30: 21000000 INFO @ Sun, 18 Mar 2018 10:48:32: 20000000 INFO @ Sun, 18 Mar 2018 10:48:35: 22000000 INFO @ Sun, 18 Mar 2018 10:48:37: 22000000 INFO @ Sun, 18 Mar 2018 10:48:40: 21000000 INFO @ Sun, 18 Mar 2018 10:48:42: 23000000 INFO @ Sun, 18 Mar 2018 10:48:45: 23000000 INFO @ Sun, 18 Mar 2018 10:48:47: 22000000 INFO @ Sun, 18 Mar 2018 10:48:49: 24000000 INFO @ Sun, 18 Mar 2018 10:48:52: 24000000 INFO @ Sun, 18 Mar 2018 10:48:55: 23000000 INFO @ Sun, 18 Mar 2018 10:48:56: 25000000 INFO @ Sun, 18 Mar 2018 10:48:59: 25000000 INFO @ Sun, 18 Mar 2018 10:49:02: 24000000 INFO @ Sun, 18 Mar 2018 10:49:03: 26000000 INFO @ Sun, 18 Mar 2018 10:49:07: 26000000 INFO @ Sun, 18 Mar 2018 10:49:10: 25000000 INFO @ Sun, 18 Mar 2018 10:49:10: 27000000 INFO @ Sun, 18 Mar 2018 10:49:14: 27000000 INFO @ Sun, 18 Mar 2018 10:49:17: 26000000 INFO @ Sun, 18 Mar 2018 10:49:17: 28000000 INFO @ Sun, 18 Mar 2018 10:49:22: 28000000 INFO @ Sun, 18 Mar 2018 10:49:22: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 10:49:22: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 10:49:22: #1 total tags in treatment: 28663283 INFO @ Sun, 18 Mar 2018 10:49:22: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:49:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 10:49:23: #1 tags after filtering in treatment: 28663146 INFO @ Sun, 18 Mar 2018 10:49:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:49:23: #1 finished! INFO @ Sun, 18 Mar 2018 10:49:23: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:49:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:49:25: 27000000 INFO @ Sun, 18 Mar 2018 10:49:27: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 10:49:27: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 10:49:27: #1 total tags in treatment: 28663283 INFO @ Sun, 18 Mar 2018 10:49:27: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:49:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 10:49:27: #2 number of paired peaks: 32508 INFO @ Sun, 18 Mar 2018 10:49:27: start model_add_line... INFO @ Sun, 18 Mar 2018 10:49:28: start X-correlation... INFO @ Sun, 18 Mar 2018 10:49:28: end of X-cor INFO @ Sun, 18 Mar 2018 10:49:28: #2 finished! INFO @ Sun, 18 Mar 2018 10:49:28: #2 predicted fragment length is 270 bps INFO @ Sun, 18 Mar 2018 10:49:28: #2 alternative fragment length(s) may be 270 bps INFO @ Sun, 18 Mar 2018 10:49:28: #2.2 Generate R script for model : SRX3087683.10_model.r INFO @ Sun, 18 Mar 2018 10:49:28: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:49:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:49:28: #1 tags after filtering in treatment: 28663146 INFO @ Sun, 18 Mar 2018 10:49:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:49:28: #1 finished! INFO @ Sun, 18 Mar 2018 10:49:28: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:49:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:49:31: #2 number of paired peaks: 32508 INFO @ Sun, 18 Mar 2018 10:49:31: start model_add_line... INFO @ Sun, 18 Mar 2018 10:49:32: start X-correlation... INFO @ Sun, 18 Mar 2018 10:49:32: end of X-cor INFO @ Sun, 18 Mar 2018 10:49:32: #2 finished! INFO @ Sun, 18 Mar 2018 10:49:32: #2 predicted fragment length is 270 bps INFO @ Sun, 18 Mar 2018 10:49:32: #2 alternative fragment length(s) may be 270 bps INFO @ Sun, 18 Mar 2018 10:49:32: #2.2 Generate R script for model : SRX3087683.20_model.r INFO @ Sun, 18 Mar 2018 10:49:32: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:49:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:49:32: 28000000 INFO @ Sun, 18 Mar 2018 10:49:37: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 10:49:37: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 10:49:37: #1 total tags in treatment: 28663283 INFO @ Sun, 18 Mar 2018 10:49:37: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:49:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 10:49:38: #1 tags after filtering in treatment: 28663146 INFO @ Sun, 18 Mar 2018 10:49:38: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:49:38: #1 finished! INFO @ Sun, 18 Mar 2018 10:49:38: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:49:38: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:49:42: #2 number of paired peaks: 32508 INFO @ Sun, 18 Mar 2018 10:49:42: start model_add_line... INFO @ Sun, 18 Mar 2018 10:49:42: start X-correlation... INFO @ Sun, 18 Mar 2018 10:49:42: end of X-cor INFO @ Sun, 18 Mar 2018 10:49:42: #2 finished! INFO @ Sun, 18 Mar 2018 10:49:42: #2 predicted fragment length is 270 bps INFO @ Sun, 18 Mar 2018 10:49:42: #2 alternative fragment length(s) may be 270 bps INFO @ Sun, 18 Mar 2018 10:49:42: #2.2 Generate R script for model : SRX3087683.05_model.r INFO @ Sun, 18 Mar 2018 10:49:42: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:49:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:50:38: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:50:44: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:50:52: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:51:20: #4 Write output xls file... SRX3087683.10_peaks.xls INFO @ Sun, 18 Mar 2018 10:51:20: #4 Write peak in narrowPeak format file... SRX3087683.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:51:20: #4 Write summits bed file... SRX3087683.10_summits.bed INFO @ Sun, 18 Mar 2018 10:51:20: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (1850 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 10:51:23: #4 Write output xls file... SRX3087683.20_peaks.xls INFO @ Sun, 18 Mar 2018 10:51:23: #4 Write peak in narrowPeak format file... SRX3087683.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:51:23: #4 Write summits bed file... SRX3087683.20_summits.bed INFO @ Sun, 18 Mar 2018 10:51:23: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (161 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 10:51:29: #4 Write output xls file... SRX3087683.05_peaks.xls INFO @ Sun, 18 Mar 2018 10:51:30: #4 Write peak in narrowPeak format file... SRX3087683.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:51:30: #4 Write summits bed file... SRX3087683.05_summits.bed INFO @ Sun, 18 Mar 2018 10:51:30: Done! pass1 - making usageList (63 chroms): 2 millis pass2 - checking and writing primary data (7878 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。