Job ID = 9029816 sra ファイルのダウンロード中... Completed: 919175K bytes transferred in 10 seconds (700506K 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 28061 0 28061 0 0 3540 0 --:--:-- 0:00:07 --:--:-- 20724 100 29932 0 29932 0 0 3699 0 --:--:-- 0:00:08 --:--:-- 19705 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 40748256 spots for /home/okishinya/chipatlas/results/dm3/SRX2172428/SRR4252439.sra Written 40748256 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: 00:13:12 40748256 reads; of these: 40748256 (100.00%) were unpaired; of these: 2776387 (6.81%) aligned 0 times 31359828 (76.96%) aligned exactly 1 time 6612041 (16.23%) aligned >1 times 93.19% overall alignment rate Time searching: 00:13:12 Overall time: 00:13:12 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 16 files... [bam_rmdupse_core] 14195444 / 37971869 = 0.3738 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 15:47:12: # Command line: callpeak -t SRX2172428.bam -f BAM -g dm -n SRX2172428.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2172428.05 # format = BAM # ChIP-seq file = ['SRX2172428.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 15:47:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:47:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:47:12: # Command line: callpeak -t SRX2172428.bam -f BAM -g dm -n SRX2172428.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2172428.10 # format = BAM # ChIP-seq file = ['SRX2172428.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 15:47:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:47:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:47:12: # Command line: callpeak -t SRX2172428.bam -f BAM -g dm -n SRX2172428.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2172428.20 # format = BAM # ChIP-seq file = ['SRX2172428.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 15:47:12: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:47:12: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:47:18: 1000000 INFO @ Sat, 03 Jun 2017 15:47:18: 1000000 INFO @ Sat, 03 Jun 2017 15:47:19: 1000000 INFO @ Sat, 03 Jun 2017 15:47:24: 2000000 INFO @ Sat, 03 Jun 2017 15:47:24: 2000000 INFO @ Sat, 03 Jun 2017 15:47:25: 2000000 INFO @ Sat, 03 Jun 2017 15:47:30: 3000000 INFO @ Sat, 03 Jun 2017 15:47:30: 3000000 INFO @ Sat, 03 Jun 2017 15:47:32: 3000000 INFO @ Sat, 03 Jun 2017 15:47:36: 4000000 INFO @ Sat, 03 Jun 2017 15:47:38: 4000000 INFO @ Sat, 03 Jun 2017 15:47:39: 4000000 INFO @ Sat, 03 Jun 2017 15:47:43: 5000000 INFO @ Sat, 03 Jun 2017 15:47:46: 5000000 INFO @ Sat, 03 Jun 2017 15:47:46: 5000000 INFO @ Sat, 03 Jun 2017 15:47:49: 6000000 INFO @ Sat, 03 Jun 2017 15:47:53: 6000000 INFO @ Sat, 03 Jun 2017 15:47:54: 6000000 INFO @ Sat, 03 Jun 2017 15:47:56: 7000000 INFO @ Sat, 03 Jun 2017 15:48:00: 7000000 INFO @ Sat, 03 Jun 2017 15:48:02: 7000000 INFO @ Sat, 03 Jun 2017 15:48:03: 8000000 INFO @ Sat, 03 Jun 2017 15:48:08: 8000000 INFO @ Sat, 03 Jun 2017 15:48:11: 9000000 INFO @ Sat, 03 Jun 2017 15:48:11: 8000000 INFO @ Sat, 03 Jun 2017 15:48:16: 9000000 INFO @ Sat, 03 Jun 2017 15:48:18: 10000000 INFO @ Sat, 03 Jun 2017 15:48:20: 9000000 INFO @ Sat, 03 Jun 2017 15:48:24: 10000000 INFO @ Sat, 03 Jun 2017 15:48:25: 11000000 INFO @ Sat, 03 Jun 2017 15:48:27: 10000000 INFO @ Sat, 03 Jun 2017 15:48:32: 12000000 INFO @ Sat, 03 Jun 2017 15:48:32: 11000000 INFO @ Sat, 03 Jun 2017 15:48:34: 11000000 INFO @ Sat, 03 Jun 2017 15:48:39: 13000000 INFO @ Sat, 03 Jun 2017 15:48:40: 12000000 INFO @ Sat, 03 Jun 2017 15:48:41: 12000000 INFO @ Sat, 03 Jun 2017 15:48:46: 14000000 INFO @ Sat, 03 Jun 2017 15:48:48: 13000000 INFO @ Sat, 03 Jun 2017 15:48:48: 13000000 INFO @ Sat, 03 Jun 2017 15:48:53: 15000000 INFO @ Sat, 03 Jun 2017 15:48:55: 14000000 INFO @ Sat, 03 Jun 2017 15:48:56: 14000000 INFO @ Sat, 03 Jun 2017 15:49:00: 16000000 INFO @ Sat, 03 Jun 2017 15:49:02: 15000000 INFO @ Sat, 03 Jun 2017 15:49:04: 15000000 INFO @ Sat, 03 Jun 2017 15:49:07: 17000000 INFO @ Sat, 03 Jun 2017 15:49:09: 16000000 INFO @ Sat, 03 Jun 2017 15:49:11: 16000000 INFO @ Sat, 03 Jun 2017 15:49:14: 18000000 INFO @ Sat, 03 Jun 2017 15:49:16: 17000000 INFO @ Sat, 03 Jun 2017 15:49:19: 17000000 INFO @ Sat, 03 Jun 2017 15:49:21: 19000000 INFO @ Sat, 03 Jun 2017 15:49:22: 18000000 INFO @ Sat, 03 Jun 2017 15:49:26: 18000000 INFO @ Sat, 03 Jun 2017 15:49:28: 20000000 INFO @ Sat, 03 Jun 2017 15:49:29: 19000000 INFO @ Sat, 03 Jun 2017 15:49:34: 19000000 INFO @ Sat, 03 Jun 2017 15:49:35: 21000000 INFO @ Sat, 03 Jun 2017 15:49:36: 20000000 INFO @ Sat, 03 Jun 2017 15:49:42: 20000000 INFO @ Sat, 03 Jun 2017 15:49:42: 22000000 INFO @ Sat, 03 Jun 2017 15:49:43: 21000000 INFO @ Sat, 03 Jun 2017 15:49:49: 23000000 INFO @ Sat, 03 Jun 2017 15:49:49: 21000000 INFO @ Sat, 03 Jun 2017 15:49:50: 22000000 INFO @ Sat, 03 Jun 2017 15:49:54: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:49:54: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:49:54: #1 total tags in treatment: 23776425 INFO @ Sat, 03 Jun 2017 