Job ID = 9159849 sra ファイルのダウンロード中... Completed: 1907788K bytes transferred in 19 seconds (782809K bits/sec), in 1 file, 2 directories. 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... Written 29586965 spots for /home/okishinya/chipatlas/results/dm3/SRX749036/SRR1636764.sra Written 29586965 spots total 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:36:40 29586965 reads; of these: 29586965 (100.00%) were paired; of these: 6261942 (21.16%) aligned concordantly 0 times 21260554 (71.86%) aligned concordantly exactly 1 time 2064469 (6.98%) aligned concordantly >1 times ---- 6261942 pairs aligned concordantly 0 times; of these: 26376 (0.42%) aligned discordantly 1 time ---- 6235566 pairs aligned 0 times concordantly or discordantly; of these: 12471132 mates make up the pairs; of these: 11580349 (92.86%) aligned 0 times 776964 (6.23%) aligned exactly 1 time 113819 (0.91%) aligned >1 times 80.43% overall alignment rate Time searching: 00:36:41 Overall time: 00:36:41 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] 6101129 / 23345046 = 0.2613 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 @ Wed, 28 Jun 2017 01:07:52: # Command line: callpeak -t SRX749036.bam -f BAM -g dm -n SRX749036.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749036.20 # format = BAM # ChIP-seq file = ['SRX749036.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 @ Wed, 28 Jun 2017 01:07:52: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:07:52: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:07:52: # Command line: callpeak -t SRX749036.bam -f BAM -g dm -n SRX749036.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749036.10 # format = BAM # ChIP-seq file = ['SRX749036.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 @ Wed, 28 Jun 2017 01:07:52: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:07:52: # Command line: callpeak -t SRX749036.bam -f BAM -g dm -n SRX749036.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749036.05 # format = BAM # ChIP-seq file = ['SRX749036.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 @ Wed, 28 Jun 2017 01:07:52: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:07:52: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:07:52: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:07:58: 1000000 INFO @ Wed, 28 Jun 2017 01:07:59: 1000000 INFO @ Wed, 28 Jun 2017 01:07:59: 1000000 INFO @ Wed, 28 Jun 2017 01:08:04: 2000000 INFO @ Wed, 28 Jun 2017 01:08:05: 2000000 INFO @ Wed, 28 Jun 2017 01:08:05: 2000000 INFO @ Wed, 28 Jun 2017 01:08:10: 3000000 INFO @ Wed, 28 Jun 2017 01:08:11: 3000000 INFO @ Wed, 28 Jun 2017 01:08:11: 3000000 INFO @ Wed, 28 Jun 2017 01:08:16: 4000000 INFO @ Wed, 28 Jun 2017 01:08:17: 4000000 INFO @ Wed, 28 Jun 2017 01:08:17: 4000000 INFO @ Wed, 28 Jun 2017 01:08:22: 5000000 INFO @ Wed, 28 Jun 2017 01:08:23: 5000000 INFO @ Wed, 28 Jun 2017 01:08:23: 5000000 INFO @ Wed, 28 Jun 2017 01:08:28: 6000000 INFO @ Wed, 28 Jun 2017 01:08:29: 6000000 INFO @ Wed, 28 Jun 2017 01:08:29: 6000000 INFO @ Wed, 28 Jun 2017 01:08:34: 7000000 INFO @ Wed, 28 Jun 2017 01:08:35: 7000000 INFO @ Wed, 28 Jun 2017 01:08:35: 7000000 INFO @ Wed, 28 Jun 2017 01:08:40: 8000000 INFO @ Wed, 28 Jun 2017 01:08:42: 8000000 INFO @ Wed, 28 Jun 2017 01:08:42: 8000000 INFO @ Wed, 28 Jun 2017 01:08:46: 9000000 INFO @ Wed, 28 Jun 2017 01:08:48: 9000000 INFO @ Wed, 28 Jun 2017 01:08:48: 9000000 INFO @ Wed, 28 Jun 2017 01:08:52: 10000000 INFO @ Wed, 28 Jun 2017 01:08:54: 10000000 INFO @ Wed, 28 Jun 2017 01:08:54: 10000000 INFO @ Wed, 28 Jun 2017 01:08:58: 11000000 INFO @ Wed, 28 Jun 2017 01:09:00: 11000000 INFO @ Wed, 28 Jun 2017 01:09:00: 11000000 INFO @ Wed, 28 Jun 2017 01:09:04: 12000000 INFO @ Wed, 28 Jun 2017 01:09:05: 12000000 INFO @ Wed, 28 Jun 2017 01:09:05: 12000000 INFO @ Wed, 28 Jun 2017 01:09:10: 13000000 INFO @ Wed, 28 Jun 2017 01:09:11: 13000000 INFO @ Wed, 28 Jun 2017 01:09:11: 13000000 INFO @ Wed, 28 Jun 2017 01:09:15: 14000000 INFO @ Wed, 28 Jun 2017 01:09:17: 14000000 INFO @ Wed, 28 Jun 2017 01:09:17: 14000000 INFO @ Wed, 28 Jun 2017 01:09:21: 15000000 INFO @ Wed, 28 Jun 2017 01:09:23: 15000000 INFO @ Wed, 28 Jun 2017 01:09:23: 15000000 INFO @ Wed, 28 Jun 2017 01:09:27: 16000000 INFO @ Wed, 28 Jun 2017 01:09:29: 16000000 INFO @ Wed, 28 Jun 2017 01:09:29: 16000000 INFO @ Wed, 28 Jun 2017 01:09:33: 17000000 INFO @ Wed, 28 Jun 2017 01:09:35: 17000000 INFO @ Wed, 28 Jun 2017 01:09:35: 17000000 INFO @ Wed, 28 Jun 2017 01:09:39: 18000000 INFO @ Wed, 28 Jun 2017 01:09:41: 18000000 INFO @ Wed, 28 Jun 2017 01:09:41: 18000000 INFO @ Wed, 28 Jun 2017 01:09:46: 19000000 INFO @ Wed, 28 Jun 2017 01:09:48: 19000000 INFO @ Wed, 28 Jun 2017 01:09:48: 19000000 INFO @ Wed, 28 Jun 2017 01:09:52: 20000000 INFO @ Wed, 28 Jun 2017 01:09:54: 20000000 INFO @ Wed, 28 Jun 2017 01:09:54: 20000000 INFO @ Wed, 28 Jun 2017 01:09:58: 21000000 INFO @ Wed, 28 Jun 2017 01:10:00: 21000000 INFO @ Wed, 28 Jun 2017 01:10:01: 21000000 INFO @ Wed, 28 Jun 2017 01:10:04: 22000000 INFO @ Wed, 28 Jun 2017 01:10:06: 22000000 INFO @ Wed, 28 Jun 2017 01:10:07: 22000000 INFO @ Wed, 28 Jun 2017 01:10:10: 23000000 INFO @ Wed, 28 Jun 2017 01:10:13: 23000000 INFO @ Wed, 28 Jun 2017 01:10:13: 23000000 INFO @ Wed, 28 Jun 2017 01:10:16: 24000000 INFO @ Wed, 28 Jun 2017 01:10:19: 24000000 INFO @ Wed, 28 Jun 2017 01:10:19: 24000000 INFO @ Wed, 28 Jun 2017 01:10:22: 25000000 INFO @ Wed, 28 Jun 2017 01:10:25: 25000000 INFO @ Wed, 28 Jun 2017 01:10:26: 25000000 INFO @ Wed, 28 Jun 2017 01:10:28: 26000000 INFO @ Wed, 28 Jun 2017 01:10:32: 26000000 INFO @ Wed, 28 Jun 2017 01:10:32: 26000000 INFO @ Wed, 28 Jun 2017 01:10:34: 27000000 INFO @ Wed, 28 Jun 2017 01:10:38: 27000000 INFO @ Wed, 28 Jun 2017 01:10:39: 27000000 INFO @ Wed, 28 Jun 2017 01:10:40: 28000000 INFO @ Wed, 28 Jun 2017 01:10:45: 28000000 INFO @ Wed, 28 Jun 2017 01:10:45: 28000000 INFO @ Wed, 28 Jun 2017 01:10:46: 29000000 INFO @ Wed, 28 Jun 2017 01:10:51: 29000000 INFO @ Wed, 28 Jun 2017 01:10:52: 29000000 INFO @ Wed, 28 Jun 2017 01:10:52: 30000000 INFO @ Wed, 28 Jun 2017 01:10:58: 30000000 INFO @ Wed, 28 Jun 2017 01:10:58: 30000000 INFO @ Wed, 28 Jun 2017 01:10:58: 31000000 INFO @ Wed, 28 Jun 2017 01:11:04: 31000000 INFO @ Wed, 28 Jun 2017 01:11:04: 32000000 INFO @ Wed, 28 Jun 2017 01:11:05: 31000000 INFO @ Wed, 28 Jun 2017 01:11:10: 32000000 INFO @ Wed, 28 Jun 2017 01:11:11: 33000000 INFO @ Wed, 28 Jun 2017 01:11:11: 32000000 INFO @ Wed, 28 Jun 2017 01:11:17: 34000000 INFO @ Wed, 28 Jun 2017 01:11:17: 33000000 INFO @ Wed, 28 Jun 2017 01:11:18: 33000000 INFO @ Wed, 28 Jun 2017 01:11:23: 35000000 INFO @ Wed, 28 Jun 2017 01:11:23: 34000000 INFO @ Wed, 28 Jun 2017 01:11:24: 34000000 INFO @ Wed, 28 Jun 2017 01:11:25: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:11:25: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:11:25: #1 total tags in treatment: 17228770 INFO @ Wed, 28 Jun 2017 01:11:25: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:11:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:11:26: #1 tags after filtering in treatment: 6980726 INFO @ Wed, 28 Jun 2017 01:11:26: #1 Redundant rate of treatment: 0.59 INFO @ Wed, 28 Jun 2017 01:11:26: #1 finished! INFO @ Wed, 28 Jun 2017 01:11:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:11:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:11:27: #2 number of paired peaks: 9400 INFO @ Wed, 28 Jun 2017 01:11:27: start model_add_line... INFO @ Wed, 28 Jun 2017 01:11:27: start X-correlation... INFO @ Wed, 28 Jun 2017 01:11:27: end of X-cor INFO @ Wed, 28 Jun 2017 01:11:27: #2 finished! INFO @ Wed, 28 Jun 2017 01:11:27: #2 predicted fragment length is 126 bps INFO @ Wed, 28 Jun 2017 01:11:27: #2 alternative fragment length(s) may be 126 bps INFO @ Wed, 28 Jun 2017 01:11:27: #2.2 Generate R script for model : SRX749036.10_model.r INFO @ Wed, 28 Jun 2017 01:11:27: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:11:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:11:29: 35000000 INFO @ Wed, 28 Jun 2017 01:11:30: 35000000 