Job ID = 10487600 sra ファイルのダウンロード中... Completed: 1216112K bytes transferred in 24 seconds (408968K 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 44172325 spots for /home/okishinya/chipatlas/results/rn6/SRX3087680/SRR5927316.sra Written 44172325 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:56:53 44172325 reads; of these: 44172325 (100.00%) were unpaired; of these: 1693386 (3.83%) aligned 0 times 34627064 (78.39%) aligned exactly 1 time 7851875 (17.78%) aligned >1 times 96.17% overall alignment rate Time searching: 00:56:54 Overall time: 00:56:54 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] 3668264 / 42478939 = 0.0864 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 10:55:14: # Command line: callpeak -t SRX3087680.bam -f BAM -g 2.15e9 -n SRX3087680.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3087680.10 # format = BAM # ChIP-seq file = ['SRX3087680.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 10:55:14: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:55:14: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:55:14: # Command line: callpeak -t SRX3087680.bam -f BAM -g 2.15e9 -n SRX3087680.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3087680.05 # format = BAM # ChIP-seq file = ['SRX3087680.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 10:55:14: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:55:14: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:55:14: # Command line: callpeak -t SRX3087680.bam -f BAM -g 2.15e9 -n SRX3087680.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3087680.20 # format = BAM # ChIP-seq file = ['SRX3087680.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 10:55:14: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:55:14: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:55:21: 1000000 INFO @ Sun, 18 Mar 2018 10:55:21: 1000000 INFO @ Sun, 18 Mar 2018 10:55:21: 1000000 INFO @ Sun, 18 Mar 2018 10:55:28: 2000000 INFO @ Sun, 18 Mar 2018 10:55:29: 2000000 INFO @ Sun, 18 Mar 2018 10:55:29: 2000000 INFO @ Sun, 18 Mar 2018 10:55:36: 3000000 INFO @ Sun, 18 Mar 2018 10:55:37: 3000000 INFO @ Sun, 18 Mar 2018 10:55:37: 3000000 INFO @ Sun, 18 Mar 2018 10:55:43: 4000000 INFO @ Sun, 18 Mar 2018 10:55:44: 4000000 INFO @ Sun, 18 Mar 2018 10:55:44: 4000000 INFO @ Sun, 18 Mar 2018 10:55:50: 5000000 INFO @ Sun, 18 Mar 2018 10:55:51: 5000000 INFO @ Sun, 18 Mar 2018 10:55:52: 5000000 INFO @ Sun, 18 Mar 2018 10:55:57: 6000000 INFO @ Sun, 18 Mar 2018 10:55:59: 6000000 INFO @ Sun, 18 Mar 2018 10:55:59: 6000000 INFO @ Sun, 18 Mar 2018 10:56:04: 7000000 INFO @ Sun, 18 Mar 2018 10:56:06: 7000000 INFO @ Sun, 18 Mar 2018 10:56:07: 7000000 INFO @ Sun, 18 Mar 2018 10:56:11: 8000000 INFO @ Sun, 18 Mar 2018 10:56:13: 8000000 INFO @ Sun, 18 Mar 2018 10:56:14: 8000000 INFO @ Sun, 18 Mar 2018 10:56:18: 9000000 INFO @ Sun, 18 Mar 2018 10:56:21: 9000000 INFO @ Sun, 18 Mar 2018 10:56:23: 9000000 INFO @ Sun, 18 Mar 2018 10:56:25: 10000000 INFO @ Sun, 18 Mar 2018 10:56:29: 10000000 INFO @ Sun, 18 Mar 2018 10:56:31: 10000000 INFO @ Sun, 18 Mar 2018 10:56:32: 11000000 INFO @ Sun, 18 Mar 2018 10:56:37: 11000000 INFO @ Sun, 18 Mar 2018 10:56:39: 12000000 INFO @ Sun, 18 Mar 2018 10:56:39: 11000000 INFO @ Sun, 18 Mar 2018 10:56:45: 12000000 INFO @ Sun, 18 Mar 2018 10:56:45: 13000000 INFO @ Sun, 18 Mar 2018 10:56:46: 12000000 INFO @ Sun, 18 Mar 2018 10:56:53: 13000000 INFO @ Sun, 18 Mar 2018 10:56:53: 14000000 INFO @ Sun, 18 Mar 2018 10:56:55: 13000000 INFO @ Sun, 18 Mar 2018 10:57:00: 15000000 INFO @ Sun, 18 Mar 2018 10:57:00: 14000000 INFO @ Sun, 18 Mar 2018 10:57:02: 14000000 INFO @ Sun, 18 Mar 2018 10:57:07: 16000000 INFO @ Sun, 18 Mar 2018 10:57:08: 15000000 INFO @ Sun, 18 Mar 2018 10:57:10: 15000000 INFO @ Sun, 18 Mar 2018 10:57:14: 17000000 INFO @ Sun, 18 Mar 2018 10:57:15: 16000000 INFO @ Sun, 18 Mar 2018 10:57:17: 16000000 INFO @ Sun, 18 Mar 2018 10:57:21: 18000000 INFO @ Sun, 18 Mar 2018 10:57:22: 17000000 INFO @ Sun, 18 Mar 2018 10:57:25: 