Job ID = 9029858 sra ファイルのダウンロード中... Completed: 328773K bytes transferred in 5 seconds (453451K 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 7663 0 7663 0 0 1041 0 --:--:-- 0:00:07 --:--:-- 8169 100 30318 0 30318 0 0 3703 0 --:--:-- 0:00:08 --:--:-- 17148 100 73256 0 73256 0 0 8278 0 --:--:-- 0:00:08 --:--:-- 30134 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 18083039 spots for /home/okishinya/chipatlas/results/dm3/SRX2385058/SRR5064689.sra Written 18083039 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:34 18083039 reads; of these: 18083039 (100.00%) were unpaired; of these: 1883438 (10.42%) aligned 0 times 13842436 (76.55%) aligned exactly 1 time 2357165 (13.04%) aligned >1 times 89.58% overall alignment rate Time searching: 00:05:35 Overall time: 00:05:35 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] 1936695 / 16199601 = 0.1196 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 15:41:45: # Command line: callpeak -t SRX2385058.bam -f BAM -g dm -n SRX2385058.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2385058.10 # format = BAM # ChIP-seq file = ['SRX2385058.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 15:41:45: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:41:45: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:41:45: # Command line: callpeak -t SRX2385058.bam -f BAM -g dm -n SRX2385058.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2385058.05 # format = BAM # ChIP-seq file = ['SRX2385058.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 15:41:45: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:41:45: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:41:45: # Command line: callpeak -t SRX2385058.bam -f BAM -g dm -n SRX2385058.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2385058.20 # format = BAM # ChIP-seq file = ['SRX2385058.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 15:41:45: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:41:45: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:41:50: 1000000 INFO @ Sat, 03 Jun 2017 15:41:50: 1000000 INFO @ Sat, 03 Jun 2017 15:41:50: 1000000 INFO @ Sat, 03 Jun 2017 15:41:55: 2000000 INFO @ Sat, 03 Jun 2017 15:41:56: 2000000 INFO @ Sat, 03 Jun 2017 15:41:56: 2000000 INFO @ Sat, 03 Jun 2017 15:42:00: 3000000 INFO @ Sat, 03 Jun 2017 15:42:01: 3000000 INFO @ Sat, 03 Jun 2017 15:42:02: 3000000 INFO @ Sat, 03 Jun 2017 15:42:05: 4000000 INFO @ Sat, 03 Jun 2017 15:42:07: 4000000 INFO @ Sat, 03 Jun 2017 15:42:08: 4000000 INFO @ Sat, 03 Jun 2017 15:42:10: 5000000 INFO @ Sat, 03 Jun 2017 15:42:13: 5000000 INFO @ Sat, 03 Jun 2017 15:42:14: 6000000 INFO @ Sat, 03 Jun 2017 15:42:15: 5000000 INFO @ Sat, 03 Jun 2017 15:42:19: 6000000 INFO @ Sat, 03 Jun 2017 15:42:19: 7000000 INFO @ Sat, 03 Jun 2017 15:42:21: 6000000 INFO @ Sat, 03 Jun 2017 15:42:24: 8000000 INFO @ Sat, 03 Jun 2017 15:42:25: 7000000 INFO @ Sat, 03 Jun 2017 15:42:27: 7000000 INFO @ Sat, 03 Jun 2017 15:42:29: 9000000 INFO @ Sat, 03 Jun 2017 15:42:31: 8000000 INFO @ Sat, 03 Jun 2017 15:42:34: 8000000 INFO @ Sat, 03 Jun 2017 15:42:34: 10000000 INFO @ Sat, 03 Jun 2017 15:42:37: 9000000 INFO @ Sat, 03 Jun 2017 15:42:39: 11000000 INFO @ Sat, 03 Jun 2017 15:42:40: 9000000 INFO @ Sat, 03 Jun 2017 15:42:42: 10000000 INFO @ Sat, 03 Jun 2017 15:42:45: 12000000 INFO @ Sat, 03 Jun 2017 15:42:46: 10000000 INFO @ Sat, 03 Jun 2017 15:42:48: 11000000 INFO @ Sat, 03 Jun 2017 15:42:50: 13000000 INFO @ Sat, 03 Jun 2017 15:42:53: 11000000 INFO @ Sat, 03 Jun 2017 15:42:54: 12000000 INFO @ Sat, 03 Jun 2017 15:42:55: 14000000 INFO @ Sat, 03 Jun 2017 15:42:56: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:42:56: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:42:56: #1 total tags in treatment: 14262906 INFO @ Sat, 03 Jun 2017 15:42:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:42:56: #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 15:42:59: #1 tags after filtering in treatment: 14258755 INFO @ Sat, 03 Jun 2017 15:42:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:42:59: #1 finished! INFO @ Sat, 03 Jun 2017 15:42:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:42:59: 12000000 INFO @ Sat, 03 Jun 2017 15:43:00: 13000000 INFO @ Sat, 03 Jun 2017 15:43:01: #2 number of paired peaks: 1054 INFO @ Sat, 03 Jun 2017 15:43:01: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:05: 13000000 