Job ID = 11171110 sra ファイルのダウンロード中... Completed: 1025385K bytes transferred in 15 seconds (555933K 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 22189541 spots for /home/okishinya/chipatlas/results/dm3/SRX2000506/SRR4000133.sra Written 22189541 spots for /home/okishinya/chipatlas/results/dm3/SRX2000506/SRR4000133.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: 00:40:50 22189541 reads; of these: 22189541 (100.00%) were paired; of these: 6495826 (29.27%) aligned concordantly 0 times 11985854 (54.02%) aligned concordantly exactly 1 time 3707861 (16.71%) aligned concordantly >1 times ---- 6495826 pairs aligned concordantly 0 times; of these: 87831 (1.35%) aligned discordantly 1 time ---- 6407995 pairs aligned 0 times concordantly or discordantly; of these: 12815990 mates make up the pairs; of these: 11763350 (91.79%) aligned 0 times 639549 (4.99%) aligned exactly 1 time 413091 (3.22%) aligned >1 times 73.49% overall alignment rate Time searching: 00:40:50 Overall time: 00:40:50 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] 270730 / 15719046 = 0.0172 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 12:43:56: # Command line: callpeak -t SRX2000506.bam -f BAM -g dm -n SRX2000506.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2000506.20 # format = BAM # ChIP-seq file = ['SRX2000506.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 12:43:56: # Command line: callpeak -t SRX2000506.bam -f BAM -g dm -n SRX2000506.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2000506.10 # format = BAM # ChIP-seq file = ['SRX2000506.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 12:43:56: # Command line: callpeak -t SRX2000506.bam -f BAM -g dm -n SRX2000506.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2000506.05 # format = BAM # ChIP-seq file = ['SRX2000506.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 12:43:56: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:43:56: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:43:56: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:43:56: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:43:56: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:43:56: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:44:02: 1000000 INFO @ Sat, 08 Sep 2018 12:44:02: 1000000 INFO @ Sat, 08 Sep 2018 12:44:02: 1000000 INFO @ Sat, 08 Sep 2018 12:44:09: 2000000 INFO @ Sat, 08 Sep 2018 12:44:09: 2000000 INFO @ Sat, 08 Sep 2018 12:44:09: 2000000 INFO @ Sat, 08 Sep 2018 12:44:15: 3000000 INFO @ Sat, 08 Sep 2018 12:44:15: 3000000 INFO @ Sat, 08 Sep 2018 12:44:16: 3000000 INFO @ Sat, 08 Sep 2018 12:44:21: 4000000 INFO @ Sat, 08 Sep 2018 12:44:22: 4000000 INFO @ Sat, 08 Sep 2018 12:44:22: 4000000 INFO @ Sat, 08 Sep 2018 12:44:28: 5000000 INFO @ Sat, 08 Sep 2018 12:44:29: 5000000 INFO @ Sat, 08 Sep 2018 12:44:29: 5000000 INFO @ Sat, 08 Sep 2018 12:44:34: 6000000 INFO @ Sat, 08 Sep 2018 12:44:35: 6000000 INFO @ Sat, 08 Sep 2018 12:44:36: 6000000 INFO @ Sat, 08 Sep 2018 12:44:40: 7000000 INFO @ Sat, 08 Sep 2018 12:44:42: 7000000 INFO @ Sat, 08 Sep 2018 12:44:42: 7000000 INFO @ Sat, 08 Sep 2018 12:44:47: 8000000 INFO @ Sat, 08 Sep 2018 12:44:49: 8000000 INFO @ Sat, 08 Sep 2018 12:44:49: 8000000 INFO @ Sat, 08 Sep 2018 12:44:53: 9000000 INFO @ Sat, 08 Sep 2018 12:44:55: 9000000 INFO @ Sat, 08 Sep 2018 12:44:56: 9000000 INFO @ Sat, 08 Sep 2018 12:44:59: 10000000 INFO @ Sat, 08 Sep 2018 12:45:02: 10000000 INFO @ Sat, 08 Sep 2018 12:45:03: 10000000 INFO @ Sat, 08 Sep 2018 12:45:06: 11000000 INFO @ Sat, 08 Sep 2018 12:45:09: 11000000 INFO @ Sat, 08 Sep 2018 12:45:10: 11000000 INFO @ Sat, 08 Sep 2018 12:45:12: 12000000 INFO @ Sat, 08 Sep 2018 12:45:15: 12000000 INFO @ Sat, 08 Sep 2018 12:45:16: 12000000 INFO @ Sat, 08 Sep 2018 12:45:18: 13000000 INFO @ Sat, 08 Sep 2018 12:45:22: 13000000 INFO @ Sat, 08 Sep 2018 12:45:23: 13000000 INFO @ Sat, 08 Sep 