Job ID = 11171112 sra ファイルのダウンロード中... Completed: 1201467K bytes transferred in 15 seconds (637533K 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 25193928 spots for /home/okishinya/chipatlas/results/dm3/SRX2000508/SRR4000135.sra Written 25193928 spots for /home/okishinya/chipatlas/results/dm3/SRX2000508/SRR4000135.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:43:01 25193928 reads; of these: 25193928 (100.00%) were paired; of these: 8625916 (34.24%) aligned concordantly 0 times 12376254 (49.12%) aligned concordantly exactly 1 time 4191758 (16.64%) aligned concordantly >1 times ---- 8625916 pairs aligned concordantly 0 times; of these: 68458 (0.79%) aligned discordantly 1 time ---- 8557458 pairs aligned 0 times concordantly or discordantly; of these: 17114916 mates make up the pairs; of these: 16073821 (93.92%) aligned 0 times 632385 (3.69%) aligned exactly 1 time 408710 (2.39%) aligned >1 times 68.10% overall alignment rate Time searching: 00:43:01 Overall time: 00:43:02 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 16 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] 282639 / 16588960 = 0.0170 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, 08 Sep 2018 12:48:10: # Command line: callpeak -t SRX2000508.bam -f BAM -g dm -n SRX2000508.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2000508.10 # format = BAM # ChIP-seq file = ['SRX2000508.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 @ Sat, 08 Sep 2018 12:48:10: # Command line: callpeak -t SRX2000508.bam -f BAM -g dm -n SRX2000508.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2000508.20 # format = BAM # ChIP-seq file = ['SRX2000508.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 @ Sat, 08 Sep 2018 12:48:10: # Command line: callpeak -t SRX2000508.bam -f BAM -g dm -n SRX2000508.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2000508.05 # format = BAM # ChIP-seq file = ['SRX2000508.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 @ Sat, 08 Sep 2018 12:48:10: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:48:10: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:48:10: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:48:10: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:48:10: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:48:10: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:48:16: 1000000 INFO @ Sat, 08 Sep 2018 12:48:16: 1000000 INFO @ Sat, 08 Sep 2018 12:48:16: 1000000 INFO @ Sat, 08 Sep 2018 12:48:22: 2000000 INFO @ Sat, 08 Sep 2018 12:48:22: 2000000 INFO @ Sat, 08 Sep 2018 12:48:23: 2000000 INFO @ Sat, 08 Sep 2018 12:48:28: 3000000 INFO @ Sat, 08 Sep 2018 12:48:28: 3000000 INFO @ Sat, 08 Sep 2018 12:48:29: 3000000 INFO @ Sat, 08 Sep 2018 12:48:34: 4000000 INFO @ Sat, 08 Sep 2018 12:48:35: 4000000 INFO @ Sat, 08 Sep 2018 12:48:36: 4000000 INFO @ Sat, 08 Sep 2018 12:48:40: 5000000 INFO @ Sat, 08 Sep 2018 12:48:41: 5000000 INFO @ Sat, 08 Sep 2018 12:48:43: 5000000 INFO @ Sat, 08 Sep 2018 12:48:45: 6000000 INFO @ Sat, 08 Sep 2018 12:48:47: 6000000 INFO @ Sat, 08 Sep 2018 12:48:49: 6000000 INFO @ Sat, 08 Sep 2018 12:48:51: 7000000 INFO @ Sat, 08 Sep 2018 12:48:53: 7000000 INFO @ Sat, 08 Sep 2018 12:48:56: 7000000 INFO @ Sat, 08 Sep 2018 12:48:57: 8000000 INFO @ Sat, 08 Sep 2018 12:48:59: 8000000 INFO @ Sat, 08 Sep 2018 12:49:02: 8000000 INFO @ Sat, 08 Sep 2018 12:49:03: 9000000 INFO @ Sat, 08 Sep 2018 12:49:05: 9000000 INFO @ Sat, 08 Sep 2018 12:49:09: 10000000 INFO @ Sat, 08 Sep 2018 12:49:09: 9000000 INFO @ Sat, 08 Sep 2018 12:49:11: 10000000 INFO @ Sat, 08 Sep 2018 12:49:14: 11000000 INFO @ Sat, 08 Sep 2018 12:49:15: 10000000 INFO @ Sat, 08 Sep 2018 12:49:17: 11000000 INFO @ Sat, 08 Sep 2018 12:49:20: 12000000 INFO @ Sat, 08 Sep 2018 12:49:22: 11000000 INFO @ Sat, 08 Sep 2018 12:49:23: 12000000 INFO @ Sat, 08 Sep 2018 12:49:26: 13000000 INFO @ Sat, 08 Sep 2018 12:49:28: 12000000 INFO @ Sat, 08 Sep 2018 12:49:30: 13000000 INFO @ Sat, 08 Sep 2018 12:49:32: 14000000 INFO @ Sat, 08 Sep 2018 12:49:35: 13000000 INFO @ Sat, 08 Sep 2018 12:49:36: 14000000 INFO @ Sat, 08 Sep 2018 12:49:38: 15000000 INFO @ Sat, 08 Sep 2018 12:49:42: 14000000 INFO @ Sat, 08 Sep 2018 12:49:42: 15000000 INFO @ Sat, 08 Sep 2018 12:49:44: 16000000 INFO @ Sat, 08 Sep 2018 12:49:48: 16000000 INFO @ Sat, 08 Sep 2018 12:49:48: 15000000 INFO @ Sat, 08 Sep 2018 12:49:49: 17000000 INFO @ Sat, 08 Sep 2018 12:49:54: 17000000 INFO @ Sat, 08 Sep 2018 12:49:55: 16000000 INFO @ Sat, 08 Sep 2018 12:49:55: 18000000 INFO @ Sat, 08 Sep 2018 12:50:01: 18000000 INFO @ Sat, 08 Sep 2018 12:50:01: 19000000 INFO @ Sat, 08 Sep 2018 12:50:02: 17000000 INFO @ Sat, 08 Sep 2018 12:50:07: 19000000 INFO @ Sat, 08 Sep 2018 12:50:07: 20000000 INFO @ Sat, 08 Sep 2018 12:50:08: 18000000 INFO @ Sat, 08 Sep 2018 12:50:13: 21000000 INFO @ Sat, 08 Sep 2018 12:50:13: 20000000 INFO @ Sat, 08 Sep 2018 12:50:15: 19000000 INFO @ Sat, 08 Sep 2018 12:50:19: 22000000 INFO @ Sat, 08 Sep 2018 12:50:19: 21000000 INFO @ Sat, 08 Sep 2018 12:50:22: 20000000 INFO @ Sat, 08 Sep 2018 12:50:25: 23000000 INFO @ Sat, 08 Sep 2018 12:50:25: 22000000 INFO @ Sat, 08 Sep 2018 12:50:28: 21000000 INFO @ Sat, 08 Sep 2018 12:50:30: 24000000 INFO @ Sat, 08 Sep 2018 12:50:31: 23000000 INFO @ Sat, 08 Sep 2018 12:50:35: 22000000 INFO @ Sat, 08 Sep 2018 12:50:36: 25000000 INFO @ Sat, 08 Sep 2018 12:50:37: 24000000 INFO @ Sat, 08 Sep 2018 12:50:41: 23000000 INFO @ Sat, 08 Sep 2018 12:50:42: 26000000 INFO @ Sat, 08 Sep 2018 12:50:44: 25000000 INFO @ Sat, 08 Sep 2018 12:50:48: 27000000 INFO @ Sat, 08 Sep 2018 12:50:48: 24000000 INFO @ Sat, 08 Sep 2018 12:50:50: 26000000 INFO @ Sat, 08 Sep 2018 12:50:54: 28000000 INFO @ Sat, 08 Sep 2018 12:50:55: 25000000 INFO @ Sat, 08 Sep 2018 12:50:55: 27000000 INFO @ Sat, 08 Sep 2018 12:51:00: 29000000 INFO @ Sat, 08 Sep 2018 12:51:01: 28000000 INFO @ Sat, 08 Sep 2018 12:51:02: 26000000 INFO @ Sat, 08 Sep 2018 12:51:06: 30000000 INFO @ Sat, 08 Sep 2018 12:51:07: 29000000 INFO @ Sat, 08 Sep 2018 12:51:09: 27000000 INFO @ Sat, 08 Sep 2018 12:51:13: 31000000 INFO @ Sat, 08 Sep 2018 12:51:13: 30000000 INFO @ Sat, 08 Sep 2018 12:51:15: 28000000 INFO @ Sat, 08 Sep 2018 12:51:19: 32000000 INFO @ Sat, 08 Sep 2018 12:51:19: 31000000 INFO @ Sat, 08 Sep 2018 12:51:22: 29000000 INFO @ Sat, 08 Sep 2018 12:51:24: 32000000 INFO @ Sat, 08 Sep 2018 12:51:25: 33000000 INFO @ Sat, 08 Sep 2018 12:51:29: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 12:51:29: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 12:51:29: #1 total tags in treatment: 16285677 INFO @ Sat, 08 Sep 2018 12:51:29: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:51:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:51:29: 30000000 INFO @ Sat, 08 Sep 2018 12:51:30: #1 tags after filtering in treatment: 14252764 INFO @ Sat, 08 Sep 2018 12:51:30: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 08 Sep 2018 12:51:30: #1 finished! INFO @ Sat, 08 Sep 2018 12:51:30: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:51:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:51:30: 33000000 INFO @ Sat, 08 Sep 2018 12:51:31: #2 number of paired peaks: 2897 INFO @ Sat, 08 Sep 2018 12:51:31: start model_add_line... INFO @ Sat, 08 Sep 2018 12:51:31: start X-correlation... INFO @ Sat, 08 Sep 2018 12:51:31: end of X-cor INFO @ Sat, 08 Sep 2018 12:51:31: #2 finished! INFO @ Sat, 08 Sep 2018 12:51:31: #2 predicted fragment length is 182 bps INFO @ Sat, 08 Sep 2018 12:51:31: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 08 Sep 2018 12:51:31: #2.2 Generate R script for model : SRX2000508.05_model.r INFO @ Sat, 08 Sep 2018 12:51:31: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:51:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:51:35: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 12:51:35: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 12:51:35: #1 total tags in treatment: 16285677 