Job ID = 9730459 sra ファイルのダウンロード中... Completed: 770639K bytes transferred in 46 seconds (134694K bits/sec), in 1 file, 2 directories. 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... Written 22789041 spots for /home/okishinya/chipatlas/results/dm3/SRX2829099/SRR5569909.sra Written 22789041 spots total 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: 00:11:30 22789041 reads; of these: 22789041 (100.00%) were unpaired; of these: 1387261 (6.09%) aligned 0 times 12056476 (52.90%) aligned exactly 1 time 9345304 (41.01%) aligned >1 times 93.91% overall alignment rate Time searching: 00:11:30 Overall time: 00:11:30 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] 14384219 / 21401780 = 0.6721 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 Sep 2017 01:11:55: # Command line: callpeak -t SRX2829099.bam -f BAM -g dm -n SRX2829099.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2829099.05 # format = BAM # ChIP-seq file = ['SRX2829099.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 Sep 2017 01:11:55: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:11:55: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:11:55: # Command line: callpeak -t SRX2829099.bam -f BAM -g dm -n SRX2829099.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2829099.20 # format = BAM # ChIP-seq file = ['SRX2829099.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 Sep 2017 01:11:55: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:11:55: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:11:55: # Command line: callpeak -t SRX2829099.bam -f BAM -g dm -n SRX2829099.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2829099.10 # format = BAM # ChIP-seq file = ['SRX2829099.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 Sep 2017 01:11:55: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:11:55: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:12:01: 1000000 INFO @ Sun, 03 Sep 2017 01:12:01: 1000000 INFO @ Sun, 03 Sep 2017 01:12:01: 1000000 INFO @ Sun, 03 Sep 2017 01:12:07: 2000000 INFO @ Sun, 03 Sep 2017 01:12:08: 2000000 INFO @ Sun, 03 Sep 2017 01:12:08: 2000000 INFO @ Sun, 03 Sep 2017 01:12:14: 3000000 INFO @ Sun, 03 Sep 2017 01:12:14: 3000000 INFO @ Sun, 03 Sep 2017 01:12:15: 3000000 INFO @ Sun, 03 Sep 2017 01:12:21: 4000000 INFO @ Sun, 03 Sep 2017 01:12:21: 4000000 INFO @ Sun, 03 Sep 2017 01:12:22: 4000000 INFO @ Sun, 03 Sep 2017 01:12:28: 5000000 INFO @ Sun, 03 Sep 2017 01:12:29: 5000000 INFO @ Sun, 03 Sep 2017 01:12:30: 5000000 INFO @ Sun, 03 Sep 2017 01:12:36: 6000000 INFO @ Sun, 03 Sep 2017 01:12:36: 6000000 INFO @ Sun, 03 Sep 2017 01:12:37: 6000000 INFO @ Sun, 03 Sep 2017 01:12:43: 7000000 INFO @ Sun, 03 Sep 2017 01:12:44: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:12:44: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:12:44: #1 total tags in treatment: 7017561 INFO @ Sun, 03 Sep 2017 01:12:44: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:12:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:12:44: #1 tags after filtering in treatment: 7017561 INFO @ Sun, 03 Sep 2017 01:12:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:12:44: #1 finished! INFO @ Sun, 03 Sep 2017 01:12:44: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:12:44: 7000000 INFO @ Sun, 03 Sep 2017 01:12:44: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:12:44: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:12:44: #1 total tags in treatment: 7017561 INFO @ Sun, 03 Sep 2017 01:12:44: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:12:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:12:44: #1 tags after filtering in treatment: 7017561 INFO @ Sun, 03 Sep 2017 01:12:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:12:44: #1 finished! INFO @ Sun, 03 Sep 2017 01:12:44: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:12:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:12:45: #2 number of paired peaks: 5580 INFO @ Sun, 03 Sep 2017 01:12:45: start model_add_line... INFO @ Sun, 03 Sep 2017 01:12:45: start X-correlation... INFO @ Sun, 03 Sep 2017 01:12:45: end of X-cor INFO @ Sun, 03 Sep 2017 01:12:45: #2 finished! INFO @ Sun, 03 Sep 2017 01:12:45: #2 predicted fragment length is 150 bps INFO @ Sun, 03 Sep 2017 01:12:45: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 03 Sep 2017 01:12:45: #2.2 Generate R script for model : SRX2829099.20_model.r INFO @ Sun, 03 Sep 2017 01:12:45: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:12:45: 7000000 INFO @ Sun, 03 Sep 2017 01:12:45: #2 number of paired peaks: 5580 INFO @ Sun, 03 Sep 2017 01:12:45: start model_add_line... INFO @ Sun, 03 Sep 2017 01:12:45: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:12:45: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:12:45: #1 total tags in treatment: 7017561 INFO @ Sun, 03 Sep 2017 01:12:45: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:12:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:12:45: start X-correlation... INFO @ Sun, 03 Sep 2017 01:12:45: end of X-cor INFO @ Sun, 03 Sep 2017 01:12:45: #2 finished! INFO @ Sun, 03 Sep 2017 01:12:45: #2 predicted fragment length is 150 bps INFO @ Sun, 03 Sep 2017 01:12:45: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 03 Sep 2017 01:12:45: #2.2 Generate R script for model : SRX2829099.05_model.r INFO @ Sun, 03 Sep 2017 01:12:45: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:12:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:12:45: #1 tags after filtering in treatment: 7017561 INFO @ Sun, 03 Sep 2017 01:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:12:45: #1 finished! INFO @ Sun, 03 Sep 2017 01:12:45: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:12:46: #2 number of paired peaks: 5580 INFO @ Sun, 03 Sep 2017 01:12:46: start model_add_line... INFO @ Sun, 03 Sep 2017 01:12:47: start X-correlation... INFO @ Sun, 03 Sep 2017 01:12:47: end of X-cor INFO @ Sun, 03 Sep 2017 01:12:47: #2 finished! INFO @ Sun, 03 Sep 2017 01:12:47: #2 predicted fragment length is 150 bps INFO @ Sun, 03 Sep 2017 01:12:47: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 03 Sep 2017 01:12:47: #2.2 Generate R script for model : SRX2829099.10_model.r INFO @ Sun, 03 Sep 2017 01:12:47: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:12:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:13:06: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:13:06: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:13:07: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:13:17: #4 Write output xls file... SRX2829099.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:17: #4 Write peak in narrowPeak format file... SRX2829099.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:17: #4 Write summits bed file... SRX2829099.05_summits.bed INFO @ Sun, 03 Sep 2017 01:13:17: #4 Write output xls file... SRX2829099.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:17: Done! INFO @ Sun, 03 Sep 2017 01:13:17: #4 Write peak in narrowPeak format file... SRX2829099.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:17: #4 Write summits bed file... SRX2829099.20_summits.bed INFO @ Sun, 03 Sep 2017 01:13:17: Done! pass1 - making usageList (13 chroms): 1 millis pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5035 records, 4 fields): 8 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (11259 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:13:18: #4 Write output xls file... SRX2829099.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:18: #4 Write peak in narrowPeak format file... SRX2829099.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:18: #4 Write summits bed file... SRX2829099.10_summits.bed INFO @ Sun, 03 Sep 2017 01:13:18: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (8086 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。