Job ID = 11171111 sra ファイルのダウンロード中... Completed: 1471653K bytes transferred in 20 seconds (596507K 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 31888245 spots for /home/okishinya/chipatlas/results/dm3/SRX2000507/SRR4000134.sra Written 31888245 spots for /home/okishinya/chipatlas/results/dm3/SRX2000507/SRR4000134.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: 00:54:55 31888245 reads; of these: 31888245 (100.00%) were paired; of these: 11830607 (37.10%) aligned concordantly 0 times 14887247 (46.69%) aligned concordantly exactly 1 time 5170391 (16.21%) aligned concordantly >1 times ---- 11830607 pairs aligned concordantly 0 times; of these: 71069 (0.60%) aligned discordantly 1 time ---- 11759538 pairs aligned 0 times concordantly or discordantly; of these: 23519076 mates make up the pairs; of these: 22303769 (94.83%) aligned 0 times 736831 (3.13%) aligned exactly 1 time 478476 (2.03%) aligned >1 times 65.03% overall alignment rate Time searching: 00:54:55 Overall time: 00:54:55 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] 390682 / 20081200 = 0.0195 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 13:02:07: # Command line: callpeak -t SRX2000507.bam -f BAM -g dm -n SRX2000507.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2000507.05 # format = BAM # ChIP-seq file = ['SRX2000507.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 13:02:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:02:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:02:07: # Command line: callpeak -t SRX2000507.bam -f BAM -g dm -n SRX2000507.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2000507.20 # format = BAM # ChIP-seq file = ['SRX2000507.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 13:02:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:02:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:02:07: # Command line: callpeak -t SRX2000507.bam -f BAM -g dm -n SRX2000507.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2000507.10 # format = BAM # ChIP-seq file = ['SRX2000507.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 13:02:07: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:02:07: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:02:13: 1000000 INFO @ Sat, 08 Sep 2018 13:02:13: 1000000 INFO @ Sat, 08 Sep 2018 13:02:13: 1000000 INFO @ Sat, 08 Sep 2018 13:02:18: 2000000 INFO @ Sat, 08 Sep 2018 13:02:19: 2000000 INFO @ Sat, 08 Sep 2018 13:02:19: 2000000 INFO @ Sat, 08 Sep 2018 13:02:24: 3000000 INFO @ Sat, 08 Sep 2018 13:02:24: 3000000 INFO @ Sat, 08 Sep 2018 13:02:24: 3000000 INFO @ Sat, 08 Sep 2018 13:02:30: 4000000 INFO @ Sat, 08 Sep 2018 13:02:30: 4000000 INFO @ Sat, 08 Sep 2018 13:02:30: 4000000 INFO @ Sat, 08 Sep 2018 13:02:36: 5000000 INFO @ Sat, 08 Sep 2018 13:02:36: 5000000 INFO @ Sat, 08 Sep 2018 13:02:36: 5000000 INFO @ Sat, 08 Sep 2018 13:02:41: 6000000 INFO @ Sat, 08 Sep 2018 13:02:42: 6000000 INFO @ Sat, 08 Sep 2018 13:02:42: 6000000 INFO @ Sat, 08 Sep 2018 13:02:47: 7000000 INFO @ Sat, 08 Sep 2018 13:02:48: 7000000 INFO @ Sat, 08 Sep 2018 13:02:48: 7000000 INFO @ Sat, 08 Sep 2018 13:02:53: 8000000 