Job ID = 11240737 sra ファイルのダウンロード中... Completed: 620777K bytes transferred in 21 seconds (238325K 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 34560344 spots for /home/okishinya/chipatlas/results/dm3/SRX4669021/SRR7817546.sra Written 34560344 spots for /home/okishinya/chipatlas/results/dm3/SRX4669021/SRR7817546.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: 00:08:43 34560344 reads; of these: 34560344 (100.00%) were unpaired; of these: 5612516 (16.24%) aligned 0 times 24374774 (70.53%) aligned exactly 1 time 4573054 (13.23%) aligned >1 times 83.76% overall alignment rate Time searching: 00:08:43 Overall time: 00:08:43 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] 13561756 / 28947828 = 0.4685 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 20:45:20: # Command line: callpeak -t SRX4669021.bam -f BAM -g dm -n SRX4669021.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669021.05 # format = BAM # ChIP-seq file = ['SRX4669021.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 20:45:20: # Command line: callpeak -t SRX4669021.bam -f BAM -g dm -n SRX4669021.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669021.10 # format = BAM # ChIP-seq file = ['SRX4669021.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 20:45:20: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:20: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:20: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:20: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:20: # Command line: callpeak -t SRX4669021.bam -f BAM -g dm -n SRX4669021.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669021.20 # format = BAM # ChIP-seq file = ['SRX4669021.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 20:45:20: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:45:20: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:45:26: 1000000 INFO @ Sun, 07 Oct 2018 20:45:26: 1000000 INFO @ Sun, 07 Oct 2018 20:45:26: 1000000 INFO @ Sun, 07 Oct 2018 20:45:33: 2000000 INFO @ Sun, 07 Oct 2018 20:45:33: 2000000 INFO @ Sun, 07 Oct 2018 20:45:33: 2000000 INFO @ Sun, 07 Oct 2018 20:45:39: 3000000 INFO @ Sun, 07 Oct 2018 20:45:39: 3000000 INFO @ Sun, 07 Oct 2018 20:45:39: 3000000 INFO @ Sun, 07 Oct 2018 20:45:45: 4000000 INFO @ Sun, 07 Oct 2018 20:45:45: 4000000 INFO @ Sun, 07 Oct 2018 20:45:45: 4000000 INFO @ Sun, 07 Oct 2018 20:45:52: 5000000 INFO @ Sun, 07 Oct 2018 20:45:52: 5000000 INFO @ Sun, 07 Oct 2018 20:45:52: 5000000 INFO @ Sun, 07 Oct 2018 20:45:58: 6000000 INFO @ Sun, 07 Oct 2018 20:45:58: 6000000 INFO @ Sun, 07 Oct 2018 20:45:58: 6000000 INFO @ Sun, 07 Oct 2018 20:46:04: 7000000 INFO @ Sun, 07 Oct 2018 20:46:04: 7000000 INFO @ Sun, 07 Oct 2018 20:46:04: 7000000 INFO @ Sun, 07 Oct 2018 20:46:11: 8000000 INFO @ Sun, 07 Oct 2018 20:46:11: 8000000 INFO @ Sun, 07 Oct 2018 20:46:11: 8000000 INFO @ Sun, 07 Oct 2018 20:46:17: 9000000 INFO @ Sun, 07 Oct 2018 20:46:17: 9000000 INFO @ Sun, 07 Oct 2018 20:46:17: 9000000 INFO @ Sun, 07 Oct 2018 20:46:23: 10000000 INFO @ Sun, 07 Oct 2018 20:46:23: 10000000 INFO @ Sun, 07 Oct 2018 20:46:23: 10000000 INFO @ Sun, 07 Oct 2018 20:46:30: 11000000 INFO @ Sun, 07 Oct 2018 20:46:30: 11000000 INFO @ Sun, 07 Oct 2018 20:46:30: 11000000 INFO @ Sun, 07 Oct 2018 20:46:36: 12000000 INFO @ Sun, 07 Oct 2018 20:46:36: 12000000 INFO @ Sun, 07 Oct 2018 20:46:36: 12000000 INFO @ Sun, 07 Oct 2018 20:46:42: 13000000 INFO @ Sun, 07 Oct 2018 20:46:43: 13000000 INFO @ Sun, 07 Oct 2018 20:46:43: 13000000 INFO @ Sun, 07 Oct 2018 20:46:49: 14000000 INFO @ Sun, 07 Oct 2018 20:46:49: 14000000 INFO @ Sun, 07 Oct 2018 20:46:49: 14000000 INFO @ Sun, 07 Oct 2018 20:46:55: 15000000 INFO @ Sun, 07 Oct 2018 20:46:55: 15000000 INFO @ Sun, 07 Oct 2018 20:46:56: 15000000 INFO @ Sun, 07 Oct 2018 20:46:58: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:46:58: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:46:58: #1 total tags in treatment: 15386072 INFO @ Sun, 07 Oct 2018 20:46:58: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:58: #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 20:46:58: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:46:58: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:46:58: #1 total tags in treatment: 15386072 INFO @ Sun, 07 Oct 2018 20:46:58: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:58: #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 20:46:58: #1 tags after filtering in treatment: 15386072 INFO @ Sun, 07 Oct 2018 20:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:58: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:58: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:58: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 20:46:58: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 20:46:58: #1 total tags in treatment: 15386072 INFO @ Sun, 07 Oct 2018 20:46:58: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:46:58: #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 20:46:58: #1 tags after filtering in treatment: 15386072 INFO @ Sun, 07 Oct 2018 20:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:58: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:58: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:58: #1 tags after filtering in treatment: 15386072 INFO @ Sun, 07 Oct 2018 20:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:46:58: #1 finished! INFO @ Sun, 07 Oct 2018 20:46:58: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:46:59: #2 number of paired peaks: 1837 INFO @ Sun, 07 Oct 2018 20:46:59: start model_add_line... INFO @ Sun, 07 Oct 2018 20:46:59: #2 number of paired peaks: 1837 INFO @ Sun, 07 Oct 2018 20:46:59: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:00: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:00: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:00: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:00: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:00: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:00: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:00: #2 predicted fragment length is 173 bps INFO @ Sun, 07 Oct 2018 20:47:00: #2 predicted fragment length is 173 bps INFO @ Sun, 07 Oct 2018 20:47:00: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 07 Oct 2018 20:47:00: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 07 Oct 2018 20:47:00: #2.2 Generate R script for model : SRX4669021.05_model.r INFO @ Sun, 07 Oct 2018 20:47:00: #2.2 Generate R script for model : SRX4669021.20_model.r INFO @ Sun, 07 Oct 2018 20:47:00: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:00: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:00: #2 number of paired peaks: 1837 INFO @ Sun, 07 Oct 2018 20:47:00: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:00: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:00: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:00: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:00: #2 predicted fragment length is 173 bps INFO @ Sun, 07 Oct 2018 20:47:00: #2 alternative fragment length(s) may be 173 bps INFO @ Sun, 07 Oct 2018 20:47:00: #2.2 Generate R script for model : SRX4669021.10_model.r INFO @ Sun, 07 Oct 2018 20:47:00: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:40: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:40: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:40: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write output xls file... SRX4669021.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write peak in narrowPeak format file... SRX4669021.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write summits bed file... SRX4669021.10_summits.bed INFO @ Sun, 07 Oct 2018 20:48:00: Done! INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write output xls file... SRX4669021.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write peak in narrowPeak format file... SRX4669021.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write summits bed file... SRX4669021.05_summits.bed INFO @ Sun, 07 Oct 2018 20:48:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9284 records, 4 fields): 13 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (13479 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:01: #4 Write output xls file... SRX4669021.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:01: #4 Write peak in narrowPeak format file... SRX4669021.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:01: #4 Write summits bed file... SRX4669021.20_summits.bed INFO @ Sun, 07 Oct 2018 20:48:01: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5479 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。