Job ID = 11240822 sra ファイルのダウンロード中... Completed: 511807K bytes transferred in 8 seconds (511655K 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 13756405 spots for /home/okishinya/chipatlas/results/dm3/SRX4798869/SRR7965200.sra Written 13756405 spots for /home/okishinya/chipatlas/results/dm3/SRX4798869/SRR7965200.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: 00:02:43 13756405 reads; of these: 13756405 (100.00%) were unpaired; of these: 5259579 (38.23%) aligned 0 times 7819145 (56.84%) aligned exactly 1 time 677681 (4.93%) aligned >1 times 61.77% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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_rmdupse_core] 2124523 / 8496826 = 0.2500 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 20:52:38: # Command line: callpeak -t SRX4798869.bam -f BAM -g dm -n SRX4798869.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798869.05 # format = BAM # ChIP-seq file = ['SRX4798869.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 20:52:38: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:52:38: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:52:38: # Command line: callpeak -t SRX4798869.bam -f BAM -g dm -n SRX4798869.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798869.20 # format = BAM # ChIP-seq file = ['SRX4798869.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 20:52:38: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:52:38: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:52:38: # Command line: callpeak -t SRX4798869.bam -f BAM -g dm -n SRX4798869.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798869.10 # format = BAM # ChIP-seq file = ['SRX4798869.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 20:52:38: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:52:38: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:52:45: 1000000 INFO @ Sun, 07 Oct 2018 20:52:45: 1000000 INFO @ Sun, 07 Oct 2018 20:52:45: 1000000 INFO @ Sun, 07 Oct 2018 20:52:52: 2000000 INFO @ Sun, 07 Oct 2018 20:52:52: 2000000 INFO @ Sun, 07 Oct 2018 20:52:53: 2000000 INFO @ Sun, 07 Oct 2018 20:52:58: 3000000 INFO @ Sun, 07 Oct 2018 20:53:00: 3000000 INFO @ Sun, 07 Oct 2018 20:53:00: 3000000 INFO @ Sun, 07 Oct 2018 20:53:05: 4000000 INFO @ Sun, 07 Oct 2018 20:53:07: 4000000 INFO @ Sun, 07 Oct 2018 20:53:08: 4000000 INFO @ Sun, 07 Oct 2018 20:53:12: 5000000 INFO @ Sun, 07 Oct 2018 20:53:14: 5000000 INFO @ Sun, 07 Oct 2018 20:53:16: 5000000 INFO @ Sun, 07 Oct 2018 20:53:19: 6000000 INFO @ Sun, 07 Oct 2018 20:53:21: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:53:21: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:53:21: #1 total tags in treatment: 6372303 INFO @ Sun, 07 Oct 2018 20:53:21: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:53:21: #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 20:53:21: #1 tags after filtering in treatment: 6372303 INFO @ Sun, 07 Oct 2018 20:53:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:53:21: #1 finished! INFO @ Sun, 07 Oct 2018 20:53:21: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:53:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:53:21: 6000000 INFO @ Sun, 07 Oct 2018 20:53:22: #2 number of paired peaks: 1418 INFO @ Sun, 07 Oct 2018 20:53:22: start model_add_line... INFO @ Sun, 07 Oct 2018 20:53:22: start X-correlation... INFO @ Sun, 07 Oct 2018 20:53:22: end of X-cor INFO @ Sun, 07 Oct 2018 20:53:22: #2 finished! INFO @ Sun, 07 Oct 2018 20:53:22: #2 predicted fragment length is 198 bps INFO @ Sun, 07 Oct 2018 20:53:22: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 07 Oct 2018 20:53:22: #2.2 Generate R script for model : SRX4798869.20_model.r INFO @ Sun, 07 Oct 2018 20:53:22: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:53:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:53:24: 6000000 INFO @ Sun, 07 Oct 2018 20:53:24: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:53:24: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:53:24: #1 total tags in treatment: 6372303 INFO @ Sun, 07 Oct 2018 20:53:24: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:53:24: #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 20:53:24: #1 tags after filtering in treatment: 6372303 INFO @ Sun, 07 Oct 2018 20:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:53:24: #1 finished! INFO @ Sun, 07 Oct 2018 20:53:24: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:53:25: #2 number of paired peaks: 1418 INFO @ Sun, 07 Oct 2018 20:53:25: start model_add_line... INFO @ Sun, 07 Oct 2018 20:53:25: start X-correlation... INFO @ Sun, 07 Oct 2018 20:53:25: end of X-cor INFO @ Sun, 07 Oct 2018 20:53:25: #2 finished! INFO @ Sun, 07 Oct 2018 20:53:25: #2 predicted fragment length is 198 bps INFO @ Sun, 07 Oct 2018 20:53:25: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 07 Oct 2018 20:53:25: #2.2 Generate R script for model : SRX4798869.10_model.r INFO @ Sun, 07 Oct 2018 20:53:25: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:53:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:53:26: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:53:26: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:53:26: #1 total tags in treatment: 6372303 INFO @ Sun, 07 Oct 2018 20:53:26: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:53:26: #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 20:53:26: #1 tags after filtering in treatment: 6372303 INFO @ Sun, 07 Oct 2018 20:53:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:53:26: #1 finished! INFO @ Sun, 07 Oct 2018 20:53:26: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:53:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:53:27: #2 number of paired peaks: 1418 INFO @ Sun, 07 Oct 2018 20:53:27: start model_add_line... INFO @ Sun, 07 Oct 2018 20:53:27: start X-correlation... INFO @ Sun, 07 Oct 2018 20:53:27: end of X-cor INFO @ Sun, 07 Oct 2018 20:53:27: #2 finished! INFO @ Sun, 07 Oct 2018 20:53:27: #2 predicted fragment length is 198 bps INFO @ Sun, 07 Oct 2018 20:53:27: #2 alternative fragment length(s) may be 198 bps INFO @ Sun, 07 Oct 2018 20:53:27: #2.2 Generate R script for model : SRX4798869.05_model.r INFO @ Sun, 07 Oct 2018 20:53:27: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:53:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:53:40: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:53:42: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:53:44: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:53:49: #4 Write output xls file... SRX4798869.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:53:49: #4 Write peak in narrowPeak format file... SRX4798869.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:53:49: #4 Write summits bed file... SRX4798869.20_summits.bed INFO @ Sun, 07 Oct 2018 20:53:49: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1079 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:53:51: #4 Write output xls file... SRX4798869.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:53:51: #4 Write peak in narrowPeak format file... SRX4798869.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:53:51: #4 Write summits bed file... SRX4798869.10_summits.bed INFO @ Sun, 07 Oct 2018 20:53:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3467 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:53:54: #4 Write output xls file... SRX4798869.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:53:54: #4 Write peak in narrowPeak format file... SRX4798869.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:53:54: #4 Write summits bed file... SRX4798869.05_summits.bed INFO @ Sun, 07 Oct 2018 20:53:54: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (6997 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。