Job ID = 9730445 sra ファイルのダウンロード中... Completed: 540730K bytes transferred in 9 seconds (467714K 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 13450419 spots for /home/okishinya/chipatlas/results/dm3/SRX2559032/SRR5253496.sra Written 13450419 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: 00:21:45 13450419 reads; of these: 13450419 (100.00%) were paired; of these: 1014039 (7.54%) aligned concordantly 0 times 10593234 (78.76%) aligned concordantly exactly 1 time 1843146 (13.70%) aligned concordantly >1 times ---- 1014039 pairs aligned concordantly 0 times; of these: 216902 (21.39%) aligned discordantly 1 time ---- 797137 pairs aligned 0 times concordantly or discordantly; of these: 1594274 mates make up the pairs; of these: 1171644 (73.49%) aligned 0 times 290549 (18.22%) aligned exactly 1 time 132081 (8.28%) aligned >1 times 95.64% overall alignment rate Time searching: 00:21:45 Overall time: 00:21:45 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] 186464 / 12644667 = 0.0147 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 01:24:43: # Command line: callpeak -t SRX2559032.bam -f BAM -g dm -n SRX2559032.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2559032.05 # format = BAM # ChIP-seq file = ['SRX2559032.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 01:24:43: # Command line: callpeak -t SRX2559032.bam -f BAM -g dm -n SRX2559032.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2559032.10 # format = BAM # ChIP-seq file = ['SRX2559032.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 01:24:43: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:24:43: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:24:43: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:24:43: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:24:43: # Command line: callpeak -t SRX2559032.bam -f BAM -g dm -n SRX2559032.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2559032.20 # format = BAM # ChIP-seq file = ['SRX2559032.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 01:24:43: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:24:43: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:24:49: 1000000 INFO @ Sun, 03 Sep 2017 01:24:49: 1000000 INFO @ Sun, 03 Sep 2017 01:24:49: 1000000 INFO @ Sun, 03 Sep 2017 01:24:55: 2000000 INFO @ Sun, 03 Sep 2017 01:24:55: 2000000 INFO @ Sun, 03 Sep 2017 01:24:56: 2000000 INFO @ Sun, 03 Sep 2017 01:25:01: 3000000 INFO @ Sun, 03 Sep 2017 01:25:01: 3000000 INFO @ Sun, 03 Sep 2017 01:25:02: 3000000 INFO @ Sun, 03 Sep 2017 01:25:07: 4000000 INFO @ Sun, 03 Sep 2017 01:25:07: 4000000 INFO @ Sun, 03 Sep 2017 01:25:08: 4000000 INFO @ Sun, 03 Sep 2017 01:25:13: 5000000 INFO @ Sun, 03 Sep 2017 01:25:13: 5000000 INFO @ Sun, 03 Sep 2017 01:25:14: 5000000 INFO @ Sun, 03 Sep 2017 01:25:18: 6000000 INFO @ Sun, 03 Sep 2017 01:25:18: 6000000 INFO @ Sun, 03 Sep 2017 01:25:20: 6000000 INFO @ Sun, 03 Sep 2017 01:25:24: 7000000 INFO @ Sun, 03 Sep 2017 01:25:24: 7000000 INFO @ Sun, 03 Sep 2017 01:25:27: 7000000 INFO @ Sun, 03 Sep 2017 01:25:30: 8000000 INFO @ Sun, 03 Sep 2017 01:25:30: 8000000 INFO @ Sun, 03 Sep 2017 01:25:34: 8000000 INFO @ Sun, 03 Sep 2017 01:25:36: 9000000 INFO @ Sun, 03 Sep 2017 01:25:36: 9000000 INFO @ Sun, 03 Sep 2017 01:25:40: 9000000 INFO @ Sun, 03 Sep 2017 01:25:42: 10000000 INFO @ Sun, 03 Sep 2017 01:25:42: 10000000 INFO @ Sun, 03 Sep 2017 01:25:46: 10000000 INFO @ Sun, 03 Sep 2017 01:25:48: 11000000 INFO @ Sun, 03 Sep 2017 01:25:48: 11000000 INFO @ Sun, 03 Sep 