Job ID = 11158477 sra ファイルのダウンロード中... Completed: 1359662K bytes transferred in 23 seconds (483767K 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: PAIRED fastq に変換中... Read 21387786 spots for /home/okishinya/chipatlas/results/dm3/SRX4279657/SRR7408145.sra Written 21387786 spots for /home/okishinya/chipatlas/results/dm3/SRX4279657/SRR7408145.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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:21:24 21387786 reads; of these: 21387786 (100.00%) were paired; of these: 2709312 (12.67%) aligned concordantly 0 times 5008017 (23.42%) aligned concordantly exactly 1 time 13670457 (63.92%) aligned concordantly >1 times ---- 2709312 pairs aligned concordantly 0 times; of these: 17428 (0.64%) aligned discordantly 1 time ---- 2691884 pairs aligned 0 times concordantly or discordantly; of these: 5383768 mates make up the pairs; of these: 3168364 (58.85%) aligned 0 times 338866 (6.29%) aligned exactly 1 time 1876538 (34.86%) aligned >1 times 92.59% overall alignment rate Time searching: 02:21:25 Overall time: 02:21:25 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 20 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 638749 / 18659864 = 0.0342 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 @ Tue, 04 Sep 2018 12:13:39: # Command line: callpeak -t SRX4279657.bam -f BAM -g dm -n SRX4279657.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4279657.05 # format = BAM # ChIP-seq file = ['SRX4279657.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 04 Sep 2018 12:13:39: # Command line: callpeak -t SRX4279657.bam -f BAM -g dm -n SRX4279657.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4279657.10 # format = BAM # ChIP-seq file = ['SRX4279657.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 04 Sep 2018 12:13:39: # Command line: callpeak -t SRX4279657.bam -f BAM -g dm -n SRX4279657.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4279657.20 # format = BAM # ChIP-seq file = ['SRX4279657.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Tue, 04 Sep 2018 12:13:39: #1 read tag files... INFO @ Tue, 04 Sep 2018 12:13:39: #1 read tag files... INFO @ Tue, 04 Sep 2018 12:13:39: #1 read tag files... INFO @ Tue, 04 Sep 2018 12:13:39: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 12:13:39: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 12:13:39: #1 read treatment tags... INFO @ Tue, 04 Sep 2018 12:13:47: 1000000 INFO @ Tue, 04 Sep 2018 12:13:47: 1000000 INFO @ Tue, 04 Sep 2018 12:13:47: 1000000 INFO @ Tue, 04 Sep 2018 12:13:54: 2000000 INFO @ Tue, 04 Sep 2018 12:13:54: 2000000 INFO @ Tue, 04 Sep 2018 12:13:55: 2000000 INFO @ Tue, 04 Sep 2018 12:14:01: 3000000 INFO @ Tue, 04 Sep 2018 12:14:02: 3000000 INFO @ Tue, 04 Sep 2018 12:14:02: 3000000 INFO @ Tue, 04 Sep 2018 12:14:08: 4000000 INFO @ Tue, 04 Sep 2018 12:14:10: 4000000 INFO @ Tue, 04 Sep 2018 12:14:10: 4000000 INFO @ Tue, 04 Sep 2018 12:14:15: 5000000 INFO @ Tue, 04 Sep 2018 12:14:17: 5000000 INFO @ Tue, 04 Sep 2018 12:14:18: 5000000 INFO @ Tue, 04 Sep 2018 12:14:22: 6000000 INFO @ Tue, 04 Sep 2018 12:14:25: 6000000 INFO @ Tue, 04 Sep 2018 12:14:25: 6000000 