Job ID = 9029294 sra ファイルのダウンロード中... Completed: 416296K bytes transferred in 6 seconds (513213K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1862 0 --:--:-- 0:00:07 --:--:-- 12974 100 38317 0 38317 0 0 4411 0 --:--:-- 0:00:08 --:--:-- 18246 100 78317 0 78317 0 0 8229 0 --:--:-- 0:00:09 --:--:-- 26720 100 109k 0 109k 0 0 11159 0 --:--:-- 0:00:10 --:--:-- 32600 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 12604030 spots for /home/okishinya/chipatlas/results/dm3/SRX1537615/SRR3109310.sra Written 12604030 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: 00:05:39 12604030 reads; of these: 12604030 (100.00%) were unpaired; of these: 2060713 (16.35%) aligned 0 times 7254037 (57.55%) aligned exactly 1 time 3289280 (26.10%) aligned >1 times 83.65% overall alignment rate Time searching: 00:05:39 Overall time: 00:05:39 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] 2969422 / 10543317 = 0.2816 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 @ Sat, 03 Jun 2017 13:12:23: # Command line: callpeak -t SRX1537615.bam -f BAM -g dm -n SRX1537615.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1537615.10 # format = BAM # ChIP-seq file = ['SRX1537615.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 INFO @ Sat, 03 Jun 2017 13:12:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:23: # Command line: callpeak -t SRX1537615.bam -f BAM -g dm -n SRX1537615.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1537615.05 # format = BAM # ChIP-seq file = ['SRX1537615.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 INFO @ Sat, 03 Jun 2017 13:12:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:23: # Command line: callpeak -t SRX1537615.bam -f BAM -g dm -n SRX1537615.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1537615.20 # format = BAM # ChIP-seq file = ['SRX1537615.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 INFO @ Sat, 03 Jun 2017 13:12:23: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:12:23: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:12:30: 1000000 INFO @ Sat, 03 Jun 2017 13:12:30: 1000000 INFO @ Sat, 03 Jun 2017 13:12:30: 1000000 INFO @ Sat, 03 Jun 2017 13:12:37: 2000000 INFO @ Sat, 03 Jun 2017 13:12:37: 2000000 INFO @ Sat, 03 Jun 2017 13:12:38: 2000000 INFO @ Sat, 03 Jun 2017 13:12:44: 3000000 INFO @ Sat, 03 Jun 2017 13:12:45: 3000000 INFO @ Sat, 03 Jun 2017 13:12:45: 3000000 INFO @ Sat, 03 Jun 2017 13:12:51: 4000000 INFO @ Sat, 03 Jun 2017 13:12:52: 4000000 INFO @ Sat, 03 Jun 2017 13:12:53: 4000000 INFO @ Sat, 03 Jun 2017 13:12:58: 5000000 INFO @ Sat, 03 Jun 2017 13:12:59: 5000000 INFO @ Sat, 03 Jun 2017 13:13:00: 5000000 INFO @ Sat, 03 Jun 2017 13:13:05: 6000000 INFO @ Sat, 03 Jun 2017 13:13:07: 6000000 INFO @ Sat, 03 Jun 2017 13:13:07: 6000000 INFO @ Sat, 03 Jun 2017 13:13:12: 7000000 INFO @ Sat, 03 Jun 2017 13:13:14: 7000000 INFO @ Sat, 03 Jun 2017 13:13:15: 7000000 INFO @ Sat, 03 Jun 2017 13:13:16: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:13:16: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:13:16: #1 total tags in treatment: 7573895 INFO @ Sat, 03 Jun 2017 13:13:16: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:13:18: #1 tags after filtering in treatment: 7570580 INFO @ Sat, 03 Jun 2017 13:13:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:18: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:18: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:18: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:13:18: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:13:18: #1 total tags in treatment: 7573895 INFO @ Sat, 03 Jun 2017 13:13:18: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:13:19: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:13:19: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:13:19: #1 total tags in treatment: 7573895 INFO @ Sat, 03 Jun 2017 13:13:19: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:13:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 13:13:19: #2 number of paired peaks: 1697 INFO @ Sat, 03 Jun 2017 13:13:19: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:20: #1 tags after filtering in treatment: 7570580 INFO @ Sat, 03 Jun 2017 13:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:20: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:20: #1 tags after filtering in treatment: 7570580 INFO @ Sat, 03 Jun 2017 13:13:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:13:20: #1 finished! INFO @ Sat, 03 Jun 2017 13:13:20: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:13:21: #2 number of paired peaks: 1697 INFO @ Sat, 03 Jun 2017 13:13:21: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:22: #2 number of paired peaks: 1697 INFO @ Sat, 03 Jun 2017 13:13:22: start model_add_line... INFO @ Sat, 03 Jun 2017 13:13:29: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:29: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:29: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:29: #2 predicted fragment length is 191 bps INFO @ Sat, 03 Jun 2017 13:13:29: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 03 Jun 2017 13:13:29: #2.2 Generate R script for model : SRX1537615.10_model.r INFO @ Sat, 03 Jun 2017 13:13:29: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:31: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:31: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:31: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:31: #2 predicted fragment length is 191 bps INFO @ Sat, 03 Jun 2017 13:13:31: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 03 Jun 2017 13:13:31: #2.2 Generate R script for model : SRX1537615.05_model.r INFO @ Sat, 03 Jun 2017 13:13:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:13:31: start X-correlation... INFO @ Sat, 03 Jun 2017 13:13:31: end of X-cor INFO @ Sat, 03 Jun 2017 13:13:31: #2 finished! INFO @ Sat, 03 Jun 2017 13:13:31: #2 predicted fragment length is 191 bps INFO @ Sat, 03 Jun 2017 13:13:31: #2 alternative fragment length(s) may be 191 bps INFO @ Sat, 03 Jun 2017 13:13:31: #2.2 Generate R script for model : SRX1537615.20_model.r INFO @ Sat, 03 Jun 2017 13:13:31: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:13:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:14:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:19: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:14:49: #4 Write output xls file... SRX1537615.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:49: #4 Write peak in narrowPeak format file... SRX1537615.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:49: #4 Write summits bed file... SRX1537615.20_summits.bed INFO @ Sat, 03 Jun 2017 13:14:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2152 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:14:53: #4 Write output xls file... SRX1537615.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:53: #4 Write peak in narrowPeak format file... SRX1537615.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:53: #4 Write summits bed file... SRX1537615.10_summits.bed INFO @ Sat, 03 Jun 2017 13:14:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2680 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:14:55: #4 Write output xls file... SRX1537615.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:14:55: #4 Write peak in narrowPeak format file... SRX1537615.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:14:56: #4 Write summits bed file... SRX1537615.05_summits.bed INFO @ Sat, 03 Jun 2017 13:14:56: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3173 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。