Job ID = 11240762 sra ファイルのダウンロード中... Completed: 530712K bytes transferred in 11 seconds (382702K 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 31076831 spots for /home/okishinya/chipatlas/results/dm3/SRX4669046/SRR7817571.sra Written 31076831 spots for /home/okishinya/chipatlas/results/dm3/SRX4669046/SRR7817571.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:09 31076831 reads; of these: 31076831 (100.00%) were unpaired; of these: 3101573 (9.98%) aligned 0 times 22610768 (72.76%) aligned exactly 1 time 5364490 (17.26%) aligned >1 times 90.02% overall alignment rate Time searching: 00:09:09 Overall time: 00:09:09 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] 11138790 / 27975258 = 0.3982 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 @ Sun, 07 Oct 2018 20:45:47: # Command line: callpeak -t SRX4669046.bam -f BAM -g dm -n SRX4669046.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669046.10 # format = BAM # ChIP-seq file = ['SRX4669046.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 @ Sun, 07 Oct 2018 20:45:47: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:47: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:47: # Command line: callpeak -t SRX4669046.bam -f BAM -g dm -n SRX4669046.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669046.05 # format = BAM # ChIP-seq file = ['SRX4669046.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 @ Sun, 07 Oct 2018 20:45:47: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:47: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:47: # Command line: callpeak -t SRX4669046.bam -f BAM -g dm -n SRX4669046.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669046.20 # format = BAM # ChIP-seq file = ['SRX4669046.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 @ Sun, 07 Oct 2018 20:45:47: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:47: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:54: 1000000 INFO @ Sun, 07 Oct 2018 20:45:54: 1000000 INFO @ Sun, 07 Oct 2018 20:45:54: 1000000 INFO @ Sun, 07 Oct 2018 20:46:01: 2000000 INFO @ Sun, 07 Oct 2018 20:46:02: 2000000 INFO @ Sun, 07 Oct 2018 20:46:02: 2000000 INFO @ Sun, 07 Oct 2018 20:46:09: 3000000 INFO @ Sun, 07 Oct 2018 20:46:10: 3000000 INFO @ Sun, 07 Oct 2018 20:46:10: 3000000 INFO @ Sun, 07 Oct 2018 20:46:16: 4000000 INFO @ Sun, 07 Oct 2018 20:46:17: 4000000 INFO @ Sun, 07 Oct 2018 20:46:18: 4000000 INFO @ Sun, 07 Oct 2018 20:46:23: 5000000 INFO @ Sun, 07 Oct 2018 20:46:25: 5000000 INFO @ Sun, 07 Oct 2018 20:46:26: 5000000 INFO @ Sun, 07 Oct 2018 20:46:31: 6000000 INFO @ Sun, 07 Oct 2018 20:46:32: 6000000 INFO @ Sun, 07 Oct 2018 20:46:34: 6000000 INFO @ Sun, 07 Oct 2018 20:46:38: 7000000 INFO @ Sun, 07 Oct 2018 20:46:40: 7000000 INFO @ Sun, 07 Oct 2018 20:46:43: 7000000 INFO @ Sun, 07 Oct 2018 20:46:45: 8000000 INFO @ Sun, 07 Oct 2018 20:46:48: 8000000 INFO @ Sun, 07 Oct 2018 20:46:51: 8000000 INFO @ Sun, 07 Oct 2018 20:46:52: 9000000 INFO @ Sun, 07 Oct 2018 20:46:55: 9000000 INFO @ Sun, 07 Oct 2018 20:46:59: 9000000 INFO @ Sun, 07 Oct 2018 20:46:59: 10000000 INFO @ Sun, 07 Oct 2018 20:47:03: 10000000 INFO @ Sun, 07 Oct 2018 20:47:06: 11000000 INFO @ Sun, 07 Oct 2018 20:47:07: 10000000 INFO @ Sun, 07 Oct 2018 20:47:11: 11000000 INFO @ Sun, 07 Oct 2018 20:47:13: 12000000 INFO @ Sun, 07 Oct 2018 20:47:15: 11000000 INFO @ Sun, 07 Oct 2018 20:47:18: 12000000 INFO @ Sun, 07 Oct 2018 20:47:21: 13000000 INFO @ Sun, 07 Oct 2018 20:47:23: 12000000 INFO @ Sun, 07 Oct 2018 20:47:26: 13000000 INFO @ Sun, 07 Oct 2018 20:47:28: 14000000 INFO @ Sun, 07 Oct 2018 20:47:32: 13000000 INFO @ Sun, 07 Oct 2018 20:47:34: 14000000 INFO @ Sun, 07 Oct 2018 20:47:35: 15000000 INFO @ Sun, 07 Oct 2018 20:47:40: 14000000 INFO @ Sun, 07 Oct 2018 20:47:42: 15000000 INFO @ Sun, 07 Oct 2018 20:47:42: 16000000 INFO @ Sun, 07 Oct 2018 20:47:48: 15000000 INFO @ Sun, 07 Oct 2018 20:47:48: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:48: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:48: #1 total tags in treatment: 16836468 INFO @ Sun, 07 Oct 2018 20:47:48: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:49: #1 tags after filtering in treatment: 16836468 INFO @ Sun, 07 Oct 2018 20:47:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:49: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:49: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:49: 16000000 INFO @ Sun, 07 Oct 