INFO @ Tue, 04 Sep 2018 12:14:29: 7000000 INFO @ Tue, 04 Sep 2018 12:14:33: 7000000 INFO @ Tue, 04 Sep 2018 12:14:33: 7000000 INFO @ Tue, 04 Sep 2018 12:14:36: 8000000 INFO @ Tue, 04 Sep 2018 12:14:41: 8000000 INFO @ Tue, 04 Sep 2018 12:14:41: 8000000 INFO @ Tue, 04 Sep 2018 12:14:44: 9000000 INFO @ Tue, 04 Sep 2018 12:14:49: 9000000 INFO @ Tue, 04 Sep 2018 12:14:49: 9000000 INFO @ Tue, 04 Sep 2018 12:14:51: 10000000 INFO @ Tue, 04 Sep 2018 12:14:56: 10000000 INFO @ Tue, 04 Sep 2018 12:14:57: 10000000 INFO @ Tue, 04 Sep 2018 12:14:58: 11000000 INFO @ Tue, 04 Sep 2018 12:15:04: 11000000 INFO @ Tue, 04 Sep 2018 12:15:05: 12000000 INFO @ Tue, 04 Sep 2018 12:15:05: 11000000 INFO @ Tue, 04 Sep 2018 12:15:12: 13000000 INFO @ Tue, 04 Sep 2018 12:15:12: 12000000 INFO @ Tue, 04 Sep 2018 12:15:13: 12000000 INFO @ Tue, 04 Sep 2018 12:15:19: 14000000 INFO @ Tue, 04 Sep 2018 12:15:20: 13000000 INFO @ Tue, 04 Sep 2018 12:15:21: 13000000 INFO @ Tue, 04 Sep 2018 12:15:27: 15000000 INFO @ Tue, 04 Sep 2018 12:15:28: 14000000 INFO @ Tue, 04 Sep 2018 12:15:29: 14000000 INFO @ Tue, 04 Sep 2018 12:15:34: 16000000 INFO @ Tue, 04 Sep 2018 12:15:37: 15000000 INFO @ Tue, 04 Sep 2018 12:15:37: 15000000 INFO @ Tue, 04 Sep 2018 12:15:41: 17000000 INFO @ Tue, 04 Sep 2018 12:15:44: 16000000 INFO @ Tue, 04 Sep 2018 12:15:45: 16000000 INFO @ Tue, 04 Sep 2018 12:15:48: 18000000 INFO @ Tue, 04 Sep 2018 12:15:52: 17000000 INFO @ Tue, 04 Sep 2018 12:15:53: 17000000 INFO @ Tue, 04 Sep 2018 12:15:55: 19000000 INFO @ Tue, 04 Sep 2018 12:16:00: 18000000 INFO @ Tue, 04 Sep 2018 12:16:01: 18000000 INFO @ Tue, 04 Sep 2018 12:16:02: 20000000 INFO @ Tue, 04 Sep 2018 12:16:08: 19000000 INFO @ Tue, 04 Sep 2018 12:16:09: 19000000 INFO @ Tue, 04 Sep 2018 12:16:09: 21000000 INFO @ Tue, 04 Sep 2018 12:16:17: 20000000 INFO @ Tue, 04 Sep 2018 12:16:17: 22000000 INFO @ Tue, 04 Sep 2018 12:16:17: 20000000 INFO @ Tue, 04 Sep 2018 12:16:24: 23000000 INFO @ Tue, 04 Sep 2018 12:16:24: 21000000 INFO @ Tue, 04 Sep 2018 12:16:25: 21000000 INFO @ Tue, 04 Sep 2018 12:16:31: 24000000 INFO @ Tue, 04 Sep 2018 12:16:32: 22000000 INFO @ Tue, 04 Sep 2018 12:16:33: 22000000 INFO @ Tue, 04 Sep 2018 12:16:38: 25000000 INFO @ Tue, 04 Sep 2018 12:16:40: 23000000 INFO @ Tue, 04 Sep 2018 12:16:40: 23000000 INFO @ Tue, 04 Sep 2018 12:16:45: 26000000 INFO @ Tue, 04 Sep 2018 12:16:47: 24000000 INFO @ Tue, 04 Sep 2018 12:16:48: 24000000 INFO @ Tue, 04 Sep 2018 12:16:52: 27000000 INFO @ Tue, 04 Sep 2018 12:16:55: 25000000 INFO @ Tue, 04 Sep 2018 12:16:55: 25000000 INFO @ Tue, 04 Sep 2018 12:16:59: 28000000 INFO @ Tue, 04 Sep 2018 12:17:03: 26000000 INFO @ Tue, 04 Sep 2018 12:17:03: 26000000 INFO @ Tue, 04 Sep 2018 12:17:06: 29000000 INFO @ Tue, 04 Sep 2018 12:17:10: 27000000 INFO @ Tue, 04 Sep 2018 12:17:10: 27000000 INFO @ Tue, 04 Sep 2018 12:17:14: 30000000 INFO @ Tue, 04 Sep 2018 12:17:18: 28000000 INFO @ Tue, 04 Sep 2018 12:17:18: 28000000 INFO @ Tue, 04 Sep 2018 12:17:21: 31000000 INFO @ Tue, 04 Sep 2018 12:17:25: 29000000 INFO @ Tue, 04 Sep 2018 12:17:25: 29000000 INFO @ Tue, 04 Sep 2018 12:17:28: 32000000 INFO @ Tue, 04 Sep 2018 12:17:32: 30000000 INFO @ Tue, 04 