Job ID = 9730439 sra ファイルのダウンロード中... Completed: 481706K bytes transferred in 10 seconds (389488K 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 12822273 spots for /home/okishinya/chipatlas/results/dm3/SRX2559026/SRR5253491.sra Written 12822273 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:47:41 12822273 reads; of these: 12822273 (100.00%) were paired; of these: 957088 (7.46%) aligned concordantly 0 times 6048016 (47.17%) aligned concordantly exactly 1 time 5817169 (45.37%) aligned concordantly >1 times ---- 957088 pairs aligned concordantly 0 times; of these: 202526 (21.16%) aligned discordantly 1 time ---- 754562 pairs aligned 0 times concordantly or discordantly; of these: 1509124 mates make up the pairs; of these: 753314 (49.92%) aligned 0 times 233949 (15.50%) aligned exactly 1 time 521861 (34.58%) aligned >1 times 97.06% overall alignment rate Time searching: 00:47:41 Overall time: 00:47:41 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 12 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] 988653 / 12047684 = 0.0821 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 @ Sun, 03 Sep 2017 01:49:28: # Command line: callpeak -t SRX2559026.bam -f BAM -g dm -n SRX2559026.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2559026.10 # format = BAM # ChIP-seq file = ['SRX2559026.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 @ Sun, 03 Sep 2017 01:49:28: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:49:28: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:49:28: # Command line: callpeak -t SRX2559026.bam -f BAM -g dm -n SRX2559026.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2559026.05 # format = BAM # ChIP-seq file = ['SRX2559026.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 @ Sun, 03 Sep 2017 01:49:28: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:49:28: # Command line: callpeak -t SRX2559026.bam -f BAM -g dm -n SRX2559026.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2559026.20 # format = BAM # ChIP-seq file = ['SRX2559026.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 @ Sun, 03 Sep 2017 01:49:28: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:49:28: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:49:28: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:49:34: 1000000 INFO @ Sun, 03 Sep 2017 01:49:34: 1000000 INFO @ Sun, 03 Sep 2017 01:49:34: 1000000 INFO @ Sun, 03 Sep 2017 01:49:39: 2000000 INFO @ Sun, 03 Sep 2017 01:49:39: 2000000 INFO @ Sun, 03 Sep 2017 01:49:40: 2000000 INFO @ Sun, 03 Sep 2017 01:49:45: 3000000 INFO @ Sun, 03 Sep 2017 01:49:46: 3000000 INFO @ Sun, 03 Sep 2017 01:49:47: 3000000 INFO @ Sun, 03 Sep 2017 01:49:52: 4000000 INFO @ Sun, 03 Sep 2017 01:49:52: 4000000 INFO @ Sun, 03 Sep 2017 01:49:54: 4000000 INFO @ Sun, 03 Sep 2017 01:49:58: 5000000 INFO @ Sun, 03 Sep 2017 01:49:58: 5000000 INFO @ Sun, 03 Sep 2017 01:50:01: 5000000 INFO @ Sun, 03 Sep 2017 01:50:04: 6000000 INFO @ Sun, 03 Sep 2017 01:50:05: 6000000 INFO @ Sun, 03 Sep 2017 01:50:07: 6000000 INFO @ Sun, 03 Sep 2017 01:50:10: 7000000 INFO @ Sun, 03 Sep 2017 01:50:11: 7000000 INFO @ Sun, 03 Sep 2017 01:50:14: 7000000 INFO @ Sun, 03 Sep 2017 01:50:16: 8000000 INFO @ Sun, 03 Sep 2017 01:50:18: 8000000 INFO @ Sun, 03 Sep 2017 01:50:21: 8000000 INFO @ Sun, 03 Sep 2017 01:50:22: 9000000 INFO @ Sun, 03 Sep 2017 01:50:24: 9000000 INFO @ Sun, 03 Sep 2017 01:50:27: 9000000 INFO @ Sun, 03 Sep 2017 01:50:28: 10000000 INFO @ Sun, 03 Sep 2017 01:50:30: 10000000 INFO @ Sun, 03 Sep 2017 01:50:33: 10000000 INFO @ Sun, 03 Sep 2017 01:50:34: 11000000 INFO @ Sun, 03 Sep 2017 01:50:37: 11000000 INFO @ Sun, 03 Sep 2017 01:50:39: 12000000 INFO @ Sun, 03 Sep 2017 01:50:40: 11000000 INFO @ Sun, 03 Sep 2017 01:50:43: 12000000 INFO @ Sun, 03 Sep 2017 01:50:46: 13000000 INFO @ Sun, 03 Sep 2017 01:50:47: 12000000 INFO @ Sun, 03 Sep 2017 01:50:49: 13000000 INFO @ Sun, 03 Sep 2017 01:50:52: 14000000 INFO @ Sun, 03 Sep 2017 01:50:54: 13000000 INFO @ Sun, 03 Sep 2017 01:50:55: 14000000 INFO @ Sun, 03 Sep 2017 01:50:59: 15000000 INFO @ Sun, 03 Sep 2017 01:51:00: 14000000 INFO @ Sun, 03 Sep 2017 01:51:01: 15000000 INFO @ Sun, 03 Sep 2017 01:51:05: 16000000 INFO @ Sun, 03 Sep 2017 01:51:07: 16000000 INFO @ Sun, 03 Sep 2017 01:51:07: 15000000 INFO @ Sun, 03 Sep 2017 01:51:12: 17000000 INFO @ Sun, 03 Sep 2017 01:51:12: 17000000 INFO @ Sun, 03 Sep 2017 01:51:13: 16000000 INFO @ Sun, 03 Sep 2017 01:51:18: 18000000 INFO @ Sun, 03 Sep 2017 01:51:18: 18000000 INFO @ Sun, 03 Sep 2017 01:51:20: 17000000 INFO @ Sun, 03 Sep 2017 01:51:24: 19000000 INFO @ Sun, 03 Sep 2017 01:51:25: 19000000 INFO @ Sun, 03 Sep 2017 01:51:27: 18000000 INFO @ Sun, 03 Sep 2017 01:51:30: 20000000 INFO @ Sun, 03 Sep 2017 01:51:32: 20000000 INFO @ Sun, 03 Sep 2017 01:51:34: 19000000 INFO @ Sun, 03 Sep 2017 01:51:36: 21000000 INFO @ Sun, 03 Sep 2017 01:51:38: 21000000 INFO @ Sun, 03 Sep 2017 01:51:40: 20000000 INFO @ Sun, 03 Sep 2017 01:51:41: 22000000 INFO @ Sun, 03 Sep 2017 01:51:45: 22000000 INFO @ Sun, 03 Sep 2017 01:51:47: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:51:47: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:51:47: #1 total tags in treatment: 10879658 INFO @ Sun, 03 Sep 2017 01:51:47: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:51:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:51:47: #1 tags after filtering in treatment: 9307564 INFO @ Sun, 03 Sep 2017 01:51:47: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Sep 2017 01:51:47: #1 finished! INFO @ Sun, 03 Sep 2017 01:51:47: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:51:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:51:47: 21000000 INFO @ Sun, 03 Sep 2017 01:51:48: #2 number of paired peaks: 6706 INFO @ Sun, 03 Sep 2017 01:51:48: start model_add_line... INFO @ Sun, 03 Sep 2017 01:51:48: start X-correlation... INFO @ Sun, 03 Sep 2017 01:51:48: end of X-cor INFO @ Sun, 03 Sep 2017 01:51:49: #2 finished! INFO @ Sun, 03 Sep 2017 01:51:49: #2 predicted fragment length is 172 bps INFO @ Sun, 03 Sep 2017 01:51:49: #2 alternative fragment length(s) may be 4,172 bps INFO @ Sun, 03 Sep 2017 01:51:49: #2.2 Generate R script for model : SRX2559026.10_model.r INFO @ Sun, 03 Sep 2017 01:51:49: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:51:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:51:51: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:51:51: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:51:51: #1 total tags in treatment: 10879658 INFO @ Sun, 03 Sep 2017 01:51:51: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:51:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:51:51: #1 tags after filtering in treatment: 9307564 INFO @ Sun, 03 Sep 2017 01:51:51: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Sep 2017 01:51:51: #1 finished! INFO @ Sun, 03 Sep 2017 01:51:51: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:51:53: #2 number of paired peaks: 6706 INFO @ Sun, 03 Sep 2017 01:51:53: start model_add_line... INFO @ Sun, 03 Sep 2017 01:51:53: start X-correlation... INFO @ Sun, 03 Sep 2017 01:51:53: end of X-cor INFO @ Sun, 03 Sep 2017 01:51:53: #2 finished! INFO @ Sun, 03 Sep 2017 01:51:53: #2 predicted fragment length is 172 bps INFO @ Sun, 03 Sep 2017 01:51:53: #2 alternative fragment length(s) may be 4,172 bps INFO @ Sun, 03 Sep 2017 01:51:53: #2.2 Generate R script for model : SRX2559026.20_model.r INFO @ Sun, 03 Sep 2017 01:51:53: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:51:53: 22000000 INFO @ Sun, 03 Sep 2017 01:51:59: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:51:59: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:51:59: #1 total tags in treatment: 10879658 INFO @ Sun, 03 Sep 2017 01:51:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:51:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:51:59: #1 tags after filtering in treatment: 9307564 INFO @ Sun, 03 Sep 2017 01:51:59: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Sep 2017 01:51:59: #1 finished! INFO @ Sun, 03 Sep 2017 01:51:59: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:51:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:52:00: #2 number of paired peaks: 6706 INFO @ Sun, 03 Sep 2017 01:52:00: start model_add_line... INFO @ Sun, 03 Sep 2017 01:52:01: start X-correlation... INFO @ Sun, 03 Sep 2017 01:52:01: end of X-cor INFO @ Sun, 03 Sep 2017 01:52:01: #2 finished! INFO @ Sun, 03 Sep 2017 01:52:01: #2 predicted fragment length is 172 bps INFO @ Sun, 03 Sep 2017 01:52:01: #2 alternative fragment length(s) may be 4,172 bps INFO @ Sun, 03 Sep 2017 01:52:01: #2.2 Generate R script for model : SRX2559026.05_model.r INFO @ Sun, 03 Sep 2017 01:52:01: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:52:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:52:18: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:52:22: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:52:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:52:31: #4 Write output xls file... SRX2559026.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:52:31: #4 Write peak in narrowPeak format file... SRX2559026.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:52:31: #4 Write summits bed file... SRX2559026.10_summits.bed INFO @ Sun, 03 Sep 2017 01:52:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3260 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:52:34: #4 Write output xls file... SRX2559026.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:52:34: #4 Write peak in narrowPeak format file... SRX2559026.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:52:34: #4 Write summits bed file... SRX2559026.20_summits.bed INFO @ Sun, 03 Sep 2017 01:52:34: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1712 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:52:42: #4 Write output xls file... SRX2559026.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:52:42: #4 Write peak in narrowPeak format file... SRX2559026.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:52:42: #4 Write summits bed file... SRX2559026.05_summits.bed INFO @ Sun, 03 Sep 2017 01:52:42: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6154 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。