Job ID = 9159843 sra ファイルのダウンロード中... Completed: 751527K bytes transferred in 9 seconds (645633K 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 11417129 spots for /home/okishinya/chipatlas/results/dm3/SRX749026/SRR1636754.sra Written 11417129 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: 00:22:46 11417129 reads; of these: 11417129 (100.00%) were paired; of these: 840007 (7.36%) aligned concordantly 0 times 8670795 (75.95%) aligned concordantly exactly 1 time 1906327 (16.70%) aligned concordantly >1 times ---- 840007 pairs aligned concordantly 0 times; of these: 114339 (13.61%) aligned discordantly 1 time ---- 725668 pairs aligned 0 times concordantly or discordantly; of these: 1451336 mates make up the pairs; of these: 870096 (59.95%) aligned 0 times 394703 (27.20%) aligned exactly 1 time 186537 (12.85%) aligned >1 times 96.19% overall alignment rate Time searching: 00:22:46 Overall time: 00:22:46 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] 1353493 / 10679173 = 0.1267 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 00:42:58: # Command line: callpeak -t SRX749026.bam -f BAM -g dm -n SRX749026.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749026.05 # format = BAM # ChIP-seq file = ['SRX749026.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 00:42:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:42:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:42:58: # Command line: callpeak -t SRX749026.bam -f BAM -g dm -n SRX749026.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749026.10 # format = BAM # ChIP-seq file = ['SRX749026.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 00:42:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:42:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:42:58: # Command line: callpeak -t SRX749026.bam -f BAM -g dm -n SRX749026.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749026.20 # format = BAM # ChIP-seq file = ['SRX749026.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 00:42:58: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:42:58: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:43:06: 1000000 INFO @ Wed, 28 Jun 2017 00:43:06: 1000000 INFO @ Wed, 28 Jun 2017 00:43:06: 1000000 INFO @ Wed, 28 Jun 2017 00:43:13: 2000000 INFO @ Wed, 28 Jun 2017 00:43:14: 2000000 INFO @ Wed, 28 Jun 2017 00:43:14: 2000000 INFO @ Wed, 28 Jun 2017 00:43:21: 3000000 INFO @ Wed, 28 Jun 2017 00:43:21: 3000000 INFO @ Wed, 28 Jun 2017 00:43:21: 3000000 INFO @ Wed, 28 Jun 2017 00:43:28: 4000000 INFO @ Wed, 28 Jun 2017 00:43:29: 4000000 INFO @ Wed, 28 Jun 2017 00:43:29: 4000000 INFO @ Wed, 28 Jun 2017 00:43:35: 5000000 INFO @ Wed, 28 Jun 2017 00:43:37: 5000000 INFO @ Wed, 28 Jun 2017 00:43:37: 5000000 INFO @ Wed, 28 Jun 2017 00:43:42: 6000000 INFO @ Wed, 28 Jun 2017 00:43:45: 6000000 INFO @ Wed, 28 Jun 2017 00:43:45: 6000000 INFO @ Wed, 28 Jun 2017 00:43:50: 7000000 INFO @ Wed, 28 Jun 2017 00:43:52: 7000000 INFO @ Wed, 28 Jun 2017 00:43:52: 7000000 INFO @ Wed, 28 Jun 2017 00:43:57: 8000000 INFO @ Wed, 28 Jun 2017 00:44:00: 8000000 INFO @ Wed, 28 Jun 2017 00:44:00: 8000000 INFO @ Wed, 28 Jun 2017 00:44:04: 9000000 INFO @ Wed, 28 Jun 2017 00:44:07: 9000000 INFO @ Wed, 28 Jun 2017 00:44:08: 9000000 INFO @ Wed, 28 Jun 2017 00:44:12: 10000000 INFO @ Wed, 28 Jun 2017 00:44:15: 10000000 INFO @ Wed, 28 Jun 2017 00:44:15: 10000000 INFO @ Wed, 28 Jun 2017 00:44:19: 11000000 INFO @ Wed, 28 Jun 2017 00:44:23: 11000000 INFO @ Wed, 28 Jun 2017 00:44:23: 11000000 INFO @ Wed, 28 Jun 2017 00:44:26: 12000000 INFO @ Wed, 28 Jun 2017 00:44:30: 12000000 INFO @ Wed, 28 Jun 2017 00:44:30: 12000000 INFO @ Wed, 28 Jun 2017 00:44:34: 13000000 INFO @ Wed, 28 Jun 2017 00:44:38: 13000000 INFO @ Wed, 28 Jun 2017 00:44:38: 13000000 INFO @ Wed, 28 Jun 2017 00:44:41: 14000000 INFO @ Wed, 28 Jun 2017 00:44:46: 14000000 INFO @ Wed, 28 Jun 2017 00:44:46: 14000000 INFO @ Wed, 28 Jun 2017 00:44:48: 15000000 INFO @ Wed, 28 Jun 2017 00:44:54: 15000000 INFO @ Wed, 28 Jun 2017 00:44:54: 15000000 INFO @ Wed, 28 Jun 2017 00:44:56: 16000000 INFO @ Wed, 28 Jun 2017 00:45:01: 16000000 INFO @ Wed, 28 Jun 2017 00:45:01: 16000000 INFO @ Wed, 28 Jun 2017 00:45:03: 17000000 INFO @ Wed, 28 Jun 2017 00:45:09: 17000000 INFO @ Wed, 28 Jun 2017 00:45:09: 17000000 INFO @ Wed, 28 Jun 2017 00:45:10: 18000000 INFO @ Wed, 28 Jun 2017 00:45:17: 18000000 INFO @ Wed, 28 Jun 2017 00:45:17: 18000000 INFO @ Wed, 28 Jun 2017 00:45:18: 19000000 INFO @ Wed, 28 Jun 2017 00:45:20: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:45:20: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:45:20: #1 total tags in treatment: 9228392 INFO @ Wed, 28 Jun 2017 00:45:20: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:45:20: #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 00:45:20: #1 tags after filtering in treatment: 7475589 INFO @ Wed, 28 Jun 