Sep 2018 12:17:32: 30000000 INFO @ Tue, 04 Sep 2018 12:17:35: 33000000 INFO @ Tue, 04 Sep 2018 12:17:40: 31000000 INFO @ Tue, 04 Sep 2018 12:17:40: 31000000 INFO @ Tue, 04 Sep 2018 12:17:42: 34000000 INFO @ Tue, 04 Sep 2018 12:17:48: 32000000 INFO @ Tue, 04 Sep 2018 12:17:48: 32000000 INFO @ Tue, 04 Sep 2018 12:17:49: 35000000 INFO @ Tue, 04 Sep 2018 12:17:55: 33000000 INFO @ Tue, 04 Sep 2018 12:17:55: 33000000 INFO @ Tue, 04 Sep 2018 12:17:56: 36000000 INFO @ Tue, 04 Sep 2018 12:18:03: 34000000 INFO @ Tue, 04 Sep 2018 12:18:03: 34000000 INFO @ Tue, 04 Sep 2018 12:18:03: 37000000 INFO @ Tue, 04 Sep 2018 12:18:10: 38000000 INFO @ Tue, 04 Sep 2018 12:18:10: 35000000 INFO @ Tue, 04 Sep 2018 12:18:10: 35000000 INFO @ Tue, 04 Sep 2018 12:18:13: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 12:18:13: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 12:18:13: #1 total tags in treatment: 18039878 INFO @ Tue, 04 Sep 2018 12:18:13: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 12:18:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 12:18:13: #1 tags after filtering in treatment: 14184993 INFO @ Tue, 04 Sep 2018 12:18:13: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 04 Sep 2018 12:18:13: #1 finished! INFO @ Tue, 04 Sep 2018 12:18:13: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 12:18:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 12:18:15: #2 number of paired peaks: 7832 INFO @ Tue, 04 Sep 2018 12:18:15: start model_add_line... INFO @ Tue, 04 Sep 2018 12:18:15: start X-correlation... INFO @ Tue, 04 Sep 2018 12:18:15: end of X-cor INFO @ Tue, 04 Sep 2018 12:18:15: #2 finished! INFO @ Tue, 04 Sep 2018 12:18:15: #2 predicted fragment length is 158 bps INFO @ Tue, 04 Sep 2018 12:18:15: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 04 Sep 2018 12:18:15: #2.2 Generate R script for model : SRX4279657.05_model.r INFO @ Tue, 04 Sep 2018 12:18:15: #3 Call peaks... INFO @ Tue, 04 Sep 2018 12:18:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 12:18:18: 36000000 INFO @ Tue, 04 Sep 2018 12:18:18: 36000000 INFO @ Tue, 04 Sep 2018 12:18:26: 37000000 INFO @ Tue, 04 Sep 2018 12:18:26: 37000000 INFO @ Tue, 04 Sep 2018 12:18:34: 38000000 INFO @ Tue, 04 Sep 2018 12:18:34: 38000000 INFO @ Tue, 04 Sep 2018 12:18:36: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 12:18:36: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 12:18:36: #1 total tags in treatment: 18039878 INFO @ Tue, 04 Sep 2018 12:18:36: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 12:18:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 12:18:36: #1 tag size is determined as 78 bps INFO @ Tue, 04 Sep 2018 12:18:36: #1 tag size = 78 INFO @ Tue, 04 Sep 2018 12:18:36: #1 total tags in treatment: 18039878 INFO @ Tue, 04 Sep 2018 12:18:36: #1 user defined the maximum tags... INFO @ Tue, 04 Sep 2018 12:18:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 04 Sep 2018 12:18:37: #1 tags after filtering in treatment: 14184993 INFO @ Tue, 04 Sep 2018 12:18:37: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 04 Sep 2018 12:18:37: #1 finished! INFO @ Tue, 04 Sep 2018 