INFO @ Sat, 08 Sep 2018 12:51:35: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:51:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:51:35: #1 tags after filtering in treatment: 14252764 INFO @ Sat, 08 Sep 2018 12:51:35: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 08 Sep 2018 12:51:35: #1 finished! INFO @ Sat, 08 Sep 2018 12:51:35: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:51:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:51:35: 31000000 INFO @ Sat, 08 Sep 2018 12:51:36: #2 number of paired peaks: 2897 INFO @ Sat, 08 Sep 2018 12:51:36: start model_add_line... INFO @ Sat, 08 Sep 2018 12:51:37: start X-correlation... INFO @ Sat, 08 Sep 2018 12:51:37: end of X-cor INFO @ Sat, 08 Sep 2018 12:51:37: #2 finished! INFO @ Sat, 08 Sep 2018 12:51:37: #2 predicted fragment length is 182 bps INFO @ Sat, 08 Sep 2018 12:51:37: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 08 Sep 2018 12:51:37: #2.2 Generate R script for model : SRX2000508.20_model.r INFO @ Sat, 08 Sep 2018 12:51:37: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:51:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:51:42: 32000000 INFO @ Sat, 08 Sep 2018 12:51:48: 33000000 INFO @ Sat, 08 Sep 2018 12:51:53: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 12:51:53: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 12:51:53: #1 total tags in treatment: 16285677 INFO @ Sat, 08 Sep 2018 12:51:53: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:51:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 12:51:53: #1 tags after filtering in treatment: 14252764 INFO @ Sat, 08 Sep 2018 12:51:53: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 08 Sep 2018 12:51:53: #1 finished! INFO @ Sat, 08 Sep 2018 12:51:53: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:51:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:51:54: #2 number of paired peaks: 2897 INFO @ Sat, 08 Sep 2018 12:51:54: start model_add_line... INFO @ Sat, 08 Sep 2018 12:51:55: start X-correlation... INFO @ Sat, 08 Sep 2018 12:51:55: end of X-cor INFO @ Sat, 08 Sep 2018 12:51:55: #2 finished! INFO @ Sat, 08 Sep 2018 12:51:55: #2 predicted fragment length is 182 bps INFO @ Sat, 08 Sep 2018 12:51:55: #2 alternative fragment length(s) may be 182 bps INFO @ Sat, 08 Sep 2018 12:51:55: #2.2 Generate R script for model : SRX2000508.10_model.r INFO @ Sat, 08 Sep 2018 12:51:55: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:51:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:52:13: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:52:17: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:52:33: #4 Write output xls file... SRX2000508.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:52:33: #4 Write peak in narrowPeak format file... SRX2000508.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:52:33: #4 Write summits bed file... SRX2000508.05_summits.bed INFO @ Sat, 08 Sep 2018 12:52:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8088 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:52:34: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:52:35: #4 Write output xls file... SRX2000508.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:52:36: #4 Write peak in narrowPeak format file... SRX2000508.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:52:36: #4 Write summits bed file... SRX2000508.20_summits.bed INFO @ Sat, 08 Sep 2018 12:52:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4058 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:52:55: #4 Write output xls file... SRX2000508.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:52:55: #4 Write peak in narrowPeak format file... SRX2000508.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:52:55: #4 Write summits bed file... SRX2000508.10_summits.bed INFO @ Sat, 08 Sep 2018 12:52:55: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6271 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。