Job ID = 11240801 sra ファイルのダウンロード中... Completed: 664022K bytes transferred in 12 seconds (426336K 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 18882033 spots for /home/okishinya/chipatlas/results/dm3/SRX4798848/SRR7965221.sra Written 18882033 spots for /home/okishinya/chipatlas/results/dm3/SRX4798848/SRR7965221.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: 00:03:04 18882033 reads; of these: 18882033 (100.00%) were unpaired; of these: 11250113 (59.58%) aligned 0 times 7169412 (37.97%) aligned exactly 1 time 462508 (2.45%) aligned >1 times 40.42% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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_rmdupse_core] 2305758 / 7631920 = 0.3021 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 20:46:55: # Command line: callpeak -t SRX4798848.bam -f BAM -g dm -n SRX4798848.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798848.05 # format = BAM # ChIP-seq file = ['SRX4798848.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 20:46:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:46:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:46:55: # Command line: callpeak -t SRX4798848.bam -f BAM -g dm -n SRX4798848.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798848.20 # format = BAM # ChIP-seq file = ['SRX4798848.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 20:46:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:46:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:46:55: # Command line: callpeak -t SRX4798848.bam -f BAM -g dm -n SRX4798848.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798848.10 # format = BAM # ChIP-seq file = ['SRX4798848.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 20:46:55: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:46:55: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:47:02: 1000000 INFO @ Sun, 07 Oct 2018 20:47:03: 1000000 INFO @ Sun, 07 Oct 2018 20:47:03: 1000000 INFO @ Sun, 07 Oct 2018 20:47:08: 2000000 INFO @ Sun, 07 Oct 2018 20:47:10: 2000000 INFO @ Sun, 07 Oct 2018 20:47:10: 2000000 INFO @ Sun, 07 Oct 2018 20:47:15: 3000000 INFO @ Sun, 07 Oct 2018 20:47:17: 3000000 INFO @ Sun, 07 Oct 2018 20:47:17: 3000000 INFO @ Sun, 07 Oct 2018 20:47:21: 4000000 INFO @ Sun, 07 Oct 2018 20:47:25: 4000000 INFO @ Sun, 07 Oct 2018 20:47:25: 4000000 INFO @ Sun, 07 Oct 2018 20:47:28: 5000000 INFO @ Sun, 07 Oct 2018 20:47:30: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:47:30: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:47:30: #1 total tags in treatment: 5326162 INFO @ Sun, 07 Oct 2018 20:47:30: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:30: #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 20:47:30: #1 tags after filtering in treatment: 5326162 INFO @ Sun, 07 Oct 2018 20:47:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:30: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:30: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:31: #2 number of paired peaks: 5639 INFO @ Sun, 07 Oct 2018 20:47:31: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:31: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:31: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:31: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:31: #2 predicted fragment length is 171 bps INFO @ Sun, 07 Oct 2018 20:47:31: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 07 Oct 2018 20:47:31: #2.2 Generate R script for model : SRX4798848.05_model.r INFO @ Sun, 07 Oct 2018 20:47:31: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:32: 5000000 INFO @ Sun, 07 Oct 2018 20:47:32: 5000000 INFO @ Sun, 07 Oct 2018 20:47:34: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:47:34: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:47:34: #1 total tags in treatment: 5326162 INFO @ Sun, 07 Oct 2018 20:47:34: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:34: #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 20:47:34: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:47:34: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:47:34: #1 total tags in treatment: 5326162 INFO @ Sun, 07 Oct 2018 20:47:34: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:47:34: #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 20:47:34: #1 tags after filtering in treatment: 5326162 INFO @ Sun, 07 Oct 2018 20:47:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:34: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:34: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:34: #1 tags after filtering in treatment: 5326162 INFO @ Sun, 07 Oct 2018 20:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:47:34: #1 finished! INFO @ Sun, 07 Oct 2018 20:47:34: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:47:35: #2 number of paired peaks: 5639 INFO @ Sun, 07 Oct 2018 20:47:35: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:35: #2 number of paired peaks: 5639 INFO @ Sun, 07 Oct 2018 20:47:35: start model_add_line... INFO @ Sun, 07 Oct 2018 20:47:35: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:35: start X-correlation... INFO @ Sun, 07 Oct 2018 20:47:35: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:35: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:35: end of X-cor INFO @ Sun, 07 Oct 2018 20:47:35: #2 predicted fragment length is 171 bps INFO @ Sun, 07 Oct 2018 20:47:35: #2 finished! INFO @ Sun, 07 Oct 2018 20:47:35: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 07 Oct 2018 20:47:35: #2 predicted fragment length is 171 bps INFO @ Sun, 07 Oct 2018 20:47:35: #2.2 Generate R script for model : SRX4798848.20_model.r INFO @ Sun, 07 Oct 2018 20:47:35: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 07 Oct 2018 20:47:35: #2.2 Generate R script for model : SRX4798848.10_model.r INFO @ Sun, 07 Oct 2018 20:47:35: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:35: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:47:47: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:52: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:52: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:47:55: #4 Write output xls file... SRX4798848.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:47:55: #4 Write peak in narrowPeak format file... SRX4798848.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:47:55: #4 Write summits bed file... SRX4798848.05_summits.bed INFO @ Sun, 07 Oct 2018 20:47:55: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9723 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write output xls file... SRX4798848.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write peak in narrowPeak format file... SRX4798848.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write summits bed file... SRX4798848.20_summits.bed INFO @ Sun, 07 Oct 2018 20:48:00: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (4375 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write output xls file... SRX4798848.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write peak in narrowPeak format file... SRX4798848.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:48:00: #4 Write summits bed file... SRX4798848.10_summits.bed INFO @ Sun, 07 Oct 2018 20:48:00: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6826 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。