2018 20:47:50: #2 number of paired peaks: 1720 INFO @ Sun, 07 Oct 2018 20:47:50: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:50: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:50: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:50: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:50: #2 predicted fragment length is 157 bps INFO @ Sun, 07 Oct 2018 20:47:50: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 07 Oct 2018 20:47:50: #2.2 Generate R script for model : SRX4669046.05_model.r INFO @ Sun, 07 Oct 2018 20:47:50: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:55: 16000000 INFO @ Sun, 07 Oct 2018 20:47:55: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:47:55: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:47:55: #1 total tags in treatment: 16836468 INFO @ Sun, 07 Oct 2018 20:47:55: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:47:55: #1 tags after filtering in treatment: 16836468 INFO @ Sun, 07 Oct 2018 20:47:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:55: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:55: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:56: #2 number of paired peaks: 1720 INFO @ Sun, 07 Oct 2018 20:47:56: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:57: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:57: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:57: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:57: #2 predicted fragment length is 157 bps INFO @ Sun, 07 Oct 2018 20:47:57: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 07 Oct 2018 20:47:57: #2.2 Generate R script for model : SRX4669046.10_model.r INFO @ Sun, 07 Oct 2018 20:47:57: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:00: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:48:00: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:48:00: #1 total tags in treatment: 16836468 INFO @ Sun, 07 Oct 2018 20:48:00: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:48:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:48:00: #1 tags after filtering in treatment: 16836468 INFO @ Sun, 07 Oct 2018 20:48:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:48:00: #1 finished! INFO @ Sun, 07 Oct 2018 20:48:00: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:48:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:48:02: #2 number of paired peaks: 1720 INFO @ Sun, 07 Oct 2018 20:48:02: start model_add_line... INFO @ Sun, 07 Oct 2018 20:48:02: start X-correlation... INFO @ Sun, 07 Oct 2018 20:48:02: end of X-cor INFO @ Sun, 07 Oct 2018 20:48:02: #2 finished! INFO @ Sun, 07 Oct 2018 20:48:02: #2 predicted fragment length is 157 bps INFO @ Sun, 07 Oct 2018 20:48:02: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 07 Oct 2018 20:48:02: #2.2 Generate R script for model : SRX4669046.20_model.r INFO @ Sun, 07 Oct 2018 20:48:02: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:48:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:48:34: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:40: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:46: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:49:00: #4 Write output xls file... SRX4669046.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:00: #4 Write peak in narrowPeak format file... SRX4669046.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:49:00: #4 Write summits bed file... SRX4669046.05_summits.bed INFO @ Sun, 07 Oct 2018 20:49:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11685 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:49:04: #4 Write output xls file... SRX4669046.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:04: #4 Write peak in narrowPeak format file... SRX4669046.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:49:04: #4 Write summits bed file... SRX4669046.10_summits.bed INFO @ Sun, 07 Oct 2018 20:49:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8460 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:49:08: #4 Write output xls file... SRX4669046.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:49:08: #4 Write peak in narrowPeak format file... SRX4669046.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:49:08: #4 Write summits bed file... SRX4669046.20_summits.bed INFO @ Sun, 07 Oct 2018 20:49:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4860 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。