17000000 INFO @ Sun, 18 Mar 2018 10:57:27: 19000000 INFO @ Sun, 18 Mar 2018 10:57:30: 18000000 INFO @ Sun, 18 Mar 2018 10:57:32: 18000000 INFO @ Sun, 18 Mar 2018 10:57:34: 20000000 INFO @ Sun, 18 Mar 2018 10:57:37: 19000000 INFO @ Sun, 18 Mar 2018 10:57:40: 19000000 INFO @ Sun, 18 Mar 2018 10:57:41: 21000000 INFO @ Sun, 18 Mar 2018 10:57:45: 20000000 INFO @ Sun, 18 Mar 2018 10:57:48: 20000000 INFO @ Sun, 18 Mar 2018 10:57:48: 22000000 INFO @ Sun, 18 Mar 2018 10:57:52: 21000000 INFO @ Sun, 18 Mar 2018 10:57:55: 23000000 INFO @ Sun, 18 Mar 2018 10:57:55: 21000000 INFO @ Sun, 18 Mar 2018 10:58:00: 22000000 INFO @ Sun, 18 Mar 2018 10:58:02: 24000000 INFO @ Sun, 18 Mar 2018 10:58:03: 22000000 INFO @ Sun, 18 Mar 2018 10:58:07: 23000000 INFO @ Sun, 18 Mar 2018 10:58:09: 25000000 INFO @ Sun, 18 Mar 2018 10:58:11: 23000000 INFO @ Sun, 18 Mar 2018 10:58:15: 24000000 INFO @ Sun, 18 Mar 2018 10:58:16: 26000000 INFO @ Sun, 18 Mar 2018 10:58:19: 24000000 INFO @ Sun, 18 Mar 2018 10:58:23: 25000000 INFO @ Sun, 18 Mar 2018 10:58:23: 27000000 INFO @ Sun, 18 Mar 2018 10:58:27: 25000000 INFO @ Sun, 18 Mar 2018 10:58:30: 28000000 INFO @ Sun, 18 Mar 2018 10:58:30: 26000000 INFO @ Sun, 18 Mar 2018 10:58:35: 26000000 INFO @ Sun, 18 Mar 2018 10:58:37: 29000000 INFO @ Sun, 18 Mar 2018 10:58:38: 27000000 INFO @ Sun, 18 Mar 2018 10:58:43: 27000000 INFO @ Sun, 18 Mar 2018 10:58:44: 30000000 INFO @ Sun, 18 Mar 2018 10:58:46: 28000000 INFO @ Sun, 18 Mar 2018 10:58:50: 28000000 INFO @ Sun, 18 Mar 2018 10:58:51: 31000000 INFO @ Sun, 18 Mar 2018 10:58:54: 29000000 INFO @ Sun, 18 Mar 2018 10:58:58: 32000000 INFO @ Sun, 18 Mar 2018 10:58:58: 29000000 INFO @ Sun, 18 Mar 2018 10:59:01: 30000000 INFO @ Sun, 18 Mar 2018 10:59:05: 33000000 INFO @ Sun, 18 Mar 2018 10:59:06: 30000000 INFO @ Sun, 18 Mar 2018 10:59:09: 31000000 INFO @ Sun, 18 Mar 2018 10:59:12: 34000000 INFO @ Sun, 18 Mar 2018 10:59:14: 31000000 INFO @ Sun, 18 Mar 2018 10:59:17: 32000000 INFO @ Sun, 18 Mar 2018 10:59:19: 35000000 INFO @ Sun, 18 Mar 2018 10:59:22: 32000000 INFO @ Sun, 18 Mar 2018 10:59:24: 33000000 INFO @ Sun, 18 Mar 2018 10:59:26: 36000000 INFO @ Sun, 18 Mar 2018 10:59:30: 33000000 INFO @ Sun, 18 Mar 2018 10:59:32: 34000000 INFO @ Sun, 18 Mar 2018 10:59:33: 37000000 INFO @ Sun, 18 Mar 2018 10:59:38: 34000000 INFO @ Sun, 18 Mar 2018 10:59:40: 35000000 INFO @ Sun, 18 Mar 2018 10:59:40: 38000000 INFO @ Sun, 18 Mar 2018 10:59:46: 35000000 INFO @ Sun, 18 Mar 2018 10:59:46: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 10:59:46: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 10:59:46: #1 total tags in treatment: 38810675 INFO @ Sun, 18 Mar 2018 10:59:46: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:59:46: #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 10:59:47: #1 tags after filtering in treatment: 38810580 INFO @ Sun, 18 Mar 2018 10:59:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:59:47: #1 finished! INFO @ Sun, 18 Mar 2018 10:59:47: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:59:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:59:48: 36000000 INFO @ Sun, 18 Mar 2018 10:59:53: #2 number of paired peaks: 46016 INFO @ Sun, 18 Mar 2018 10:59:53: start model_add_line... INFO @ Sun, 18 Mar 2018 10:59:54: start X-correlation... INFO @ Sun, 18 Mar 2018 10:59:54: end of X-cor INFO @ Sun, 18 Mar 2018 10:59:54: #2 finished! INFO @ Sun, 18 Mar 2018 10:59:54: #2 predicted fragment length is 263 bps INFO @ Sun, 18 Mar 2018 10:59:54: #2 alternative fragment length(s) may be 263 bps INFO @ Sun, 18 Mar 2018 10:59:54: #2.2 Generate R script for model : SRX3087680.10_model.r INFO @ Sun, 18 Mar 2018 10:59:54: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:59:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:59:54: 36000000 INFO @ Sun, 18 Mar 2018 10:59:55: 37000000 INFO @ Sun, 18 Mar 2018 11:00:02: 37000000 INFO @ Sun, 18 Mar 2018 11:00:03: 38000000 INFO @ Sun, 18 Mar 2018 11:00:10: 38000000 INFO @ Sun, 18 Mar 2018 