2018 12:45:25: 14000000 INFO @ Sat, 08 Sep 2018 12:45:28: 14000000 INFO @ Sat, 08 Sep 2018 12:45:30: 14000000 INFO @ Sat, 08 Sep 2018 12:45:31: 15000000 INFO @ Sat, 08 Sep 2018 12:45:35: 15000000 INFO @ Sat, 08 Sep 2018 12:45:37: 15000000 INFO @ Sat, 08 Sep 2018 12:45:38: 16000000 INFO @ Sat, 08 Sep 2018 12:45:42: 16000000 INFO @ Sat, 08 Sep 2018 12:45:43: 16000000 INFO @ Sat, 08 Sep 2018 12:45:44: 17000000 INFO @ Sat, 08 Sep 2018 12:45:48: 17000000 INFO @ Sat, 08 Sep 2018 12:45:50: 17000000 INFO @ Sat, 08 Sep 2018 12:45:50: 18000000 INFO @ Sat, 08 Sep 2018 12:45:55: 18000000 INFO @ Sat, 08 Sep 2018 12:45:57: 18000000 INFO @ Sat, 08 Sep 2018 12:45:57: 19000000 INFO @ Sat, 08 Sep 2018 12:46:01: 19000000 INFO @ Sat, 08 Sep 2018 12:46:03: 20000000 INFO @ Sat, 08 Sep 2018 12:46:04: 19000000 INFO @ Sat, 08 Sep 2018 12:46:08: 20000000 INFO @ Sat, 08 Sep 2018 12:46:10: 21000000 INFO @ Sat, 08 Sep 2018 12:46:10: 20000000 INFO @ Sat, 08 Sep 2018 12:46:15: 21000000 INFO @ Sat, 08 Sep 2018 12:46:16: 22000000 INFO @ Sat, 08 Sep 2018 12:46:17: 21000000 INFO @ Sat, 08 Sep 2018 12:46:21: 22000000 INFO @ Sat, 08 Sep 2018 12:46:23: 23000000 INFO @ Sat, 08 Sep 2018 12:46:24: 22000000 INFO @ Sat, 08 Sep 2018 12:46:28: 23000000 INFO @ Sat, 08 Sep 2018 12:46:29: 24000000 INFO @ Sat, 08 Sep 2018 12:46:31: 23000000 INFO @ Sat, 08 Sep 2018 12:46:35: 24000000 INFO @ Sat, 08 Sep 2018 12:46:35: 25000000 INFO @ Sat, 08 Sep 2018 12:46:38: 24000000 INFO @ Sat, 08 Sep 2018 12:46:41: 25000000 INFO @ Sat, 08 Sep 2018 12:46:42: 26000000 INFO @ Sat, 08 Sep 2018 12:46:45: 25000000 INFO @ Sat, 08 Sep 2018 12:46:48: 26000000 INFO @ Sat, 08 Sep 2018 12:46:49: 27000000 INFO @ Sat, 08 Sep 2018 12:46:52: 26000000 INFO @ Sat, 08 Sep 2018 12:46:54: 27000000 INFO @ Sat, 08 Sep 2018 12:46:55: 28000000 INFO @ Sat, 08 Sep 2018 12:46:59: 27000000 INFO @ Sat, 08 Sep 2018 12:47:01: 28000000 INFO @ Sat, 08 Sep 2018 12:47:02: 29000000 INFO @ Sat, 08 Sep 2018 12:47:06: 28000000 INFO @ Sat, 08 Sep 2018 12:47:08: 29000000 INFO @ Sat, 08 Sep 2018 12:47:09: 30000000 INFO @ Sat, 08 Sep 2018 12:47:12: 29000000 INFO @ Sat, 08 Sep 2018 12:47:14: 30000000 INFO @ Sat, 08 Sep 2018 12:47:16: 31000000 INFO @ Sat, 08 Sep 2018 12:47:19: 30000000 INFO @ Sat, 08 Sep 2018 12:47:21: 31000000 INFO @ Sat, 08 Sep 2018 12:47:22: 32000000 INFO @ Sat, 08 Sep 2018 12:47:23: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 12:47:23: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 12:47:23: #1 total tags in treatment: 15423356 INFO @ Sat, 08 Sep 2018 12:47:23: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:47:23: #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 12:47:23: #1 tags after filtering in treatment: 13252669 INFO @ Sat, 08 Sep 2018 12:47:23: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 08 Sep 2018 12:47:23: #1 finished! INFO @ Sat, 08 Sep 2018 12:47:23: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:47:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:47:24: #2 number of paired peaks: 3160 INFO @ Sat, 08 Sep 2018 12:47:24: start model_add_line... INFO @ Sat, 08 Sep 2018 12:47:24: start X-correlation... INFO @ Sat, 08 Sep 2018 12:47:24: end of X-cor INFO @ Sat, 08 Sep 2018 12:47:24: #2 finished! INFO @ Sat, 08 Sep 2018 12:47:24: #2 predicted fragment length is 192 bps INFO @ Sat, 08 Sep 2018 12:47:24: #2 alternative fragment length(s) may be 192 bps INFO @ Sat, 08 Sep 2018 12:47:24: #2.2 Generate R script for model : SRX2000506.10_model.r INFO @ Sat, 08 Sep 2018 12:47:24: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:47:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:47:26: 31000000 INFO @ Sat, 08 Sep 2018 12:47:27: 32000000 INFO @ Sat, 08 Sep 2018 12:47:28: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 12:47:28: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 12:47:28: #1 total tags in treatment: 15423356 INFO @ Sat, 