Job ID = 9159842 sra ファイルのダウンロード中... Completed: 950407K bytes transferred in 10 seconds (713880K 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 15304534 spots for /home/okishinya/chipatlas/results/dm3/SRX749025/SRR1636753.sra Written 15304534 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: 00:37:29 15304534 reads; of these: 15304534 (100.00%) were paired; of these: 2423602 (15.84%) aligned concordantly 0 times 9241167 (60.38%) aligned concordantly exactly 1 time 3639765 (23.78%) aligned concordantly >1 times ---- 2423602 pairs aligned concordantly 0 times; of these: 31048 (1.28%) aligned discordantly 1 time ---- 2392554 pairs aligned 0 times concordantly or discordantly; of these: 4785108 mates make up the pairs; of these: 4430977 (92.60%) aligned 0 times 253186 (5.29%) aligned exactly 1 time 100945 (2.11%) aligned >1 times 85.52% overall alignment rate Time searching: 00:37:29 Overall time: 00:37:29 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] 3664253 / 12901303 = 0.2840 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 00:58:43: # Command line: callpeak -t SRX749025.bam -f BAM -g dm -n SRX749025.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749025.05 # format = BAM # ChIP-seq file = ['SRX749025.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 00:58:43: # Command line: callpeak -t SRX749025.bam -f BAM -g dm -n SRX749025.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749025.20 # format = BAM # ChIP-seq file = ['SRX749025.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 00:58:43: # Command line: callpeak -t SRX749025.bam -f BAM -g dm -n SRX749025.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749025.10 # format = BAM # ChIP-seq file = ['SRX749025.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 00:58:43: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:43: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:43: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:43: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:43: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:43: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:50: 1000000 INFO @ Wed, 28 Jun 2017 00:58:50: 1000000 INFO @ Wed, 28 Jun 2017 00:58:51: 1000000 INFO @ Wed, 28 Jun 2017 00:58:56: 2000000 INFO @ Wed, 28 Jun 2017 00:58:58: 2000000 INFO @ Wed, 28 Jun 2017 00:58:58: 2000000 INFO @ Wed, 28 Jun 2017 00:59:03: 3000000 INFO @ Wed, 28 Jun 2017 00:59:05: 3000000 INFO @ Wed, 28 Jun 2017 00:59:06: 3000000 INFO @ Wed, 28 Jun 2017 00:59:10: 4000000 INFO @ Wed, 28 Jun 2017 00:59:13: 4000000 INFO @ Wed, 28 Jun 2017 00:59:14: 4000000 INFO @ Wed, 28 Jun 2017 00:59:16: 5000000 INFO @ Wed, 28 Jun 2017 00:59:20: 5000000 INFO @ Wed, 28 Jun 2017 00:59:22: 5000000 INFO @ Wed, 28 Jun 2017 00:59:23: 6000000 INFO @ Wed, 28 Jun 2017 00:59:27: 6000000 INFO @ Wed, 28 Jun 2017 00:59:29: 7000000 INFO @ Wed, 28 Jun 2017 00:59:30: 6000000 INFO @ Wed, 28 Jun 2017 00:59:35: 7000000 INFO @ Wed, 28 Jun 2017 00:59:36: 8000000 INFO @ Wed, 28 Jun 2017 00:59:38: 7000000 INFO @ Wed, 28 Jun 2017 00:59:42: 8000000 INFO @ Wed, 28 Jun 2017 00:59:42: 9000000 INFO @ Wed, 28 Jun 2017 00:59:46: 8000000 INFO @ Wed, 28 Jun 2017 00:59:49: 10000000 INFO @ Wed, 28 Jun 2017 00:59:50: 9000000 INFO @ Wed, 28 Jun 2017 00:59:54: 9000000 INFO @ Wed, 28 Jun 2017 00:59:55: 11000000 INFO @ Wed, 28 Jun 2017 00:59:57: 10000000 INFO @ Wed, 28 Jun 2017 01:00:02: 12000000 INFO @ Wed, 28 Jun 2017 01:00:02: 10000000 INFO @ Wed, 28 Jun 2017 01:00:04: 11000000 INFO @ Wed, 28 Jun 2017 01:00:08: 13000000 INFO @ Wed, 28 Jun 2017 01:00:10: 11000000 INFO @ Wed, 28 Jun 2017 01:00:12: 12000000 INFO @ Wed, 28 Jun 2017 01:00:15: 14000000 INFO @ Wed, 28 Jun 2017 01:00:18: 12000000 INFO @ Wed, 28 Jun 2017 01:00:19: 13000000 INFO @ Wed, 28 Jun 2017 01:00:21: 15000000 INFO @ Wed, 28 Jun 2017 01:00:26: 13000000 INFO @ Wed, 28 Jun 2017 01:00:27: 14000000 INFO @ Wed, 28 Jun 2017 01:00:28: 16000000 INFO @ Wed, 28 Jun 2017 01:00:34: 14000000 INFO @ Wed, 28 Jun 2017 01:00:34: 15000000 INFO @ Wed, 28 Jun 2017 01:00:34: 17000000 INFO @ Wed, 28 Jun 2017 01:00:41: 18000000 INFO @ Wed, 28 Jun 2017 01:00:41: 16000000 INFO @ Wed, 28 Jun 2017 01:00:42: 15000000 INFO @ Wed, 28 Jun 2017 01:00:46: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:00:46: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:00:46: #1 total tags in treatment: 9218672 INFO @ Wed, 28 Jun 2017 01:00:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:00:46: #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 01:00:47: #1 tags after filtering in treatment: 8509833 INFO @ Wed, 28 Jun 2017 01:00:47: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 01:00:47: #1 finished! INFO @ Wed, 28 Jun 2017 01:00:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:00:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:00:47: #2 number of paired peaks: 1619 INFO @ Wed, 28 Jun 2017 01:00:47: start model_add_line... INFO @ Wed, 28 Jun 2017 01:00:48: start X-correlation... INFO @ Wed, 28 Jun 2017 01:00:48: end of X-cor INFO @ Wed, 28 Jun 2017 01:00:48: #2 finished! INFO @ Wed, 28 Jun 2017 01:00:48: #2 predicted fragment length is 168 bps INFO @ Wed, 28 Jun 2017 01:00:48: #2 alternative fragment length(s) may be 168 bps INFO @ Wed, 28 Jun 2017 01:00:48: #2.2 Generate R script for model : SRX749025.10_model.r INFO @ Wed, 28 Jun 2017 01:00:48: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:00:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:00:49: 17000000 INFO @ Wed, 28 Jun 2017 01:00:50: 16000000 INFO @ Wed, 28 Jun 2017 01:00:56: 18000000 INFO @ Wed, 28 Jun 2017 01:00:58: 17000000 INFO @ Wed, 28 Jun 2017 01:01:03: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:01:03: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:01:03: #1 total tags in treatment: 9218672 INFO @ Wed, 28 Jun 2017 01:01:03: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:01:03: #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 01:01:03: #1 tags after filtering in treatment: 8509833 INFO @ Wed, 28 Jun 2017 01:01:03: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 01:01:03: #1 finished! INFO @ Wed, 28 Jun 2017 01:01:03: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:01:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:01:04: #2 number of paired peaks: 1619 INFO @ Wed, 28 Jun 2017 01:01:04: start model_add_line... INFO @ Wed, 28 Jun 2017 01:01:04: start X-correlation... INFO @ Wed, 28 Jun 2017 01:01:04: end of X-cor INFO @ Wed, 28 Jun 2017 01:01:04: #2 finished! INFO @ Wed, 28 Jun 2017 01:01:04: #2 predicted fragment length is 168 bps INFO @ Wed, 28 Jun 2017 01:01:04: #2 alternative fragment length(s) may be 168 bps INFO @ Wed, 28 Jun 2017 01:01:04: #2.2 Generate R script for model : SRX749025.20_model.r INFO @ Wed, 28 Jun 2017 01:01:04: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:01:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:01:05: 18000000 INFO @ Wed, 28 Jun 2017 01:01:09: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:01:11: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:01:11: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:01:11: #1 total tags in treatment: 9218672 INFO @ Wed, 28 Jun 2017 01:01:11: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:01:11: #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 01:01:11: #1 tags after filtering in treatment: 8509833 INFO @ Wed, 28 Jun 2017 01:01:11: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 01:01:11: #1 finished! INFO @ Wed, 28 Jun 2017 01:01:11: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:01:11: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:01:12: #2 number of paired peaks: 1619 INFO @ Wed, 28 Jun 2017 01:01:12: start model_add_line... INFO @ Wed, 28 Jun 2017 01:01:12: start X-correlation... INFO @ Wed, 28 Jun 2017 01:01:12: end of X-cor INFO @ Wed, 28 Jun 2017 01:01:12: #2 finished! INFO @ Wed, 28 Jun 2017 01:01:12: #2 predicted fragment length is 168 bps INFO @ Wed, 28 Jun 2017 01:01:12: #2 alternative fragment length(s) may be 168 bps INFO @ Wed, 28 Jun 2017 01:01:12: #2.2 Generate R script for model : SRX749025.05_model.r INFO @ Wed, 28 Jun 2017 01:01:12: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:01:12: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:01:20: #4 Write output xls file... SRX749025.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:01:20: #4 Write peak in narrowPeak format file... SRX749025.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:01:20: #4 Write summits bed file... SRX749025.10_summits.bed INFO @ Wed, 28 Jun 2017 01:01:21: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4214 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:01:25: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:01:34: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:01:36: #4 Write output xls file... SRX749025.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:01:36: #4 Write peak in narrowPeak format file... SRX749025.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:01:36: #4 Write summits bed file... SRX749025.20_summits.bed INFO @ Wed, 28 Jun 2017 01:01:36: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2746 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:01:46: #4 Write output xls file... SRX749025.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:01:46: #4 Write peak in narrowPeak format file... SRX749025.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:01:46: #4 Write summits bed file... SRX749025.05_summits.bed INFO @ Wed, 28 Jun 2017 01:01:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6086 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。