11:00:10: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:00:10: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:00:10: #1 total tags in treatment: 38810675 INFO @ Sun, 18 Mar 2018 11:00:10: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:00:10: #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 11:00:11: #1 tags after filtering in treatment: 38810580 INFO @ Sun, 18 Mar 2018 11:00:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:00:11: #1 finished! INFO @ Sun, 18 Mar 2018 11:00:11: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:00:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:00:17: #1 tag size is determined as 61 bps INFO @ Sun, 18 Mar 2018 11:00:17: #1 tag size = 61 INFO @ Sun, 18 Mar 2018 11:00:17: #1 total tags in treatment: 38810675 INFO @ Sun, 18 Mar 2018 11:00:17: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 11:00:17: #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 11:00:17: #2 number of paired peaks: 46016 INFO @ Sun, 18 Mar 2018 11:00:17: start model_add_line... INFO @ Sun, 18 Mar 2018 11:00:17: start X-correlation... INFO @ Sun, 18 Mar 2018 11:00:17: end of X-cor INFO @ Sun, 18 Mar 2018 11:00:17: #2 finished! INFO @ Sun, 18 Mar 2018 11:00:17: #2 predicted fragment length is 263 bps INFO @ Sun, 18 Mar 2018 11:00:17: #2 alternative fragment length(s) may be 263 bps INFO @ Sun, 18 Mar 2018 11:00:17: #2.2 Generate R script for model : SRX3087680.20_model.r INFO @ Sun, 18 Mar 2018 11:00:17: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:00:18: #1 tags after filtering in treatment: 38810580 INFO @ Sun, 18 Mar 2018 11:00:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 11:00:18: #1 finished! INFO @ Sun, 18 Mar 2018 11:00:18: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 11:00:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 11:00:23: #2 number of paired peaks: 46016 INFO @ Sun, 18 Mar 2018 11:00:23: start model_add_line... INFO @ Sun, 18 Mar 2018 11:00:24: start X-correlation... INFO @ Sun, 18 Mar 2018 11:00:24: end of X-cor INFO @ Sun, 18 Mar 2018 11:00:24: #2 finished! INFO @ Sun, 18 Mar 2018 11:00:24: #2 predicted fragment length is 263 bps INFO @ Sun, 18 Mar 2018 11:00:24: #2 alternative fragment length(s) may be 263 bps INFO @ Sun, 18 Mar 2018 11:00:24: #2.2 Generate R script for model : SRX3087680.05_model.r INFO @ Sun, 18 Mar 2018 11:00:24: #3 Call peaks... INFO @ Sun, 18 Mar 2018 11:00:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 11:01:32: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:01:51: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:02:09: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 11:02:29: #4 Write output xls file... SRX3087680.10_peaks.xls INFO @ Sun, 18 Mar 2018 11:02:29: #4 Write peak in narrowPeak format file... SRX3087680.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:02:29: #4 Write summits bed file... SRX3087680.10_summits.bed INFO @ Sun, 18 Mar 2018 11:02:29: Done! pass1 - making usageList (53 chroms): 2 millis pass2 - checking and writing primary data (7997 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:02:57: #4 Write output xls file... SRX3087680.20_peaks.xls INFO @ Sun, 18 Mar 2018 11:02:57: #4 Write peak in narrowPeak format file... SRX3087680.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:02:57: #4 Write summits bed file... SRX3087680.20_summits.bed INFO @ Sun, 18 Mar 2018 11:02:57: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (1770 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 11:03:10: #4 Write output xls file... SRX3087680.05_peaks.xls INFO @ Sun, 18 Mar 2018 11:03:10: #4 Write peak in narrowPeak format file... SRX3087680.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 11:03:10: #4 Write summits bed file... SRX3087680.05_summits.bed INFO @ Sun, 18 Mar 2018 11:03:10: Done! pass1 - making usageList (97 chroms): 4 millis pass2 - checking and writing primary data (17463 records, 4 fields): 24 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。