15:49:54: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:49:54: #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 15:49:57: 22000000 INFO @ Sat, 03 Jun 2017 15:49:57: 23000000 INFO @ Sat, 03 Jun 2017 15:49:59: #1 tags after filtering in treatment: 23761316 INFO @ Sat, 03 Jun 2017 15:49:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:49:59: #1 finished! INFO @ Sat, 03 Jun 2017 15:49:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:50:02: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:50:02: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:50:02: #1 total tags in treatment: 23776425 INFO @ Sat, 03 Jun 2017 15:50:02: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:50:02: #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 15:50:03: #2 number of paired peaks: 4545 INFO @ Sat, 03 Jun 2017 15:50:03: start model_add_line... INFO @ Sat, 03 Jun 2017 15:50:04: 23000000 INFO @ Sat, 03 Jun 2017 15:50:07: #1 tags after filtering in treatment: 23761316 INFO @ Sat, 03 Jun 2017 15:50:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:50:07: #1 finished! INFO @ Sat, 03 Jun 2017 15:50:07: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:50:10: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 15:50:10: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 15:50:10: #1 total tags in treatment: 23776425 INFO @ Sat, 03 Jun 2017 15:50:10: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:50:10: #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 15:50:13: #2 number of paired peaks: 4545 INFO @ Sat, 03 Jun 2017 15:50:13: start model_add_line... INFO @ Sat, 03 Jun 2017 15:50:15: #1 tags after filtering in treatment: 23761316 INFO @ Sat, 03 Jun 2017 15:50:15: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:50:15: #1 finished! INFO @ Sat, 03 Jun 2017 15:50:15: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:50:20: #2 number of paired peaks: 4545 INFO @ Sat, 03 Jun 2017 15:50:21: start model_add_line... INFO @ Sat, 03 Jun 2017 15:51:02: start X-correlation... INFO @ Sat, 03 Jun 2017 15:51:02: end of X-cor INFO @ Sat, 03 Jun 2017 15:51:02: #2 finished! INFO @ Sat, 03 Jun 2017 15:51:02: #2 predicted fragment length is 162 bps INFO @ Sat, 03 Jun 2017 15:51:02: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 03 Jun 2017 15:51:02: #2.2 Generate R script for model : SRX2172428.10_model.r INFO @ Sat, 03 Jun 2017 15:51:02: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:51:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:51:10: start X-correlation... INFO @ Sat, 03 Jun 2017 15:51:10: end of X-cor INFO @ Sat, 03 Jun 2017 15:51:10: #2 finished! INFO @ Sat, 03 Jun 2017 15:51:10: #2 predicted fragment length is 162 bps INFO @ Sat, 03 Jun 2017 15:51:10: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 03 Jun 2017 15:51:10: #2.2 Generate R script for model : SRX2172428.05_model.r INFO @ Sat, 03 Jun 2017 15:51:10: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:51:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:51:20: start X-correlation... INFO @ Sat, 03 Jun 2017 15:51:20: end of X-cor INFO @ Sat, 03 Jun 2017 15:51:20: #2 finished! INFO @ Sat, 03 Jun 2017 15:51:20: #2 predicted fragment length is 162 bps INFO @ Sat, 03 Jun 2017 15:51:20: #2 alternative fragment length(s) may be 162 bps INFO @ Sat, 03 Jun 2017 15:51:20: #2.2 Generate R script for model : SRX2172428.20_model.r INFO @ Sat, 03 Jun 2017 15:51:20: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:51:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:53:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:53:20: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:53:28: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:54:55: #4 Write output xls file... SRX2172428.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:54:55: #4 Write peak in narrowPeak format file... SRX2172428.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:54:55: #4 Write summits bed file... SRX2172428.10_summits.bed INFO @ Sat, 03 Jun 2017 15:54:56: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (13766 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:55:11: #4 Write output xls file... SRX2172428.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:55:11: #4 Write peak in narrowPeak format file... SRX2172428.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:55:12: #4 Write summits bed file... SRX2172428.20_summits.bed INFO @ Sat, 03 Jun 2017 15:55:12: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11560 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:55:12: #4 Write output xls file... SRX2172428.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:55:13: #4 Write peak in narrowPeak format file... SRX2172428.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:55:13: #4 Write summits bed file... SRX2172428.05_summits.bed INFO @ Sat, 03 Jun 2017 15:55:13: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15689 records, 4 fields): 20 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。