Job ID = 9371930 sra ファイルのダウンロード中... Completed: 1918195K bytes transferred in 52 seconds (296788K bits/sec), in 2 files, 3 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 10140757 spots for /home/okishinya/chipatlas/results/dm3/SRX2548341/SRR5241483.sra Written 10140757 spots total Written 11543730 spots for /home/okishinya/chipatlas/results/dm3/SRX2548341/SRR5241484.sra Written 11543730 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 02:38:14 21684487 reads; of these: 21684487 (100.00%) were paired; of these: 7148562 (32.97%) aligned concordantly 0 times 5510451 (25.41%) aligned concordantly exactly 1 time 9025474 (41.62%) aligned concordantly >1 times ---- 7148562 pairs aligned concordantly 0 times; of these: 1049407 (14.68%) aligned discordantly 1 time ---- 6099155 pairs aligned 0 times concordantly or discordantly; of these: 12198310 mates make up the pairs; of these: 7455037 (61.12%) aligned 0 times 650461 (5.33%) aligned exactly 1 time 4092812 (33.55%) aligned >1 times 82.81% overall alignment rate Time searching: 02:38:15 Overall time: 02:38:15 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] 637713 / 15521418 = 0.0411 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 @ Fri, 04 Aug 2017 17:46:41: # Command line: callpeak -t SRX2548341.bam -f BAM -g dm -n SRX2548341.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2548341.10 # format = BAM # ChIP-seq file = ['SRX2548341.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 @ Fri, 04 Aug 2017 17:46:41: #1 read tag files... INFO @ Fri, 04 Aug 2017 17:46:41: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 17:46:41: # Command line: callpeak -t SRX2548341.bam -f BAM -g dm -n SRX2548341.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2548341.05 # format = BAM # ChIP-seq file = ['SRX2548341.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 @ Fri, 04 Aug 2017 17:46:41: #1 read tag files... INFO @ Fri, 04 Aug 2017 17:46:41: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 17:46:41: # Command line: callpeak -t SRX2548341.bam -f BAM -g dm -n SRX2548341.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2548341.20 # format = BAM # ChIP-seq file = ['SRX2548341.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 @ Fri, 04 Aug 2017 17:46:41: #1 read tag files... INFO @ Fri, 04 Aug 2017 17:46:41: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 17:46:49: 1000000 INFO @ Fri, 04 Aug 2017 17:46:49: 1000000 INFO @ Fri, 04 Aug 2017 17:46:49: 1000000 INFO @ Fri, 04 Aug 2017 17:46:57: 2000000 INFO @ Fri, 04 Aug 2017 17:46:57: 2000000 INFO @ Fri, 04 Aug 2017 17:46:58: 2000000 INFO @ Fri, 04 Aug 2017 17:47:05: 3000000 INFO @ Fri, 04 Aug 2017 17:47:06: 3000000 INFO @ Fri, 04 Aug 2017 17:47:06: 3000000 INFO @ Fri, 04 Aug 2017 17:47:13: 4000000 INFO @ Fri, 04 Aug 2017 17:47:14: 4000000 INFO @ Fri, 04 Aug 2017 17:47:14: 4000000 INFO @ Fri, 04 Aug 2017 17:47:22: 5000000 INFO @ Fri, 04 Aug 2017 17:47:22: 5000000 INFO @ Fri, 04 Aug 2017 17:47:22: 5000000 INFO @ Fri, 04 Aug 2017 17:47:30: 6000000 INFO @ Fri, 04 Aug 2017 17:47:30: 6000000 INFO @ Fri, 04 Aug 2017 17:47:31: 6000000 INFO @ Fri, 04 Aug 2017 17:47:38: 7000000 INFO @ Fri, 04 Aug 2017 17:47:39: 7000000 INFO @ Fri, 04 Aug 2017 17:47:40: 7000000 INFO @ Fri, 04 Aug 2017 17:47:45: 8000000 INFO @ Fri, 04 Aug 2017 17:47:47: 8000000 INFO @ Fri, 04 Aug 2017 17:47:49: 8000000 INFO @ Fri, 04 Aug 2017 17:47:54: 9000000 INFO @ Fri, 04 Aug 2017 17:47:56: 9000000 INFO @ Fri, 04 Aug 2017 17:47:58: 9000000 INFO @ Fri, 04 Aug 2017 17:48:01: 10000000 INFO @ Fri, 04 Aug 2017 17:48:04: 10000000 INFO @ Fri, 04 Aug 2017 17:48:07: 10000000 INFO @ Fri, 04 Aug 2017 17:48:09: 11000000 INFO @ Fri, 04 Aug 2017 17:48:13: 11000000 INFO @ Fri, 04 Aug 2017 17:48:15: 11000000 INFO @ Fri, 04 Aug 2017 17:48:17: 12000000 INFO @ Fri, 04 Aug 2017 17:48:21: 12000000 INFO @ Fri, 04 Aug 2017 17:48:24: 12000000 INFO @ Fri, 04 Aug 2017 17:48:25: 13000000 INFO @ Fri, 04 Aug 2017 17:48:30: 13000000 INFO @ Fri, 04 Aug 2017 17:48:33: 