INFO @ Sat, 08 Sep 2018 13:02:54: 8000000 INFO @ Sat, 08 Sep 2018 13:02:54: 8000000 INFO @ Sat, 08 Sep 2018 13:02:59: 9000000 INFO @ Sat, 08 Sep 2018 13:02:59: 9000000 INFO @ Sat, 08 Sep 2018 13:02:59: 9000000 INFO @ Sat, 08 Sep 2018 13:03:04: 10000000 INFO @ Sat, 08 Sep 2018 13:03:05: 10000000 INFO @ Sat, 08 Sep 2018 13:03:05: 10000000 INFO @ Sat, 08 Sep 2018 13:03:10: 11000000 INFO @ Sat, 08 Sep 2018 13:03:11: 11000000 INFO @ Sat, 08 Sep 2018 13:03:11: 11000000 INFO @ Sat, 08 Sep 2018 13:03:16: 12000000 INFO @ Sat, 08 Sep 2018 13:03:17: 12000000 INFO @ Sat, 08 Sep 2018 13:03:17: 12000000 INFO @ Sat, 08 Sep 2018 13:03:22: 13000000 INFO @ Sat, 08 Sep 2018 13:03:23: 13000000 INFO @ Sat, 08 Sep 2018 13:03:23: 13000000 INFO @ Sat, 08 Sep 2018 13:03:27: 14000000 INFO @ Sat, 08 Sep 2018 13:03:29: 14000000 INFO @ Sat, 08 Sep 2018 13:03:29: 14000000 INFO @ Sat, 08 Sep 2018 13:03:33: 15000000 INFO @ Sat, 08 Sep 2018 13:03:34: 15000000 INFO @ Sat, 08 Sep 2018 13:03:34: 15000000 INFO @ Sat, 08 Sep 2018 13:03:39: 16000000 INFO @ Sat, 08 Sep 2018 13:03:40: 16000000 INFO @ Sat, 08 Sep 2018 13:03:40: 16000000 INFO @ Sat, 08 Sep 2018 13:03:45: 17000000 INFO @ Sat, 08 Sep 2018 13:03:46: 17000000 INFO @ Sat, 08 Sep 2018 13:03:46: 17000000 INFO @ Sat, 08 Sep 2018 13:03:50: 18000000 INFO @ Sat, 08 Sep 2018 13:03:51: 18000000 INFO @ Sat, 08 Sep 2018 13:03:51: 18000000 INFO @ Sat, 08 Sep 2018 13:03:56: 19000000 INFO @ Sat, 08 Sep 2018 13:03:57: 19000000 INFO @ Sat, 08 Sep 2018 13:03:57: 19000000 INFO @ Sat, 08 Sep 2018 13:04:02: 20000000 INFO @ Sat, 08 Sep 2018 13:04:03: 20000000 INFO @ Sat, 08 Sep 2018 13:04:03: 20000000 INFO @ Sat, 08 Sep 2018 13:04:08: 21000000 INFO @ Sat, 08 Sep 2018 13:04:09: 21000000 INFO @ Sat, 08 Sep 2018 13:04:09: 21000000 INFO @ Sat, 08 Sep 2018 13:04:13: 22000000 INFO @ Sat, 08 Sep 2018 13:04:14: 22000000 INFO @ Sat, 08 Sep 2018 13:04:14: 22000000 INFO @ Sat, 08 Sep 2018 13:04:19: 23000000 INFO @ Sat, 08 Sep 2018 13:04:20: 23000000 INFO @ Sat, 08 Sep 2018 13:04:20: 23000000 INFO @ Sat, 08 Sep 2018 13:04:25: 24000000 INFO @ Sat, 08 Sep 2018 13:04:26: 24000000 INFO @ Sat, 08 Sep 2018 13:04:26: 24000000 INFO @ Sat, 08 Sep 2018 13:04:31: 25000000 INFO @ Sat, 08 Sep 2018 13:04:32: 25000000 INFO @ Sat, 08 Sep 2018 13:04:32: 25000000 INFO @ Sat, 08 Sep 2018 13:04:36: 26000000 INFO @ Sat, 08 Sep 2018 13:04:37: 26000000 INFO @ Sat, 08 Sep 2018 13:04:37: 26000000 INFO @ Sat, 08 Sep 2018 13:04:42: 27000000 INFO @ Sat, 08 Sep 2018 13:04:43: 27000000 INFO @ Sat, 08 Sep 2018 13:04:43: 27000000 INFO @ Sat, 08 Sep 2018 13:04:48: 28000000 INFO @ Sat, 08 Sep 2018 13:04:49: 28000000 INFO @ Sat, 08 Sep 2018 13:04:49: 28000000 INFO @ Sat, 08 Sep 2018 13:04:54: 29000000 INFO @ Sat, 08 Sep 2018 13:04:55: 29000000 INFO @ Sat, 08 Sep 2018 13:04:55: 29000000 INFO @ Sat, 08 Sep 2018 13:04:59: 30000000 INFO @ Sat, 08 Sep 2018 13:05:00: 30000000 INFO @ Sat, 08 Sep 2018 13:05:00: 30000000 INFO @ Sat, 08 Sep 2018 13:05:05: 31000000 INFO @ Sat, 08 Sep 2018 13:05:06: 31000000 INFO @ Sat, 08 Sep 2018 13:05:06: 31000000 INFO @ Sat, 08 Sep 2018 13:05:11: 32000000 INFO @ Sat, 08 Sep 2018 13:05:12: 