Job ID = 10714566 sra ファイルのダウンロード中... Completed: 260519K bytes transferred in 15 seconds (137531K 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 13486424 spots for /home/okishinya/chipatlas/results/dm3/SRX4053300/SRR7132413.sra Written 13486424 spots for /home/okishinya/chipatlas/results/dm3/SRX4053300/SRR7132413.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: 00:03:18 13486424 reads; of these: 13486424 (100.00%) were unpaired; of these: 2049013 (15.19%) aligned 0 times 10521633 (78.02%) aligned exactly 1 time 915778 (6.79%) aligned >1 times 84.81% overall alignment rate Time searching: 00:03:18 Overall time: 00:03:18 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] 5701353 / 11437411 = 0.4985 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, 03 Jun 2018 13:35:08: # Command line: callpeak -t SRX4053300.bam -f BAM -g dm -n SRX4053300.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053300.20 # format = BAM # ChIP-seq file = ['SRX4053300.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, 03 Jun 2018 13:35:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:08: # Command line: callpeak -t SRX4053300.bam -f BAM -g dm -n SRX4053300.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053300.05 # format = BAM # ChIP-seq file = ['SRX4053300.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, 03 Jun 2018 13:35:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:08: # Command line: callpeak -t SRX4053300.bam -f BAM -g dm -n SRX4053300.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053300.10 # format = BAM # ChIP-seq file = ['SRX4053300.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, 03 Jun 2018 13:35:08: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:35:08: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:35:14: 1000000 INFO @ Sun, 03 Jun 2018 13:35:15: 1000000 INFO @ Sun, 03 Jun 2018 13:35:15: 1000000 INFO @ Sun, 03 Jun 2018 13:35:21: 2000000 INFO @ Sun, 03 Jun 2018 13:35:21: 2000000 INFO @ Sun, 03 Jun 2018 13:35:22: 2000000 INFO @ Sun, 03 Jun 2018 13:35:28: 3000000 INFO @ Sun, 03 Jun 2018 13:35:29: 3000000 INFO @ Sun, 03 Jun 2018 13:35:29: 3000000 INFO @ Sun, 03 Jun 2018 13:35:35: 4000000 INFO @ Sun, 03 Jun 2018 13:35:36: 4000000 INFO @ Sun, 03 Jun 2018 13:35:37: 4000000 INFO @ Sun, 03 Jun 2018 13:35:42: 5000000 INFO @ Sun, 03 Jun 2018 13:35:44: 5000000 INFO @ Sun, 03 Jun 2018 13:35:45: 5000000 INFO @ Sun, 03 Jun 2018 13:35:47: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:35:47: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:35:47: #1 total tags in treatment: 5736058 INFO @ Sun, 03 Jun 2018 13:35:47: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:35:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:35:48: #1 tags after filtering in treatment: 5736058 INFO @ Sun, 03 Jun 2018 13:35:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:35:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:35:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:35:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:35:49: #2 number of paired peaks: 9935 INFO @ Sun, 03 Jun 2018 13:35:49: start model_add_line... INFO @ Sun, 03 Jun 2018 13:35:49: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:35:49: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:35:49: #1 total tags in treatment: 5736058 INFO @ Sun, 03 Jun 2018 13:35:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:35:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:35:49: start X-correlation... INFO @ Sun, 03 Jun 2018 13:35:49: end of X-cor INFO @ Sun, 03 Jun 2018 13:35:49: #2 finished! INFO @ Sun, 03 Jun 2018 13:35:49: #2 predicted fragment length is 184 bps INFO @ Sun, 03 Jun 2018 13:35:49: #2 alternative fragment length(s) may be 184 bps INFO @ Sun, 03 Jun 2018 13:35:49: #2.2 Generate R script for model : SRX4053300.10_model.r INFO @ Sun, 03 Jun 2018 13:35:49: #1 tags after filtering in treatment: 5736058 INFO @ Sun, 03 Jun 2018 13:35:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:35:49: #1 finished! INFO @ Sun, 03 Jun 2018 13:35:49: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:35:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:35:49: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:35:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:35:50: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:35:50: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:35:50: #1 total tags in treatment: 5736058 INFO @ Sun, 03 Jun 2018 13:35:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:35:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:35:50: #1 tags after filtering in treatment: 5736058 INFO @ Sun, 03 Jun 2018 13:35:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:35:50: #1 finished! INFO @ Sun, 03 Jun 2018 13:35:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:35:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:35:50: #2 number of paired peaks: 9935 INFO @ Sun, 03 Jun 2018 13:35:50: start model_add_line... INFO @ Sun, 03 Jun 2018 13:35:50: start X-correlation... INFO @ Sun, 03 Jun 2018 13:35:50: end of X-cor INFO @ Sun, 03 Jun 2018 13:35:50: #2 finished! INFO @ Sun, 03 Jun 2018 13:35:50: #2 predicted fragment length is 184 bps INFO @ Sun, 03 Jun 2018 13:35:50: #2 alternative fragment length(s) may be 184 bps INFO @ Sun, 03 Jun 2018 13:35:50: #2.2 Generate R script for model : SRX4053300.20_model.r INFO @ Sun, 03 Jun 2018 13:35:50: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:35:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:35:51: #2 number of paired peaks: 9935 INFO @ Sun, 03 Jun 2018 13:35:51: start model_add_line... INFO @ Sun, 03 Jun 2018 13:35:52: start X-correlation... INFO @ Sun, 03 Jun 2018 13:35:52: end of X-cor INFO @ Sun, 03 Jun 2018 13:35:52: #2 finished! INFO @ Sun, 03 Jun 2018 13:35:52: #2 predicted fragment length is 184 bps INFO @ Sun, 03 Jun 2018 13:35:52: #2 alternative fragment length(s) may be 184 bps INFO @ Sun, 03 Jun 2018 13:35:52: #2.2 Generate R script for model : SRX4053300.05_model.r INFO @ Sun, 03 Jun 2018 13:35:52: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:35:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:36:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:09: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:36:16: #4 Write output xls file... SRX4053300.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:16: #4 Write peak in narrowPeak format file... SRX4053300.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:16: #4 Write summits bed file... SRX4053300.20_summits.bed INFO @ Sun, 03 Jun 2018 13:36:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5495 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:36:16: #4 Write output xls file... SRX4053300.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:16: #4 Write peak in narrowPeak format file... SRX4053300.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:16: #4 Write summits bed file... SRX4053300.10_summits.bed INFO @ Sun, 03 Jun 2018 13:36:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6131 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:36:17: #4 Write output xls file... SRX4053300.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:36:17: #4 Write peak in narrowPeak format file... SRX4053300.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:36:17: #4 Write summits bed file... SRX4053300.05_summits.bed INFO @ Sun, 03 Jun 2018 13:36:17: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6483 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。