Job ID = 9033333 sra ファイルのダウンロード中... Completed: 336245K bytes transferred in 6 seconds (420582K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 20110 0 20110 0 0 2529 0 --:--:-- 0:00:07 --:--:-- 14082 100 44726 0 44726 0 0 4999 0 --:--:-- 0:00:08 --:--:-- 18458 100 73406 0 73406 0 0 7911 0 --:--:-- 0:00:09 --:--:-- 26634 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 15324494 spots for /home/okishinya/chipatlas/results/dm3/SRX969922/SRR1931638.sra Written 15324494 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: 00:06:48 15324494 reads; of these: 15324494 (100.00%) were unpaired; of these: 784937 (5.12%) aligned 0 times 10732617 (70.04%) aligned exactly 1 time 3806940 (24.84%) aligned >1 times 94.88% overall alignment rate Time searching: 00:06:48 Overall time: 00:06:48 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] 2676455 / 14539557 = 0.1841 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, 04 Jun 2017 00:22:53: # Command line: callpeak -t SRX969922.bam -f BAM -g dm -n SRX969922.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX969922.20 # format = BAM # ChIP-seq file = ['SRX969922.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 @ Sun, 04 Jun 2017 00:22:53: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:22:53: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:22:53: # Command line: callpeak -t SRX969922.bam -f BAM -g dm -n SRX969922.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX969922.10 # format = BAM # ChIP-seq file = ['SRX969922.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 @ Sun, 04 Jun 2017 00:22:53: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:22:53: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:22:53: # Command line: callpeak -t SRX969922.bam -f BAM -g dm -n SRX969922.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX969922.05 # format = BAM # ChIP-seq file = ['SRX969922.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 @ Sun, 04 Jun 2017 00:22:53: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:22:53: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:22:58: 1000000 INFO @ Sun, 04 Jun 2017 00:22:59: 1000000 INFO @ Sun, 04 Jun 2017 00:22:59: 1000000 INFO @ Sun, 04 Jun 2017 00:23:05: 2000000 INFO @ Sun, 04 Jun 2017 00:23:05: 2000000 INFO @ Sun, 04 Jun 2017 00:23:05: 2000000 INFO @ Sun, 04 Jun 2017 00:23:11: 3000000 INFO @ Sun, 04 Jun 2017 00:23:11: 3000000 INFO @ Sun, 04 Jun 2017 00:23:11: 3000000 INFO @ Sun, 04 Jun 2017 00:23:17: 4000000 INFO @ Sun, 04 Jun 2017 00:23:17: 4000000 INFO @ Sun, 04 Jun 2017 00:23:17: 4000000 INFO @ Sun, 04 Jun 2017 00:23:23: 5000000 INFO @ Sun, 04 Jun 2017 00:23:24: 5000000 INFO @ Sun, 04 Jun 2017 00:23:24: 5000000 INFO @ Sun, 04 Jun 2017 00:23:30: 6000000 INFO @ Sun, 04 Jun 2017 00:23:30: 6000000 INFO @ Sun, 04 Jun 2017 00:23:30: 6000000 INFO @ Sun, 04 Jun 2017 00:23:36: 7000000 INFO @ Sun, 04 Jun 2017 00:23:36: 7000000 INFO @ Sun, 04 Jun 2017 00:23:36: 7000000 INFO @ Sun, 04 Jun 2017 00:23:42: 8000000 INFO @ Sun, 04 Jun 2017 00:23:43: 8000000 INFO @ Sun, 04 Jun 2017 00:23:43: 8000000 INFO @ Sun, 04 Jun 2017 00:23:49: 9000000 INFO @ Sun, 04 Jun 2017 00:23:49: 9000000 INFO @ Sun, 04 Jun 2017 00:23:49: 9000000 INFO @ Sun, 04 Jun 2017 00:23:55: 10000000 INFO @ Sun, 04 Jun 2017 00:23:55: 10000000 INFO @ Sun, 04 Jun 2017 00:23:55: 10000000 INFO @ Sun, 04 Jun 2017 00:24:01: 11000000 INFO @ Sun, 04 Jun 2017 00:24:02: 11000000 INFO @ Sun, 04 Jun 2017 00:24:02: 11000000 INFO @ Sun, 04 Jun 2017 00:24:07: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:24:07: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:24:07: #1 total tags in treatment: 11863102 INFO @ Sun, 04 Jun 2017 00:24:07: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:24:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:24:07: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:24:07: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:24:07: #1 total tags in treatment: 11863102 INFO @ Sun, 04 Jun 2017 00:24:07: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:24:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:24:07: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 00:24:07: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 00:24:07: #1 total tags in