12:18:37: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 12:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 12:18:37: #1 tags after filtering in treatment: 14184993 INFO @ Tue, 04 Sep 2018 12:18:37: #1 Redundant rate of treatment: 0.21 INFO @ Tue, 04 Sep 2018 12:18:37: #1 finished! INFO @ Tue, 04 Sep 2018 12:18:37: #2 Build Peak Model... INFO @ Tue, 04 Sep 2018 12:18:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 04 Sep 2018 12:18:38: #2 number of paired peaks: 7832 INFO @ Tue, 04 Sep 2018 12:18:38: start model_add_line... INFO @ Tue, 04 Sep 2018 12:18:38: #2 number of paired peaks: 7832 INFO @ Tue, 04 Sep 2018 12:18:38: start model_add_line... INFO @ Tue, 04 Sep 2018 12:18:39: start X-correlation... INFO @ Tue, 04 Sep 2018 12:18:39: start X-correlation... INFO @ Tue, 04 Sep 2018 12:18:39: end of X-cor INFO @ Tue, 04 Sep 2018 12:18:39: #2 finished! INFO @ Tue, 04 Sep 2018 12:18:39: #2 predicted fragment length is 158 bps INFO @ Tue, 04 Sep 2018 12:18:39: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 04 Sep 2018 12:18:39: #2.2 Generate R script for model : SRX4279657.10_model.r INFO @ Tue, 04 Sep 2018 12:18:39: end of X-cor INFO @ Tue, 04 Sep 2018 12:18:39: #2 finished! INFO @ Tue, 04 Sep 2018 12:18:39: #2 predicted fragment length is 158 bps INFO @ Tue, 04 Sep 2018 12:18:39: #2 alternative fragment length(s) may be 158 bps INFO @ Tue, 04 Sep 2018 12:18:39: #2.2 Generate R script for model : SRX4279657.20_model.r INFO @ Tue, 04 Sep 2018 12:18:39: #3 Call peaks... INFO @ Tue, 04 Sep 2018 12:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 12:18:39: #3 Call peaks... INFO @ Tue, 04 Sep 2018 12:18:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 04 Sep 2018 12:18:58: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 12:19:18: #4 Write output xls file... SRX4279657.05_peaks.xls INFO @ Tue, 04 Sep 2018 12:19:18: #4 Write peak in narrowPeak format file... SRX4279657.05_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 12:19:18: #4 Write summits bed file... SRX4279657.05_summits.bed INFO @ Tue, 04 Sep 2018 12:19:19: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (17696 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 12:19:21: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 12:19:24: #3 Call peaks for each chromosome... INFO @ Tue, 04 Sep 2018 12:19:39: #4 Write output xls file... SRX4279657.20_peaks.xls INFO @ Tue, 04 Sep 2018 12:19:39: #4 Write peak in narrowPeak format file... SRX4279657.20_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 12:19:39: #4 Write summits bed file... SRX4279657.20_summits.bed INFO @ Tue, 04 Sep 2018 12:19:39: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7269 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 04 Sep 2018 12:19:42: #4 Write output xls file... SRX4279657.10_peaks.xls INFO @ Tue, 04 Sep 2018 12:19:42: #4 Write peak in narrowPeak format file... SRX4279657.10_peaks.narrowPeak INFO @ Tue, 04 Sep 2018 12:19:42: #4 Write summits bed file... SRX4279657.10_summits.bed INFO @ Tue, 04 Sep 2018 12:19:42: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (12545 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。