2017 01:25:52: 11000000 INFO @ Sun, 03 Sep 2017 01:25:53: 12000000 INFO @ Sun, 03 Sep 2017 01:25:53: 12000000 INFO @ Sun, 03 Sep 2017 01:25:58: 12000000 INFO @ Sun, 03 Sep 2017 01:25:59: 13000000 INFO @ Sun, 03 Sep 2017 01:25:59: 13000000 INFO @ Sun, 03 Sep 2017 01:26:04: 13000000 INFO @ Sun, 03 Sep 2017 01:26:05: 14000000 INFO @ Sun, 03 Sep 2017 01:26:05: 14000000 INFO @ Sun, 03 Sep 2017 01:26:10: 14000000 INFO @ Sun, 03 Sep 2017 01:26:11: 15000000 INFO @ Sun, 03 Sep 2017 01:26:11: 15000000 INFO @ Sun, 03 Sep 2017 01:26:16: 15000000 INFO @ Sun, 03 Sep 2017 01:26:17: 16000000 INFO @ Sun, 03 Sep 2017 01:26:17: 16000000 INFO @ Sun, 03 Sep 2017 01:26:22: 16000000 INFO @ Sun, 03 Sep 2017 01:26:22: 17000000 INFO @ Sun, 03 Sep 2017 01:26:22: 17000000 INFO @ Sun, 03 Sep 2017 01:26:28: 17000000 INFO @ Sun, 03 Sep 2017 01:26:28: 18000000 INFO @ Sun, 03 Sep 2017 01:26:28: 18000000 INFO @ Sun, 03 Sep 2017 01:26:34: 19000000 INFO @ Sun, 03 Sep 2017 01:26:34: 19000000 INFO @ Sun, 03 Sep 2017 01:26:35: 18000000 INFO @ Sun, 03 Sep 2017 01:26:40: 20000000 INFO @ Sun, 03 Sep 2017 01:26:40: 20000000 INFO @ Sun, 03 Sep 2017 01:26:41: 19000000 INFO @ Sun, 03 Sep 2017 01:26:45: 21000000 INFO @ Sun, 03 Sep 2017 01:26:45: 21000000 INFO @ Sun, 03 Sep 2017 01:26:47: 20000000 INFO @ Sun, 03 Sep 2017 01:26:51: 22000000 INFO @ Sun, 03 Sep 2017 01:26:51: 22000000 INFO @ Sun, 03 Sep 2017 01:26:53: 21000000 INFO @ Sun, 03 Sep 2017 01:26:57: 23000000 INFO @ Sun, 03 Sep 2017 01:26:57: 23000000 INFO @ Sun, 03 Sep 2017 01:26:58: 22000000 INFO @ Sun, 03 Sep 2017 01:27:02: 24000000 INFO @ Sun, 03 Sep 2017 01:27:02: 24000000 INFO @ Sun, 03 Sep 2017 01:27:04: 23000000 INFO @ Sun, 03 Sep 2017 01:27:08: 25000000 INFO @ Sun, 03 Sep 2017 01:27:08: 25000000 INFO @ Sun, 03 Sep 2017 01:27:10: 24000000 INFO @ Sun, 03 Sep 2017 01:27:10: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:27:10: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:27:10: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:27:10: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:27:10: #1 total tags in treatment: 12250617 INFO @ Sun, 03 Sep 2017 01:27:10: #1 total tags in treatment: 12250617 INFO @ Sun, 03 Sep 2017 01:27:10: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:27:10: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:27:10: #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 01:27:10: #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 01:27:11: #1 tags after filtering in treatment: 10483370 INFO @ Sun, 03 Sep 2017 01:27:11: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Sep 2017 01:27:11: #1 finished! INFO @ Sun, 03 Sep 2017 01:27:11: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:27:11: #1 tags after filtering in treatment: 10483370 INFO @ Sun, 03 Sep 2017 01:27:11: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Sep 2017 01:27:11: #1 finished! INFO @ Sun, 03 Sep 2017 01:27:11: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:27:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:27:12: #2 number of paired peaks: 7617 INFO @ Sun, 03 Sep 2017 01:27:12: start model_add_line... INFO @ Sun, 03 Sep 2017 01:27:12: #2 number of paired peaks: 7617 INFO @ Sun, 03 Sep 2017 01:27:12: start model_add_line... INFO @ Sun, 03 Sep 2017 01:27:12: start X-correlation... INFO @ Sun, 03 Sep 2017 01:27:12: start X-correlation... INFO @ Sun, 03 Sep 2017 01:27:12: end of X-cor INFO @ Sun, 03 Sep 2017 01:27:12: end of X-cor INFO @ Sun, 03 Sep 2017 01:27:12: #2 finished! INFO @ Sun, 03 Sep 2017 01:27:12: #2 finished! INFO @ Sun, 03 Sep 2017 01:27:12: #2 predicted fragment length is 226 bps INFO @ Sun, 03 Sep 2017 01:27:12: #2 predicted fragment length is 226 bps INFO @ Sun, 03 Sep 2017 01:27:12: #2 alternative fragment length(s) may be 4,226 bps INFO @ Sun, 03 Sep 2017 01:27:12: #2 alternative fragment length(s) may be 4,226 bps INFO @ Sun, 03 Sep 2017 01:27:12: #2.2 Generate R script for model : SRX2559032.10_model.r INFO @ Sun, 03 Sep 2017 01:27:12: #2.2 Generate R script for model : SRX2559032.20_model.r INFO @ Sun, 03 Sep 2017 01:27:12: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:27:12: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:27:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:27:16: 25000000 INFO @ Sun, 03 Sep 2017 01:27:18: #1 tag size is determined as 50 bps INFO @ Sun, 03 Sep 2017 01:27:18: #1 tag size = 50 INFO @ Sun, 03 Sep 2017 01:27:18: #1 total tags in treatment: 12250617 INFO @ Sun, 03 Sep 2017 01:27:18: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:27:18: #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 01:27:18: #1 tags after filtering in treatment: 10483370 INFO @ Sun, 03 Sep 2017 01:27:18: #1 Redundant rate of treatment: 0.14 INFO @ Sun, 03 Sep 2017 01:27:18: #1 finished! INFO @ Sun, 03 Sep 2017 01:27:18: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:27:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:27:19: #2 number of paired peaks: 7617 INFO @ Sun, 03 Sep 2017 01:27:19: start model_add_line... INFO @ Sun, 03 Sep 2017 01:27:20: start X-correlation... INFO @ Sun, 03 Sep 2017 01:27:20: end of X-cor INFO @ Sun, 03 Sep 2017 01:27:20: #2 finished! INFO @ Sun, 03 Sep 2017 01:27:20: #2 predicted fragment length is 226 bps INFO @ Sun, 03 Sep 2017 01:27:20: #2 alternative fragment length(s) may be 4,226 bps INFO @ Sun, 03 Sep 2017 01:27:20: #2.2 Generate R script for model : SRX2559032.05_model.r INFO @ Sun, 03 Sep 2017 01:27:20: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:27:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:27:47: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:27:49: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:27:57: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:28:01: #4 Write output xls file... SRX2559032.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:28:01: #4 Write peak in narrowPeak format file... SRX2559032.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:28:01: #4 Write summits bed file... SRX2559032.10_summits.bed INFO @ Sun, 03 Sep 2017 01:28:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5160 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:28:03: #4 Write output xls file... SRX2559032.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:28:03: #4 Write peak in narrowPeak format file... SRX2559032.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:28:03: #4 Write summits bed file... SRX2559032.20_summits.bed INFO @ Sun, 03 Sep 2017 01:28:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2785 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:28:15: #4 Write output xls file... SRX2559032.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:28:15: #4 Write peak in narrowPeak format file... SRX2559032.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:28:15: #4 Write summits bed file... SRX2559032.05_summits.bed INFO @ Sun, 03 Sep 2017 01:28:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7575 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。