32000000 INFO @ Sat, 08 Sep 2018 13:05:12: 32000000 INFO @ Sat, 08 Sep 2018 13:05:17: 33000000 INFO @ Sat, 08 Sep 2018 13:05:18: 33000000 INFO @ Sat, 08 Sep 2018 13:05:18: 33000000 INFO @ Sat, 08 Sep 2018 13:05:22: 34000000 INFO @ Sat, 08 Sep 2018 13:05:23: 34000000 INFO @ Sat, 08 Sep 2018 13:05:23: 34000000 INFO @ Sat, 08 Sep 2018 13:05:28: 35000000 INFO @ Sat, 08 Sep 2018 13:05:29: 35000000 INFO @ Sat, 08 Sep 2018 13:05:29: 35000000 INFO @ Sat, 08 Sep 2018 13:05:34: 36000000 INFO @ Sat, 08 Sep 2018 13:05:35: 36000000 INFO @ Sat, 08 Sep 2018 13:05:35: 36000000 INFO @ Sat, 08 Sep 2018 13:05:40: 37000000 INFO @ Sat, 08 Sep 2018 13:05:41: 37000000 INFO @ Sat, 08 Sep 2018 13:05:41: 37000000 INFO @ Sat, 08 Sep 2018 13:05:45: 38000000 INFO @ Sat, 08 Sep 2018 13:05:46: 38000000 INFO @ Sat, 08 Sep 2018 13:05:46: 38000000 INFO @ Sat, 08 Sep 2018 13:05:51: 39000000 INFO @ Sat, 08 Sep 2018 13:05:52: 39000000 INFO @ Sat, 08 Sep 2018 13:05:52: 39000000 INFO @ Sat, 08 Sep 2018 13:05:57: 40000000 INFO @ Sat, 08 Sep 2018 13:05:58: 40000000 INFO @ Sat, 08 Sep 2018 13:05:58: 40000000 INFO @ Sat, 08 Sep 2018 13:06:01: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:06:01: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:06:01: #1 total tags in treatment: 19667400 INFO @ Sat, 08 Sep 2018 13:06:01: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:06:01: #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 13:06:02: #1 tags after filtering in treatment: 17113479 INFO @ Sat, 08 Sep 2018 13:06:02: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 08 Sep 2018 13:06:02: #1 finished! INFO @ Sat, 08 Sep 2018 13:06:02: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:06:02: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:06:02: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 13:06:02: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:06:02: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 13:06:02: #1 total tags in treatment: 19667400 INFO @ Sat, 08 Sep 2018 13:06:02: #1 total tags in treatment: 19667400 INFO @ Sat, 08 Sep 2018 13:06:02: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:06:02: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:06:02: #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 13:06:02: #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 13:06:02: #1 tags after filtering in treatment: 17113479 INFO @ Sat, 08 Sep 2018 13:06:02: #1 tags after filtering in treatment: 17113479 INFO @ Sat, 08 Sep 2018 13:06:02: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 08 Sep 2018 13:06:02: #1 Redundant rate of treatment: 0.13 INFO @ Sat, 08 Sep 2018 13:06:02: #1 finished! INFO @ Sat, 08 Sep 2018 13:06:02: #1 finished! INFO @ Sat, 08 Sep 2018 13:06:02: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:06:02: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:06:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:06:03: #2 number of paired peaks: 2331 INFO @ Sat, 08 Sep 2018 13:06:03: start model_add_line... INFO @ Sat, 08 Sep 2018 13:06:03: start X-correlation... INFO @ Sat, 08 Sep 2018 13:06:03: end of X-cor INFO @ Sat, 08 Sep 