Job ID = 10845192 sra ファイルのダウンロード中... Completed: 251076K bytes transferred in 12 seconds (164020K bits/sec), in 1 file. Completed: 338086K bytes transferred in 6 seconds (414067K bits/sec), in 1 file. 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... Read 4302457 spots for /home/okishinya/chipatlas/results/dm3/SRX3632886/SRR6655514.sra Written 4302457 spots for /home/okishinya/chipatlas/results/dm3/SRX3632886/SRR6655514.sra Read 6108427 spots for /home/okishinya/chipatlas/results/dm3/SRX3632886/SRR6655515.sra Written 6108427 spots for /home/okishinya/chipatlas/results/dm3/SRX3632886/SRR6655515.sra rm: cannot remove `[DSE]RX*': 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: 00:17:15 10410884 reads; of these: 10410884 (100.00%) were paired; of these: 1289557 (12.39%) aligned concordantly 0 times 8212551 (78.88%) aligned concordantly exactly 1 time 908776 (8.73%) aligned concordantly >1 times ---- 1289557 pairs aligned concordantly 0 times; of these: 670732 (52.01%) aligned discordantly 1 time ---- 618825 pairs aligned 0 times concordantly or discordantly; of these: 1237650 mates make up the pairs; of these: 710871 (57.44%) aligned 0 times 350324 (28.31%) aligned exactly 1 time 176455 (14.26%) aligned >1 times 96.59% overall alignment rate Time searching: 00:17:15 Overall time: 00:17:16 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] 420063 / 9684881 = 0.0434 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, 04 Jul 2018 09:50:44: # Command line: callpeak -t SRX3632886.bam -f BAM -g dm -n SRX3632886.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3632886.10 # format = BAM # ChIP-seq file = ['SRX3632886.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, 04 Jul 2018 09:50:44: # Command line: callpeak -t SRX3632886.bam -f BAM -g dm -n SRX3632886.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3632886.20 # format = BAM # ChIP-seq file = ['SRX3632886.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, 04 Jul 2018 09:50:44: # Command line: callpeak -t SRX3632886.bam -f BAM -g dm -n SRX3632886.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3632886.05 # format = BAM # ChIP-seq file = ['SRX3632886.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, 04 Jul 2018 09:50:44: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:50:44: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:50:44: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:50:44: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:50:44: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:50:44: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:50:51: 1000000 INFO @ Wed, 04 Jul 2018 09:50:52: 1000000 INFO @ Wed, 04 Jul 2018 09:50:52: 1000000 INFO @ Wed, 04 Jul 2018 09:50:58: 2000000 INFO @ Wed, 04 Jul 2018 09:50:59: 2000000 INFO @ Wed, 04 Jul 2018 09:50:59: 2000000 INFO @ Wed, 04 Jul 2018 09:51:05: 3000000 INFO @ Wed, 04 Jul 2018 09:51:06: 3000000 INFO @ Wed, 04 Jul 2018 09:51:06: 3000000 INFO @ Wed, 04 Jul 2018 09:51:11: 4000000 INFO @ Wed, 04 Jul 2018 09:51:13: 4000000 INFO @ Wed, 04 Jul 2018 09:51:13: 4000000 INFO @ Wed, 04 Jul 2018 09:51:18: 5000000 INFO @ Wed, 04 Jul 2018 09:51:20: 5000000 INFO @ Wed, 04 Jul 2018 09:51:20: 5000000 INFO @ Wed, 04 Jul 2018 09:51:25: 6000000 INFO @ Wed, 04 Jul 2018 09:51:27: 6000000 INFO @ Wed, 04 Jul 2018 09:51:27: 6000000 INFO @ Wed, 04 Jul 2018 09:51:31: 7000000 INFO @ Wed, 04 Jul 2018 09:51:34: 7000000 INFO @ Wed, 04 Jul 2018 09:51:34: 7000000 INFO @ Wed, 04 Jul 2018 09:51:38: 8000000 INFO @ Wed, 04 Jul 2018 09:51:41: 8000000 INFO @ Wed, 04 Jul 2018 09:51:41: 8000000 INFO @ Wed, 04 Jul 2018 09:51:45: 9000000 INFO @ Wed, 04 Jul 2018 09:51:48: 9000000 INFO @ Wed, 04 Jul 2018 09:51:49: 9000000 INFO @ Wed, 04 Jul 2018 09:51:51: 10000000 INFO @ Wed, 04 Jul 2018 09:51:55: 10000000 INFO @ Wed, 04 Jul 2018 09:51:56: 10000000 INFO @ Wed, 04 Jul 2018 09:51:58: 11000000 INFO @ Wed, 04 Jul 2018 09:52:03: 11000000 INFO @ Wed, 04 Jul 2018 09:52:03: 11000000 INFO @ Wed, 04 Jul 2018 09:52:04: 12000000 INFO @ Wed, 04 Jul 2018 09:52:10: 12000000 INFO @ Wed, 04 Jul 2018 09:52:11: 12000000 INFO @ Wed, 04 Jul 2018 09:52:11: 13000000 INFO @ Wed, 04 Jul 2018 09:52:17: 13000000 INFO @ Wed, 04 Jul 2018 09:52:18: 14000000 INFO @ Wed, 04 Jul 2018 09:52:18: 13000000 INFO @ Wed, 04 Jul 2018 09:52:24: 14000000 INFO @ Wed, 04 Jul 2018 09:52:24: 15000000 INFO @ Wed, 04 Jul 2018 09:52:26: 14000000 INFO @ Wed, 04 Jul 2018 09:52:31: 16000000 INFO @ Wed, 04 Jul 2018 09:52:31: 15000000 INFO @ Wed, 04 Jul 2018 09:52:34: 15000000 INFO @ Wed, 04 Jul 2018 09:52:38: 17000000 INFO @ Wed, 04 Jul 2018 09:52:39: 16000000 INFO @ Wed, 04 Jul 2018 09:52:41: 16000000 INFO @ Wed, 04 Jul 2018 09:52:44: 18000000 INFO @ Wed, 04 Jul 2018 09:52:46: 17000000 INFO @ Wed, 04 Jul 2018 09:52:49: 17000000 INFO @ Wed, 04 Jul 2018 09:52:51: 19000000 INFO @ Wed, 04 Jul 2018 09:52:53: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:52:53: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:52:53: #1 total tags in treatment: 8725331 INFO @ Wed, 04 Jul 2018 