08 Sep 2018 12:47:28: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:47:28: #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 12:47:28: #1 tags after filtering in treatment: 13252669 INFO @ Sat, 08 Sep 2018 12:47:28: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 08 Sep 2018 12:47:28: #1 finished! INFO @ Sat, 08 Sep 2018 12:47:28: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:47:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:47:30: #2 number of paired peaks: 3160 INFO @ Sat, 08 Sep 2018 12:47:30: start model_add_line... INFO @ Sat, 08 Sep 2018 12:47:30: start X-correlation... INFO @ Sat, 08 Sep 2018 12:47:30: end of X-cor INFO @ Sat, 08 Sep 2018 12:47:30: #2 finished! INFO @ Sat, 08 Sep 2018 12:47:30: #2 predicted fragment length is 192 bps INFO @ Sat, 08 Sep 2018 12:47:30: #2 alternative fragment length(s) may be 192 bps INFO @ Sat, 08 Sep 2018 12:47:30: #2.2 Generate R script for model : SRX2000506.20_model.r INFO @ Sat, 08 Sep 2018 12:47:30: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:47:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:47:32: 32000000 INFO @ Sat, 08 Sep 2018 12:47:33: #1 tag size is determined as 51 bps INFO @ Sat, 08 Sep 2018 12:47:33: #1 tag size = 51 INFO @ Sat, 08 Sep 2018 12:47:33: #1 total tags in treatment: 15423356 INFO @ Sat, 08 Sep 2018 12:47:33: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:47:33: #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 12:47:33: #1 tags after filtering in treatment: 13252669 INFO @ Sat, 08 Sep 2018 12:47:33: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 08 Sep 2018 12:47:33: #1 finished! INFO @ Sat, 08 Sep 2018 12:47:33: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:47:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:47:34: #2 number of paired peaks: 3160 INFO @ Sat, 08 Sep 2018 12:47:34: start model_add_line... INFO @ Sat, 08 Sep 2018 12:47:34: start X-correlation... INFO @ Sat, 08 Sep 2018 12:47:34: end of X-cor INFO @ Sat, 08 Sep 2018 12:47:34: #2 finished! INFO @ Sat, 08 Sep 2018 12:47:34: #2 predicted fragment length is 192 bps INFO @ Sat, 08 Sep 2018 12:47:34: #2 alternative fragment length(s) may be 192 bps INFO @ Sat, 08 Sep 2018 12:47:34: #2.2 Generate R script for model : SRX2000506.05_model.r INFO @ Sat, 08 Sep 2018 12:47:34: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:47:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:48:03: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:48:08: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:48:14: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:48:20: #4 Write output xls file... SRX2000506.10_peaks.xls INFO @ Sat, 08 Sep 2018 12:48:20: #4 Write peak in narrowPeak format file... SRX2000506.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:48:20: #4 Write summits bed file... SRX2000506.10_summits.bed INFO @ Sat, 08 Sep 2018 12:48:20: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6580 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:48:26: #4 Write output xls file... SRX2000506.20_peaks.xls INFO @ Sat, 08 Sep 2018 12:48:26: #4 Write peak in narrowPeak format file... SRX2000506.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:48:26: #4 Write summits bed file... SRX2000506.20_summits.bed INFO @ Sat, 08 Sep 2018 12:48:26: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4458 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 12:48:33: #4 Write output xls file... SRX2000506.05_peaks.xls INFO @ Sat, 08 Sep 2018 12:48:33: #4 Write peak in narrowPeak format file... SRX2000506.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 12:48:33: #4 Write summits bed file... SRX2000506.05_summits.bed INFO @ Sat, 08 Sep 2018 12:48:33: Done! pass1 - making usageList (15 chroms): 89 millis pass2 - checking and writing primary data (8424 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。