2018 13:06:03: #2 finished! INFO @ Sat, 08 Sep 2018 13:06:03: #2 predicted fragment length is 183 bps INFO @ Sat, 08 Sep 2018 13:06:03: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 08 Sep 2018 13:06:03: #2.2 Generate R script for model : SRX2000507.10_model.r INFO @ Sat, 08 Sep 2018 13:06:03: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:06:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:06:04: #2 number of paired peaks: 2331 INFO @ Sat, 08 Sep 2018 13:06:04: start model_add_line... INFO @ Sat, 08 Sep 2018 13:06:04: #2 number of paired peaks: 2331 INFO @ Sat, 08 Sep 2018 13:06:04: start model_add_line... INFO @ Sat, 08 Sep 2018 13:06:04: start X-correlation... INFO @ Sat, 08 Sep 2018 13:06:04: end of X-cor INFO @ Sat, 08 Sep 2018 13:06:04: #2 finished! INFO @ Sat, 08 Sep 2018 13:06:04: #2 predicted fragment length is 183 bps INFO @ Sat, 08 Sep 2018 13:06:04: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 08 Sep 2018 13:06:04: #2.2 Generate R script for model : SRX2000507.05_model.r INFO @ Sat, 08 Sep 2018 13:06:04: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:06:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:06:04: start X-correlation... INFO @ Sat, 08 Sep 2018 13:06:04: end of X-cor INFO @ Sat, 08 Sep 2018 13:06:04: #2 finished! INFO @ Sat, 08 Sep 2018 13:06:04: #2 predicted fragment length is 183 bps INFO @ Sat, 08 Sep 2018 13:06:04: #2 alternative fragment length(s) may be 183 bps INFO @ Sat, 08 Sep 2018 13:06:04: #2.2 Generate R script for model : SRX2000507.20_model.r INFO @ Sat, 08 Sep 2018 13:06:04: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:06:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:06:51: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:06:53: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:06:54: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:07:11: #4 Write output xls file... SRX2000507.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:07:11: #4 Write peak in narrowPeak format file... SRX2000507.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:07:11: #4 Write summits bed file... SRX2000507.10_summits.bed INFO @ Sat, 08 Sep 2018 13:07:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6372 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:07:15: #4 Write output xls file... SRX2000507.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:07:15: #4 Write peak in narrowPeak format file... SRX2000507.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:07:15: #4 Write summits bed file... SRX2000507.05_summits.bed INFO @ Sat, 08 Sep 2018 13:07:15: Done! INFO @ Sat, 08 Sep 2018 13:07:15: #4 Write output xls file... SRX2000507.20_peaks.xls pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8252 records, 4 fields): 12 millis INFO @ Sat, 08 Sep 2018 13:07:16: #4 Write peak in narrowPeak format file... SRX2000507.20_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:07:16: #4 Write summits bed file... SRX2000507.20_summits.bed INFO @ Sat, 08 Sep 2018 13:07:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4163 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。