Job ID = 10175242 sra ファイルのダウンロード中... Completed: 597120K bytes transferred in 28 seconds (168730K 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... Written 33987866 spots for /home/okishinya/chipatlas/results/dm3/SRX2804220/SRR5534648.sra Written 33987866 spots total 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:11:37 33987866 reads; of these: 33987866 (100.00%) were unpaired; of these: 8228028 (24.21%) aligned 0 times 19111439 (56.23%) aligned exactly 1 time 6648399 (19.56%) aligned >1 times 75.79% overall alignment rate Time searching: 00:11:37 Overall time: 00:11:37 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_rmdupse_core] 6939079 / 25759838 = 0.2694 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 @ Mon, 06 Nov 2017 12:01:35: # Command line: callpeak -t SRX2804220.bam -f BAM -g dm -n SRX2804220.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2804220.20 # format = BAM # ChIP-seq file = ['SRX2804220.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 @ Mon, 06 Nov 2017 12:01:35: # Command line: callpeak -t SRX2804220.bam -f BAM -g dm -n SRX2804220.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2804220.10 # format = BAM # ChIP-seq file = ['SRX2804220.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 @ Mon, 06 Nov 2017 12:01:35: # Command line: callpeak -t SRX2804220.bam -f BAM -g dm -n SRX2804220.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2804220.05 # format = BAM # ChIP-seq file = ['SRX2804220.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 @ Mon, 06 Nov 2017 12:01:35: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:01:35: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:01:35: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:01:35: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:01:35: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:01:35: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:01:43: 1000000 INFO @ Mon, 06 Nov 2017 12:01:43: 1000000 INFO @ Mon, 06 Nov 2017 12:01:43: 1000000 INFO @ Mon, 06 Nov 2017 12:01:50: 2000000 INFO @ Mon, 06 Nov 2017 12:01:50: 2000000 INFO @ Mon, 06 Nov 2017 12:01:50: 2000000 INFO @ Mon, 06 Nov 2017 12:01:57: 3000000 INFO @ Mon, 06 Nov 2017 12:01:57: 3000000 INFO @ Mon, 06 Nov 2017 12:01:57: 3000000 INFO @ Mon, 06 Nov 2017 12:02:05: 4000000 INFO @ Mon, 06 Nov 2017 12:02:05: 4000000 INFO @ Mon, 06 Nov 2017 12:02:05: 4000000 INFO @ Mon, 06 Nov 2017 12:02:12: 5000000 INFO @ Mon, 06 Nov 2017 12:02:12: 5000000 INFO @ Mon, 06 Nov 2017 12:02:12: 5000000 INFO @ Mon, 06 Nov 2017 12:02:19: 6000000 INFO @ Mon, 06 Nov 2017 12:02:19: 6000000 INFO @ Mon, 06 Nov 2017 12:02:19: 6000000 INFO @ Mon, 06 Nov 2017 12:02:26: 7000000 INFO @ Mon, 06 Nov 2017 12:02:26: 7000000 INFO @ Mon, 06 Nov 2017 12:02:26: 7000000 INFO @ Mon, 06 Nov 2017 12:02:32: 8000000 INFO @ Mon, 06 Nov 2017 12:02:32: 8000000 INFO @ Mon, 06 Nov 2017 12:02:32: 8000000 INFO @ Mon, 06 Nov 2017 12:02:39: 9000000 INFO @ Mon, 06 Nov 2017 12:02:39: 9000000 INFO @ Mon, 06 Nov 2017 12:02:39: 9000000 INFO @ Mon, 06 Nov 2017 12:02:46: 10000000 INFO @ Mon, 06 Nov 2017 12:02:46: 10000000 INFO @ Mon, 06 Nov 2017 12:02:46: 10000000 INFO @ Mon, 06 Nov 2017 12:02:53: 11000000 INFO @ Mon, 06 Nov 2017 12:02:53: 11000000 INFO @ Mon, 06 Nov 2017 12:02:53: 11000000 INFO @ Mon, 06 Nov 2017 12:02:59: 12000000 INFO @ Mon, 06 Nov 2017 12:02:59: 12000000 INFO @ Mon, 06 Nov 2017 12:02:59: 12000000 INFO @ Mon, 06 Nov 2017 12:03:06: 13000000 INFO @ Mon, 06 Nov 2017 12:03:06: 13000000 INFO @ Mon, 06 Nov 2017 12:03:06: 13000000 INFO @ Mon, 06 Nov 2017 12:03:13: 14000000 INFO @ Mon, 06 Nov 2017 12:03:13: 14000000 INFO @ Mon, 06 Nov 2017 12:03:13: 14000000 INFO @ Mon, 06 Nov 2017 12:03:20: 15000000 INFO @ Mon, 06 Nov 2017 12:03:20: 15000000 INFO @ Mon, 06 Nov 2017 12:03:20: 15000000 INFO @ Mon, 06 Nov 2017 12:03:26: 16000000 INFO @ Mon, 06 Nov 2017 12:03:27: 16000000 INFO @ Mon, 06 Nov 2017 12:03:27: 16000000 INFO @ Mon, 06 Nov 2017 12:03:33: 17000000 INFO @ Mon, 06 Nov 2017 12:03:33: 17000000 INFO @ Mon, 06 Nov 2017 12:03:33: 17000000 INFO @ Mon, 06 Nov 2017 12:03:40: 18000000 INFO @ Mon, 06 Nov 2017 12:03:40: 18000000 INFO @ Mon, 06 Nov 2017 12:03:40: 18000000 INFO @ Mon, 06 Nov 2017 12:03:45: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:03:45: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:03:45: #1 total tags in treatment: 18820759 INFO @ Mon, 06 Nov 2017 12:03:45: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:03:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:03:46: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:03:46: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:03:46: #1 total tags in treatment: 18820759 INFO @ Mon, 06 Nov 2017 12:03:46: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:03:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:03:46: #1 tag size is determined as 51 bps INFO @ Mon, 06 Nov 2017 12:03:46: #1 tag size = 51 INFO @ Mon, 06 Nov 2017 12:03:46: #1 total tags in treatment: 18820759 INFO @ Mon, 06 Nov 2017 12:03:46: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:03:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:03:46: #1 tags after filtering in treatment: 18820759 INFO @ Mon, 06 Nov 2017 12:03:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:03:46: #1 finished! INFO @ Mon, 06 Nov 2017 12:03:46: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:03:46: #1 tags after filtering in treatment: 18820759 INFO @ Mon, 06 Nov 2017 12:03:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:03:46: #1 finished! INFO @ Mon, 06 Nov 2017 12:03:46: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:03:46: #1 tags after filtering in treatment: 18820759 INFO @ Mon, 06 Nov 2017 12:03:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:03:46: #1 finished! INFO @ Mon, 06 Nov 2017 12:03:46: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:03:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:03:47: #2 number of paired peaks: 706 WARNING @ Mon, 06 Nov 2017 12:03:47: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Mon, 06 Nov 2017 12:03:47: start model_add_line... INFO @ Mon, 06 Nov 2017 12:03:47: #2 number of paired peaks: 706 WARNING @ Mon, 06 Nov 2017 12:03:47: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Mon, 06 Nov 2017 12:03:47: start model_add_line... INFO @ Mon, 06 Nov 2017 12:03:47: #2 number of paired peaks: 706 WARNING @ Mon, 06 Nov 2017 12:03:47: Fewer paired peaks (706) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 706 pairs to build model! INFO @ Mon, 06 Nov 2017 12:03:47: start model_add_line... INFO @ Mon, 06 Nov 2017 12:03:47: start X-correlation... INFO @ Mon, 06 Nov 2017 12:03:48: end of X-cor INFO @ Mon, 06 Nov 2017 12:03:48: #2 finished! INFO @ Mon, 06 Nov 2017 12:03:48: #2 predicted fragment length is 130 bps INFO @ Mon, 06 Nov 2017 12:03:48: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 06 Nov 2017 12:03:48: #2.2 Generate R script for model : SRX2804220.20_model.r INFO @ Mon, 06 Nov 2017 12:03:48: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:03:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:03:48: start X-correlation... INFO @ Mon, 06 Nov 2017 12:03:48: end of X-cor INFO @ Mon, 06 Nov 2017 12:03:48: #2 finished! INFO @ Mon, 06 Nov 2017 12:03:48: #2 predicted fragment length is 130 bps INFO @ Mon, 06 Nov 2017 12:03:48: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 06 Nov 2017 12:03:48: #2.2 Generate R script for model : SRX2804220.05_model.r INFO @ Mon, 06 Nov 2017 12:03:48: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:03:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:03:48: start X-correlation... INFO @ Mon, 06 Nov 2017 12:03:48: end of X-cor INFO @ Mon, 06 Nov 2017 12:03:48: #2 finished! INFO @ Mon, 06 Nov 2017 12:03:48: #2 predicted fragment length is 130 bps INFO @ Mon, 06 Nov 2017 12:03:48: #2 alternative fragment length(s) may be 130 bps INFO @ Mon, 06 Nov 2017 12:03:48: #2.2 Generate R script for model : SRX2804220.10_model.r INFO @ Mon, 06 Nov 2017 12:03:48: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:03:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:04:29: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:04:31: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:04:33: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:04:50: #4 Write output xls file... SRX2804220.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:04:50: #4 Write peak in narrowPeak format file... SRX2804220.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:04:50: #4 Write summits bed file... SRX2804220.20_summits.bed INFO @ Mon, 06 Nov 2017 12:04:50: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4630 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:04:53: #4 Write output xls file... SRX2804220.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:04:53: #4 Write peak in narrowPeak format file... SRX2804220.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:04:53: #4 Write summits bed file... SRX2804220.10_summits.bed INFO @ Mon, 06 Nov 2017 12:04:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7258 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:04:59: #4 Write output xls file... SRX2804220.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:04:59: #4 Write peak in narrowPeak format file... SRX2804220.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:04:59: #4 Write summits bed file... SRX2804220.05_summits.bed INFO @ Mon, 06 Nov 2017 12:04:59: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10685 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。