13000000 INFO @ Fri, 04 Aug 2017 17:48:33: 14000000 INFO @ Fri, 04 Aug 2017 17:48:38: 14000000 INFO @ Fri, 04 Aug 2017 17:48:41: 15000000 INFO @ Fri, 04 Aug 2017 17:48:42: 14000000 INFO @ Fri, 04 Aug 2017 17:48:47: 15000000 INFO @ Fri, 04 Aug 2017 17:48:49: 16000000 INFO @ Fri, 04 Aug 2017 17:48:51: 15000000 INFO @ Fri, 04 Aug 2017 17:48:55: 16000000 INFO @ Fri, 04 Aug 2017 17:48:56: 17000000 INFO @ Fri, 04 Aug 2017 17:48:59: 16000000 INFO @ Fri, 04 Aug 2017 17:49:03: 17000000 INFO @ Fri, 04 Aug 2017 17:49:04: 18000000 INFO @ Fri, 04 Aug 2017 17:49:08: 17000000 INFO @ Fri, 04 Aug 2017 17:49:11: 18000000 INFO @ Fri, 04 Aug 2017 17:49:12: 19000000 INFO @ Fri, 04 Aug 2017 17:49:16: 18000000 INFO @ Fri, 04 Aug 2017 17:49:20: 19000000 INFO @ Fri, 04 Aug 2017 17:49:20: 20000000 INFO @ Fri, 04 Aug 2017 17:49:25: 19000000 INFO @ Fri, 04 Aug 2017 17:49:28: 21000000 INFO @ Fri, 04 Aug 2017 17:49:28: 20000000 INFO @ Fri, 04 Aug 2017 17:49:34: 20000000 INFO @ Fri, 04 Aug 2017 17:49:35: 22000000 INFO @ Fri, 04 Aug 2017 17:49:37: 21000000 INFO @ Fri, 04 Aug 2017 17:49:43: 21000000 INFO @ Fri, 04 Aug 2017 17:49:43: 23000000 INFO @ Fri, 04 Aug 2017 17:49:45: 22000000 INFO @ Fri, 04 Aug 2017 17:49:51: 24000000 INFO @ Fri, 04 Aug 2017 17:49:51: 22000000 INFO @ Fri, 04 Aug 2017 17:49:53: 23000000 INFO @ Fri, 04 Aug 2017 17:49:59: 25000000 INFO @ Fri, 04 Aug 2017 17:50:00: 23000000 INFO @ Fri, 04 Aug 2017 17:50:02: 24000000 INFO @ Fri, 04 Aug 2017 17:50:07: 26000000 INFO @ Fri, 04 Aug 2017 17:50:09: 24000000 INFO @ Fri, 04 Aug 2017 17:50:10: 25000000 INFO @ Fri, 04 Aug 2017 17:50:14: 27000000 INFO @ Fri, 04 Aug 2017 17:50:18: 25000000 INFO @ Fri, 04 Aug 2017 17:50:18: 26000000 INFO @ Fri, 04 Aug 2017 17:50:22: 28000000 INFO @ Fri, 04 Aug 2017 17:50:26: 26000000 INFO @ Fri, 04 Aug 2017 17:50:27: 27000000 INFO @ Fri, 04 Aug 2017 17:50:30: 29000000 INFO @ Fri, 04 Aug 2017 17:50:34: 28000000 INFO @ Fri, 04 Aug 2017 17:50:36: 27000000 INFO @ Fri, 04 Aug 2017 17:50:39: 30000000 INFO @ Fri, 04 Aug 2017 17:50:42: 29000000 INFO @ Fri, 04 Aug 2017 17:50:46: 28000000 INFO @ Fri, 04 Aug 2017 17:50:48: 31000000 INFO @ Fri, 04 Aug 2017 17:50:51: 30000000 INFO @ Fri, 04 Aug 2017 17:50:55: 29000000 INFO @ Fri, 04 Aug 2017 17:50:56: 32000000 INFO @ Fri, 04 Aug 2017 17:50:58: 31000000 INFO @ Fri, 04 Aug 2017 17:51:03: 30000000 INFO @ Fri, 04 Aug 2017 17:51:04: 33000000 INFO @ Fri, 04 Aug 2017 17:51:07: 32000000 INFO @ Fri, 04 Aug 2017 17:51:12: 34000000 INFO @ Fri, 04 Aug 2017 17:51:12: 31000000 INFO @ Fri, 04 Aug 2017 17:51:15: 33000000 INFO @ Fri, 04 Aug 2017 17:51:17: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 17:51:17: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 17:51:17: #1 total tags in treatment: 13920974 INFO @ Fri, 04 Aug 2017 17:51:17: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 17:51:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 17:51:17: #1 tags after filtering in treatment: 11840138 INFO @ Fri, 04 Aug 2017 17:51:17: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 04 Aug 2017 17:51:17: #1 finished! INFO @ Fri, 04 Aug 2017 17:51:17: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 17:51:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 17:51:18: #2 number of paired peaks: 2762 INFO @ Fri, 04 Aug 2017 17:51:18: start model_add_line... INFO @ Fri, 04 Aug 2017 17:51:18: start X-correlation... INFO @ Fri, 04 Aug 2017 17:51:18: end of X-cor INFO @ Fri, 04 Aug 2017 17:51:18: #2 finished! INFO @ Fri, 04 Aug 2017 17:51:18: #2 predicted fragment length is 224 bps INFO @ Fri, 04 Aug 2017 17:51:18: #2 alternative fragment length(s) may be 224 bps INFO @ Fri, 04 Aug 2017 17:51:18: #2.2 Generate R script for model : SRX2548341.20_model.r INFO @ Fri, 04 Aug 2017 17:51:18: #3 Call peaks... INFO @ Fri, 04 Aug 2017 17:51:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 17:51:20: 32000000 INFO @ Fri, 04 Aug 2017 17:51:23: 34000000 INFO @ Fri, 04 Aug 2017 17:51:28: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 