Job ID = 10609093 sra ファイルのダウンロード中... Completed: 332708K bytes transferred in 40 seconds (67273K 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: SINGLE fastq に変換中... Read 16203007 spots for /home/okishinya/chipatlas/results/dm3/SRX3011231/SRR5834708.sra Written 16203007 spots for /home/okishinya/chipatlas/results/dm3/SRX3011231/SRR5834708.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 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:55 16203007 reads; of these: 16203007 (100.00%) were unpaired; of these: 144146 (0.89%) aligned 0 times 15811805 (97.59%) aligned exactly 1 time 247056 (1.52%) aligned >1 times 99.11% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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 8 files... [bam_rmdupse_core] 5514066 / 16058861 = 0.3434 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 May 2018 07:09:36: # Command line: callpeak -t SRX3011231.bam -f BAM -g dm -n SRX3011231.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011231.20 # format = BAM # ChIP-seq file = ['SRX3011231.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 May 2018 07:09:36: #1 read tag files... INFO @ Fri, 04 May 2018 07:09:36: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:09:36: # Command line: callpeak -t SRX3011231.bam -f BAM -g dm -n SRX3011231.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011231.05 # format = BAM # ChIP-seq file = ['SRX3011231.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 May 2018 07:09:36: #1 read tag files... INFO @ Fri, 04 May 2018 07:09:36: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:09:36: # Command line: callpeak -t SRX3011231.bam -f BAM -g dm -n SRX3011231.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011231.10 # format = BAM # ChIP-seq file = ['SRX3011231.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 May 2018 07:09:36: #1 read tag files... INFO @ Fri, 04 May 2018 07:09:36: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:09:43: 1000000 INFO @ Fri, 04 May 2018 07:09:43: 1000000 INFO @ Fri, 04 May 2018 07:09:43: 1000000 INFO @ Fri, 04 May 2018 07:09:50: 2000000 INFO @ Fri, 04 May 2018 07:09:50: 2000000 INFO @ Fri, 04 May 2018 07:09:50: 2000000 INFO @ Fri, 04 May 2018 07:09:56: 3000000 INFO @ Fri, 04 May 2018 07:09:57: 3000000 INFO @ Fri, 04 May 2018 07:09:57: 3000000 INFO @ Fri, 04 May 2018 07:10:03: 4000000 INFO @ Fri, 04 May 2018 07:10:04: 4000000 INFO @ Fri, 04 May 2018 07:10:04: 4000000 INFO @ Fri, 04 May 2018 07:10:10: 5000000 INFO @ Fri, 04 May 2018 07:10:10: 5000000 INFO @ Fri, 04 May 2018 07:10:10: 5000000 INFO @ Fri, 04 May 2018 07:10:17: 6000000 INFO @ Fri, 04 May 2018 07:10:17: 6000000 INFO @ Fri, 04 May 2018 07:10:17: 6000000 INFO @ Fri, 04 May 2018 07:10:24: 7000000 INFO @ Fri, 04 May 2018 07:10:24: 7000000 INFO @ Fri, 04 May 2018 07:10:24: 7000000 INFO @ Fri, 04 May 2018 07:10:31: 8000000 INFO @ Fri, 04 May 2018 07:10:31: 8000000 INFO @ Fri, 04 May 2018 07:10:31: 8000000 INFO @ Fri, 04 May 2018 07:10:38: 9000000 INFO @ Fri, 04 May 2018 07:10:38: 9000000 INFO @ Fri, 04 May 2018 07:10:38: 9000000 INFO @ Fri, 04 May 2018 07:10:45: 10000000 INFO @ Fri, 04 May 2018 07:10:45: 10000000 INFO @ Fri, 04 May 2018 07:10:45: 10000000 INFO @ Fri, 04 May 2018 07:10:48: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:10:48: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:10:48: #1 total tags in treatment: 10544795 INFO @ Fri, 04 May 2018 07:10:48: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:10:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:10:48: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:10:48: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:10:48: #1 total tags in treatment: 10544795 INFO @ Fri, 04 May 2018 07:10:48: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:10:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:10:48: #1 tags after filtering in treatment: 10544795 INFO @ Fri, 04 May 2018 07:10:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:10:48: #1 finished! INFO @ Fri, 04 May 2018 07:10:48: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:10:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:10:49: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:10:49: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:10:49: #1 total tags in treatment: 10544795 INFO @ Fri, 04 May 2018 07:10:49: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:10:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:10:49: #1 tags after filtering in treatment: 10544795 INFO @ Fri, 04 May 2018 07:10:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:10:49: #1 finished! INFO @ Fri, 04 May 2018 07:10:49: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:10:49: #1 tags after filtering in treatment: 10544795 INFO @ Fri, 04 May 2018 07:10:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:10:49: #1 finished! INFO @ Fri, 04 May 2018 07:10:49: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:10:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:10:50: #2 number of paired peaks: 6088 INFO @ Fri, 04 May 2018 07:10:50: start model_add_line... INFO @ Fri, 04 May 2018 07:10:50: #2 number of paired peaks: 6088 INFO @ Fri, 04 May 2018 07:10:50: start model_add_line... INFO @ Fri, 04 May 2018 07:10:50: start X-correlation... INFO @ Fri, 04 May 2018 07:10:50: end of X-cor INFO @ Fri, 04 May 2018 07:10:50: #2 finished! INFO @ Fri, 04 May 2018 07:10:50: #2 predicted fragment length is 189 bps INFO @ Fri, 04 May 2018 07:10:50: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 04 May 2018 07:10:50: #2.2 Generate R script for model : SRX3011231.05_model.r INFO @ Fri, 04 May 2018 07:10:50: #3 Call peaks... INFO @ Fri, 04 May 2018 07:10:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:10:50: #2 number of paired peaks: 6088 INFO @ Fri, 04 May 2018 07:10:50: start model_add_line... INFO @ Fri, 04 May 2018 07:10:50: start X-correlation... INFO @ Fri, 04 May 2018 07:10:50: end of X-cor INFO @ Fri, 04 May 2018 07:10:50: #2 finished! INFO @ Fri, 04 May 2018 07:10:50: #2 predicted fragment length is 189 bps INFO @ Fri, 04 May 2018 07:10:50: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 04 May 2018 07:10:50: #2.2 Generate R script for model : SRX3011231.20_model.r INFO @ Fri, 04 May 2018 07:10:50: #3 Call peaks... INFO @ Fri, 04 May 2018 07:10:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:10:50: start X-correlation... INFO @ Fri, 04 May 2018 07:10:50: end of X-cor INFO @ Fri, 04 May 2018 07:10:50: #2 finished! INFO @ Fri, 04 May 2018 07:10:50: #2 predicted fragment length is 189 bps INFO @ Fri, 04 May 2018 07:10:50: #2 alternative fragment length(s) may be 189 bps INFO @ Fri, 04 May 2018 07:10:50: #2.2 Generate R script for model : SRX3011231.10_model.r INFO @ Fri, 04 May 2018 07:10:50: #3 Call peaks... INFO @ Fri, 04 May 2018 07:10:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:11:25: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:11:26: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:11:26: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:11:40: #4 Write output xls file... SRX3011231.05_peaks.xls INFO @ Fri, 04 May 2018 07:11:40: #4 Write peak in narrowPeak format file... SRX3011231.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:11:40: #4 Write summits bed file... SRX3011231.05_summits.bed INFO @ Fri, 04 May 2018 07:11:40: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9629 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:11:42: #4 Write output xls file... SRX3011231.10_peaks.xls INFO @ Fri, 04 May 2018 07:11:42: #4 Write output xls file... SRX3011231.20_peaks.xls INFO @ Fri, 04 May 2018 07:11:42: #4 Write peak in narrowPeak format file... SRX3011231.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:11:42: #4 Write peak in narrowPeak format file... SRX3011231.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:11:42: #4 Write summits bed file... SRX3011231.20_summits.bed INFO @ Fri, 04 May 2018 07:11:42: #4 Write summits bed file... SRX3011231.10_summits.bed INFO @ Fri, 04 May 2018 07:11:42: Done! INFO @ Fri, 04 May 2018 07:11:42: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (5379 records, 4 fields): 8 millis pass1 - making usageList (13 chroms): 1 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (7441 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。