09:52:53: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:52:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:52:53: #1 tags after filtering in treatment: 7462064 INFO @ Wed, 04 Jul 2018 09:52:53: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 04 Jul 2018 09:52:53: #1 finished! INFO @ Wed, 04 Jul 2018 09:52:53: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:52:54: 18000000 INFO @ Wed, 04 Jul 2018 09:52:54: #2 number of paired peaks: 2430 INFO @ Wed, 04 Jul 2018 09:52:54: start model_add_line... INFO @ Wed, 04 Jul 2018 09:52:54: start X-correlation... INFO @ Wed, 04 Jul 2018 09:52:54: end of X-cor INFO @ Wed, 04 Jul 2018 09:52:54: #2 finished! INFO @ Wed, 04 Jul 2018 09:52:54: #2 predicted fragment length is 273 bps INFO @ Wed, 04 Jul 2018 09:52:54: #2 alternative fragment length(s) may be 3,273 bps INFO @ Wed, 04 Jul 2018 09:52:54: #2.2 Generate R script for model : SRX3632886.05_model.r INFO @ Wed, 04 Jul 2018 09:52:54: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:52:57: 18000000 INFO @ Wed, 04 Jul 2018 09:53:01: 19000000 INFO @ Wed, 04 Jul 2018 09:53:03: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:53:03: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:53:03: #1 total tags in treatment: 8725331 INFO @ Wed, 04 Jul 2018 09:53:03: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:53:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:53:03: #1 tags after filtering in treatment: 7462064 INFO @ Wed, 04 Jul 2018 09:53:03: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 04 Jul 2018 09:53:03: #1 finished! INFO @ Wed, 04 Jul 2018 09:53:03: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:53:03: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:53:04: #2 number of paired peaks: 2430 INFO @ Wed, 04 Jul 2018 09:53:04: start model_add_line... INFO @ Wed, 04 Jul 2018 09:53:04: start X-correlation... INFO @ Wed, 04 Jul 2018 09:53:04: end of X-cor INFO @ Wed, 04 Jul 2018 09:53:04: #2 finished! INFO @ Wed, 04 Jul 2018 09:53:04: #2 predicted fragment length is 273 bps INFO @ Wed, 04 Jul 2018 09:53:04: #2 alternative fragment length(s) may be 3,273 bps INFO @ Wed, 04 Jul 2018 09:53:04: #2.2 Generate R script for model : SRX3632886.20_model.r INFO @ Wed, 04 Jul 2018 09:53:04: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:53:04: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:53:04: 19000000 INFO @ Wed, 04 Jul 2018 09:53:06: #1 tag size is determined as 74 bps INFO @ Wed, 04 Jul 2018 09:53:06: #1 tag size = 74 INFO @ Wed, 04 Jul 2018 09:53:06: #1 total tags in treatment: 8725331 INFO @ Wed, 04 Jul 2018 09:53:06: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:53:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:53:06: #1 tags after filtering in treatment: 7462064 INFO @ Wed, 04 Jul 2018 09:53:06: #1 Redundant rate of treatment: 0.14 INFO @ Wed, 04 Jul 2018 09:53:06: #1 finished! INFO @ Wed, 04 Jul 2018 09:53:06: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:53:06: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:53:07: #2 number of paired peaks: 2430 INFO @ Wed, 04 Jul 2018 09:53:07: start model_add_line... INFO @ Wed, 04 Jul 2018 09:53:07: start X-correlation... INFO @ Wed, 04 Jul 2018 09:53:07: end of X-cor INFO @ Wed, 04 Jul 2018 09:53:07: #2 finished! INFO @ Wed, 04 Jul 2018 09:53:07: #2 predicted fragment length is 273 bps INFO @ Wed, 04 Jul 2018 09:53:07: #2 alternative fragment length(s) may be 3,273 bps INFO @ Wed, 04 Jul 2018 09:53:07: #2.2 Generate R script for model : SRX3632886.10_model.r INFO @ Wed, 04 Jul 2018 09:53:07: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:53:13: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:53:21: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:53:23: #4 Write output xls file... SRX3632886.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:53:23: #4 Write peak in narrowPeak format file... SRX3632886.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:53:23: #4 Write summits bed file... SRX3632886.05_summits.bed INFO @ Wed, 04 Jul 2018 09:53:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4338 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:53:26: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:53:30: #4 Write output xls file... SRX3632886.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:53:30: #4 Write peak in narrowPeak format file... SRX3632886.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:53:30: #4 Write summits bed file... SRX3632886.20_summits.bed INFO @ Wed, 04 Jul 2018 09:53:30: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (360 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:53:35: #4 Write output xls file... SRX3632886.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:53:35: #4 Write peak in narrowPeak format file... SRX3632886.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:53:35: #4 Write summits bed file... SRX3632886.10_summits.bed INFO @ Wed, 04 Jul 2018 09:53:35: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1726 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。