17:51:28: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 17:51:28: #1 total tags in treatment: 13920974 INFO @ Fri, 04 Aug 2017 17:51:28: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 17:51:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 17:51:28: #1 tags after filtering in treatment: 11840138 INFO @ Fri, 04 Aug 2017 17:51:28: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 04 Aug 2017 17:51:28: #1 finished! INFO @ Fri, 04 Aug 2017 17:51:28: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 17:51:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 17:51:29: 33000000 INFO @ Fri, 04 Aug 2017 17:51:29: #2 number of paired peaks: 2762 INFO @ Fri, 04 Aug 2017 17:51:29: start model_add_line... INFO @ Fri, 04 Aug 2017 17:51:30: start X-correlation... INFO @ Fri, 04 Aug 2017 17:51:30: end of X-cor INFO @ Fri, 04 Aug 2017 17:51:30: #2 finished! INFO @ Fri, 04 Aug 2017 17:51:30: #2 predicted fragment length is 224 bps INFO @ Fri, 04 Aug 2017 17:51:30: #2 alternative fragment length(s) may be 224 bps INFO @ Fri, 04 Aug 2017 17:51:30: #2.2 Generate R script for model : SRX2548341.10_model.r INFO @ Fri, 04 Aug 2017 17:51:30: #3 Call peaks... INFO @ Fri, 04 Aug 2017 17:51:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 17:51:36: 34000000 INFO @ Fri, 04 Aug 2017 17:51:41: #1 tag size is determined as 101 bps INFO @ Fri, 04 Aug 2017 17:51:41: #1 tag size = 101 INFO @ Fri, 04 Aug 2017 17:51:41: #1 total tags in treatment: 13920974 INFO @ Fri, 04 Aug 2017 17:51:41: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 17:51:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 17:51:41: #1 tags after filtering in treatment: 11840138 INFO @ Fri, 04 Aug 2017 17:51:41: #1 Redundant rate of treatment: 0.15 INFO @ Fri, 04 Aug 2017 17:51:41: #1 finished! INFO @ Fri, 04 Aug 2017 17:51:41: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 17:51:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 17:51:42: #2 number of paired peaks: 2762 INFO @ Fri, 04 Aug 2017 17:51:42: start model_add_line... INFO @ Fri, 04 Aug 2017 17:51:43: start X-correlation... INFO @ Fri, 04 Aug 2017 17:51:43: end of X-cor INFO @ Fri, 04 Aug 2017 17:51:43: #2 finished! INFO @ Fri, 04 Aug 2017 17:51:43: #2 predicted fragment length is 224 bps INFO @ Fri, 04 Aug 2017 17:51:43: #2 alternative fragment length(s) may be 224 bps INFO @ Fri, 04 Aug 2017 17:51:43: #2.2 Generate R script for model : SRX2548341.05_model.r INFO @ Fri, 04 Aug 2017 17:51:43: #3 Call peaks... INFO @ Fri, 04 Aug 2017 17:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 17:51:53: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:52:04: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:52:10: #4 Write output xls file... SRX2548341.20_peaks.xls INFO @ Fri, 04 Aug 2017 17:52:10: #4 Write peak in narrowPeak format file... SRX2548341.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:52:10: #4 Write summits bed file... SRX2548341.20_summits.bed INFO @ Fri, 04 Aug 2017 17:52:10: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4285 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 17:52:15: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 17:52:21: #4 Write output xls file... SRX2548341.10_peaks.xls INFO @ Fri, 04 Aug 2017 17:52:21: #4 Write peak in narrowPeak format file... SRX2548341.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:52:21: #4 Write summits bed file... SRX2548341.10_summits.bed INFO @ Fri, 04 Aug 2017 17:52:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6872 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 17:52:33: #4 Write output xls file... SRX2548341.05_peaks.xls INFO @ Fri, 04 Aug 2017 17:52:33: #4 Write peak in narrowPeak format file... SRX2548341.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 17:52:33: #4 Write summits bed file... SRX2548341.05_summits.bed INFO @ Fri, 04 Aug 2017 17:52:33: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10150 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。