2017 00:45:20: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 00:45:20: #1 finished! INFO @ Wed, 28 Jun 2017 00:45:20: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:45:20: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:45:21: #2 number of paired peaks: 8348 INFO @ Wed, 28 Jun 2017 00:45:21: start model_add_line... INFO @ Wed, 28 Jun 2017 00:45:21: start X-correlation... INFO @ Wed, 28 Jun 2017 00:45:21: end of X-cor INFO @ Wed, 28 Jun 2017 00:45:21: #2 finished! INFO @ Wed, 28 Jun 2017 00:45:21: #2 predicted fragment length is 186 bps INFO @ Wed, 28 Jun 2017 00:45:21: #2 alternative fragment length(s) may be 186 bps INFO @ Wed, 28 Jun 2017 00:45:21: #2.2 Generate R script for model : SRX749026.05_model.r INFO @ Wed, 28 Jun 2017 00:45:21: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:45:21: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:45:25: 19000000 INFO @ Wed, 28 Jun 2017 00:45:25: 19000000 INFO @ Wed, 28 Jun 2017 00:45:26: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:45:26: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:45:26: #1 total tags in treatment: 9228392 INFO @ Wed, 28 Jun 2017 00:45:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:45:26: #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 00:45:27: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:45:27: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:45:27: #1 total tags in treatment: 9228392 INFO @ Wed, 28 Jun 2017 00:45:27: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:45:27: #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 00:45:27: #1 tags after filtering in treatment: 7475589 INFO @ Wed, 28 Jun 2017 00:45:27: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 00:45:27: #1 finished! INFO @ Wed, 28 Jun 2017 00:45:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:45:27: #1 tags after filtering in treatment: 7475589 INFO @ Wed, 28 Jun 2017 00:45:27: #1 Redundant rate of treatment: 0.19 INFO @ Wed, 28 Jun 2017 00:45:27: #1 finished! INFO @ Wed, 28 Jun 2017 00:45:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:45:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:45:28: #2 number of paired peaks: 8348 INFO @ Wed, 28 Jun 2017 00:45:28: start model_add_line... INFO @ Wed, 28 Jun 2017 00:45:28: #2 number of paired peaks: 8348 INFO @ Wed, 28 Jun 2017 00:45:28: start model_add_line... INFO @ Wed, 28 Jun 2017 00:45:28: start X-correlation... INFO @ Wed, 28 Jun 2017 00:45:28: end of X-cor INFO @ Wed, 28 Jun 2017 00:45:28: #2 finished! INFO @ Wed, 28 Jun 2017 00:45:28: #2 predicted fragment length is 186 bps INFO @ Wed, 28 Jun 2017 00:45:28: #2 alternative fragment length(s) may be 186 bps INFO @ Wed, 28 Jun 2017 00:45:28: #2.2 Generate R script for model : SRX749026.10_model.r INFO @ Wed, 28 Jun 2017 00:45:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:45:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:45:28: start X-correlation... INFO @ Wed, 28 Jun 2017 00:45:28: end of X-cor INFO @ Wed, 28 Jun 2017 00:45:28: #2 finished! INFO @ Wed, 28 Jun 2017 00:45:28: #2 predicted fragment length is 186 bps INFO @ Wed, 28 Jun 2017 00:45:28: #2 alternative fragment length(s) may be 186 bps INFO @ Wed, 28 Jun 2017 00:45:28: #2.2 Generate R script for model : SRX749026.20_model.r INFO @ Wed, 28 Jun 2017 00:45:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:45:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:45:49: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:45:55: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:45:55: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:46:01: #4 Write output xls file... SRX749026.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:46:01: #4 Write peak in narrowPeak format file... SRX749026.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:46:01: #4 Write summits bed file... SRX749026.05_summits.bed INFO @ Wed, 28 Jun 2017 00:46:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (12284 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:46:06: #4 Write output xls file... SRX749026.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:46:06: #4 Write peak in narrowPeak format file... SRX749026.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:46:06: #4 Write summits bed file... SRX749026.20_summits.bed INFO @ Wed, 28 Jun 2017 00:46:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7611 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:46:06: #4 Write output xls file... SRX749026.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:46:06: #4 Write peak in narrowPeak format file... SRX749026.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:46:06: #4 Write summits bed file... SRX749026.10_summits.bed INFO @ Wed, 28 Jun 2017 00:46:06: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10320 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。