treatment: 11863102 INFO @ Sun, 04 Jun 2017 00:24:07: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:24:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 00:24:09: #1 tags after filtering in treatment: 11859523 INFO @ Sun, 04 Jun 2017 00:24:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:24:09: #1 finished! INFO @ Sun, 04 Jun 2017 00:24:09: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:24:10: #1 tags after filtering in treatment: 11859523 INFO @ Sun, 04 Jun 2017 00:24:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:24:10: #1 finished! INFO @ Sun, 04 Jun 2017 00:24:10: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:24:10: #1 tags after filtering in treatment: 11859523 INFO @ Sun, 04 Jun 2017 00:24:10: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:24:10: #1 finished! INFO @ Sun, 04 Jun 2017 00:24:10: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:24:11: #2 number of paired peaks: 2509 INFO @ Sun, 04 Jun 2017 00:24:11: start model_add_line... INFO @ Sun, 04 Jun 2017 00:24:12: #2 number of paired peaks: 2509 INFO @ Sun, 04 Jun 2017 00:24:12: start model_add_line... INFO @ Sun, 04 Jun 2017 00:24:13: #2 number of paired peaks: 2509 INFO @ Sun, 04 Jun 2017 00:24:13: start model_add_line... INFO @ Sun, 04 Jun 2017 00:24:27: start X-correlation... INFO @ Sun, 04 Jun 2017 00:24:27: end of X-cor INFO @ Sun, 04 Jun 2017 00:24:27: #2 finished! INFO @ Sun, 04 Jun 2017 00:24:27: #2 predicted fragment length is 203 bps INFO @ Sun, 04 Jun 2017 00:24:27: #2 alternative fragment length(s) may be 203 bps INFO @ Sun, 04 Jun 2017 00:24:27: #2.2 Generate R script for model : SRX969922.05_model.r INFO @ Sun, 04 Jun 2017 00:24:27: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:24:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:24:28: start X-correlation... INFO @ Sun, 04 Jun 2017 00:24:28: end of X-cor INFO @ Sun, 04 Jun 2017 00:24:28: #2 finished! INFO @ Sun, 04 Jun 2017 00:24:28: #2 predicted fragment length is 203 bps INFO @ Sun, 04 Jun 2017 00:24:28: #2 alternative fragment length(s) may be 203 bps INFO @ Sun, 04 Jun 2017 00:24:28: #2.2 Generate R script for model : SRX969922.20_model.r INFO @ Sun, 04 Jun 2017 00:24:28: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:24:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:24:29: start X-correlation... INFO @ Sun, 04 Jun 2017 00:24:29: end of X-cor INFO @ Sun, 04 Jun 2017 00:24:29: #2 finished! INFO @ Sun, 04 Jun 2017 00:24:29: #2 predicted fragment length is 203 bps INFO @ Sun, 04 Jun 2017 00:24:29: #2 alternative fragment length(s) may be 203 bps INFO @ Sun, 04 Jun 2017 00:24:29: #2.2 Generate R script for model : SRX969922.10_model.r INFO @ Sun, 04 Jun 2017 00:24:29: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:24:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:25:38: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:25:39: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:25:41: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:26:34: #4 Write output xls file... SRX969922.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:26:35: #4 Write peak in narrowPeak format file... SRX969922.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:26:35: #4 Write summits bed file... SRX969922.10_summits.bed INFO @ Sun, 04 Jun 2017 00:26:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6638 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:26:38: #4 Write output xls file... SRX969922.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:26:38: #4 Write peak in narrowPeak format file... SRX969922.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:26:38: #4 Write summits bed file... SRX969922.20_summits.bed INFO @ Sun, 04 Jun 2017 00:26:38: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4993 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:26:44: #4 Write output xls file... SRX969922.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:26:44: #4 Write peak in narrowPeak format file... SRX969922.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:26:44: #4 Write summits bed file... SRX969922.05_summits.bed INFO @ Sun, 04 Jun 2017 00:26:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8020 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。