INFO @ Sat, 03 Jun 2017 15:43:06: 14000000 INFO @ Sat, 03 Jun 2017 15:43:08: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:43:08: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:43:08: #1 total tags in treatment: 14262906 INFO @ Sat, 03 Jun 2017 15:43:08: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:08: #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 15:43:11: 14000000 INFO @ Sat, 03 Jun 2017 15:43:11: #1 tags after filtering in treatment: 14258755 INFO @ Sat, 03 Jun 2017 15:43:11: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:11: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:11: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:11: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:11: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:11: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:11: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Jun 2017 15:43:11: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Jun 2017 15:43:11: #2.2 Generate R script for model : SRX2385058.05_model.r INFO @ Sat, 03 Jun 2017 15:43:11: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:43:12: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:43:12: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:43:12: #1 total tags in treatment: 14262906 INFO @ Sat, 03 Jun 2017 15:43:12: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:43:12: #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 15:43:14: #2 number of paired peaks: 1054 INFO @ Sat, 03 Jun 2017 15:43:14: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:15: #1 tags after filtering in treatment: 14258755 INFO @ Sat, 03 Jun 2017 15:43:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:43:15: #1 finished! INFO @ Sat, 03 Jun 2017 15:43:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:43:17: #2 number of paired peaks: 1054 INFO @ Sat, 03 Jun 2017 15:43:17: start model_add_line... INFO @ Sat, 03 Jun 2017 15:43:23: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:23: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:23: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:23: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Jun 2017 15:43:23: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Jun 2017 15:43:23: #2.2 Generate R script for model : SRX2385058.20_model.r INFO @ Sat, 03 Jun 2017 15:43:23: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:43:27: start X-correlation... INFO @ Sat, 03 Jun 2017 15:43:27: end of X-cor INFO @ Sat, 03 Jun 2017 15:43:27: #2 finished! INFO @ Sat, 03 Jun 2017 15:43:27: #2 predicted fragment length is 123 bps INFO @ Sat, 03 Jun 2017 15:43:27: #2 alternative fragment length(s) may be 123 bps INFO @ Sat, 03 Jun 2017 15:43:27: #2.2 Generate R script for model : SRX2385058.10_model.r INFO @ Sat, 03 Jun 2017 15:43:27: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:43:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:44:32: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:44:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:44:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:45:32: #4 Write output xls file... SRX2385058.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:45:32: #4 Write peak in narrowPeak format file... SRX2385058.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:45:32: #4 Write summits bed file... SRX2385058.20_summits.bed INFO @ Sat, 03 Jun 2017 15:45:32: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2467 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:45:37: #4 Write output xls file... SRX2385058.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:45:37: #4 Write peak in narrowPeak format file... SRX2385058.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:45:37: #4 Write summits bed file... SRX2385058.05_summits.bed INFO @ Sat, 03 Jun 2017 15:45:37: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9027 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:45:47: #4 Write output xls file... SRX2385058.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:45:47: #4 Write peak in narrowPeak format file... SRX2385058.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:45:47: #4 Write summits bed file... SRX2385058.10_summits.bed INFO @ Sat, 03 Jun 2017 15:45:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5577 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。