INFO @ Wed, 28 Jun 2017 01:11:32: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:11:32: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:11:32: #1 total tags in treatment: 17228770 INFO @ Wed, 28 Jun 2017 01:11:32: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:11:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:11:32: #1 tags after filtering in treatment: 6980726 INFO @ Wed, 28 Jun 2017 01:11:32: #1 Redundant rate of treatment: 0.59 INFO @ Wed, 28 Jun 2017 01:11:32: #1 finished! INFO @ Wed, 28 Jun 2017 01:11:32: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:11:32: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:11:33: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:11:33: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:11:33: #1 total tags in treatment: 17228770 INFO @ Wed, 28 Jun 2017 01:11:33: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:11:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:11:33: #1 tags after filtering in treatment: 6980726 INFO @ Wed, 28 Jun 2017 01:11:33: #1 Redundant rate of treatment: 0.59 INFO @ Wed, 28 Jun 2017 01:11:33: #1 finished! INFO @ Wed, 28 Jun 2017 01:11:33: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:11:33: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:11:34: #2 number of paired peaks: 9400 INFO @ Wed, 28 Jun 2017 01:11:34: start model_add_line... INFO @ Wed, 28 Jun 2017 01:11:34: start X-correlation... INFO @ Wed, 28 Jun 2017 01:11:34: end of X-cor INFO @ Wed, 28 Jun 2017 01:11:34: #2 finished! INFO @ Wed, 28 Jun 2017 01:11:34: #2 predicted fragment length is 126 bps INFO @ Wed, 28 Jun 2017 01:11:34: #2 alternative fragment length(s) may be 126 bps INFO @ Wed, 28 Jun 2017 01:11:34: #2.2 Generate R script for model : SRX749036.20_model.r INFO @ Wed, 28 Jun 2017 01:11:34: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:11:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:11:35: #2 number of paired peaks: 9400 INFO @ Wed, 28 Jun 2017 01:11:35: start model_add_line... INFO @ Wed, 28 Jun 2017 01:11:35: start X-correlation... INFO @ Wed, 28 Jun 2017 01:11:35: end of X-cor INFO @ Wed, 28 Jun 2017 01:11:35: #2 finished! INFO @ Wed, 28 Jun 2017 01:11:35: #2 predicted fragment length is 126 bps INFO @ Wed, 28 Jun 2017 01:11:35: #2 alternative fragment length(s) may be 126 bps INFO @ Wed, 28 Jun 2017 01:11:35: #2.2 Generate R script for model : SRX749036.05_model.r INFO @ Wed, 28 Jun 2017 01:11:35: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:11:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:11:46: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:11:53: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:11:53: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:11:55: #4 Write output xls file... SRX749036.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:11:56: #4 Write peak in narrowPeak format file... SRX749036.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:11:56: #4 Write summits bed file... SRX749036.10_summits.bed INFO @ Wed, 28 Jun 2017 01:11:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (13340 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:12:03: #4 Write output xls file... SRX749036.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:12:03: #4 Write peak in narrowPeak format file... SRX749036.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:12:03: #4 Write summits bed file... SRX749036.05_summits.bed INFO @ Wed, 28 Jun 2017 01:12:03: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15789 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:12:04: #4 Write output xls file... SRX749036.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:12:05: #4 Write peak in narrowPeak format file... SRX749036.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:12:05: #4 Write summits bed file... SRX749036.20_summits.bed INFO @ Wed, 28 Jun 2017 01:12:05: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10759 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。