Job ID = 8696836 sra ファイルのダウンロード中... Completed: 494221K bytes transferred in 9 seconds (432395K 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 12695 0 12695 0 0 1656 0 --:--:-- 0:00:07 --:--:-- 13223 100 31474 0 31474 0 0 3614 0 --:--:-- 0:00:08 --:--:-- 15697 100 31474 0 31474 0 0 3613 0 --:--:-- 0:00:08 --:--:-- 15689 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 40289302 spots for /home/okishinya/chipatlas/results/dm3/SRX110774/SRR388356.sra Written 40289302 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: 00:33:15 40289302 reads; of these: 40289302 (100.00%) were unpaired; of these: 1775290 (4.41%) aligned 0 times 17289830 (42.91%) aligned exactly 1 time 21224182 (52.68%) aligned >1 times 95.59% overall alignment rate Time searching: 00:33:15 Overall time: 00:33:15 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] 15468973 / 38514012 = 0.4016 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 @ Fri, 10 Mar 2017 12:46:58: # Command line: callpeak -t SRX110774.bam -f BAM -g dm -n SRX110774.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110774.05 # format = BAM # ChIP-seq file = ['SRX110774.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 @ Fri, 10 Mar 2017 12:46:58: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:46:58: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:46:58: # Command line: callpeak -t SRX110774.bam -f BAM -g dm -n SRX110774.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110774.20 # format = BAM # ChIP-seq file = ['SRX110774.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 @ Fri, 10 Mar 2017 12:46:58: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:46:58: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:46:58: # Command line: callpeak -t SRX110774.bam -f BAM -g dm -n SRX110774.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110774.10 # format = BAM # ChIP-seq file = ['SRX110774.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 @ Fri, 10 Mar 2017 12:46:58: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:46:58: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:47:04: 1000000 INFO @ Fri, 10 Mar 2017 12:47:10: 1000000 INFO @ Fri, 10 Mar 2017 12:47:11: 1000000 INFO @ Fri, 10 Mar 2017 12:47:11: 2000000 INFO @ Fri, 10 Mar 2017 12:47:17: 3000000 INFO @ Fri, 10 Mar 2017 12:47:22: 2000000 INFO @ Fri, 10 Mar 2017 12:47:24: 2000000 INFO @ Fri, 10 Mar 2017 12:47:24: 4000000 INFO @ Fri, 10 Mar 2017 12:47:30: 5000000 INFO @ Fri, 10 Mar 2017 12:47:33: 3000000 INFO @ Fri, 10 Mar 2017 12:47:37: 6000000 INFO @ Fri, 10 Mar 2017 12:47:37: 3000000 INFO @ Fri, 10 Mar 2017 12:47:43: 7000000 INFO @ Fri, 10 Mar 2017 12:47:44: 4000000 INFO @ Fri, 10 Mar 2017 12:47:50: 8000000 INFO @ Fri, 10 Mar 2017 12:47:50: 4000000 INFO @ Fri, 10 Mar 2017 12:47:55: 5000000 INFO @ Fri, 10 Mar 2017 12:47:56: 9000000 INFO @ Fri, 10 Mar 2017 12:48:02: 10000000 INFO @ Fri, 10 Mar 2017 12:48:05: 5000000 INFO @ Fri, 10 Mar 2017 12:48:08: 6000000 INFO @ Fri, 10 Mar 2017 12:48:09: 11000000 INFO @ Fri, 10 Mar 2017 12:48:15: 12000000 INFO @ Fri, 10 Mar 2017 12:48:18: 6000000 INFO @ Fri, 10 Mar 2017 12:48:20: 7000000 INFO @ Fri, 10 Mar 2017 12:48:21: 13000000 INFO @ Fri, 10 Mar 2017 12:48:28: 8000000 INFO @ Fri, 10 Mar 2017 12:48:28: 14000000 INFO @ Fri, 10 Mar 2017 12:48:28: 7000000 INFO @ Fri, 10 Mar 2017 12:48:34: 15000000 INFO @ Fri, 10 Mar 2017 12:48:35: 9000000 INFO @ Fri, 10 Mar 2017 12:48:35: 8000000 INFO @ Fri, 10 Mar 2017 12:48:40: 16000000 INFO @ Fri, 10 Mar 2017 12:48:41: 10000000 INFO @ Fri, 10 Mar 2017 12:48:42: 9000000 INFO @ Fri, 10 Mar 2017 12:48:47: 17000000 INFO @ Fri, 10 Mar 2017 12:48:51: 11000000 INFO @ Fri, 10 Mar 2017 12:48:52: 10000000 INFO @ Fri, 10 Mar 2017 12:48:53: 18000000 INFO @ Fri, 10 Mar 2017 12:48:59: 19000000 INFO @ Fri, 10 Mar 2017 12:49:04: 12000000 INFO @ Fri, 10 Mar 2017 12:49:04: 11000000 INFO @ Fri, 10 Mar 2017 12:49:05: 20000000 INFO @ Fri, 10 Mar 2017 12:49:11: 21000000 INFO @ Fri, 10 Mar 2017 12:49:12: 12000000 INFO @ Fri, 10 Mar 2017 12:49:12: 13000000 INFO @ Fri, 10 Mar 2017 12:49:17: 22000000 INFO @ Fri, 10 Mar 2017 12:49:19: 13000000 INFO @ Fri, 10 Mar 2017 12:49:19: 14000000 INFO @ Fri, 10 Mar 2017 12:49:23: 23000000 INFO @ Fri, 10 Mar 2017 12:49:25: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:49:25: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:49:25: #1 total tags in treatment: 23045039 INFO @ Fri, 10 Mar 2017 12:49:25: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:49:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:49:25: 14000000 INFO @ Fri, 10 Mar 2017 12:49:25: 15000000 INFO @ Fri, 10 Mar 2017 12:49:29: #1 tags after filtering in treatment: 23045039 INFO @ Fri, 10 Mar 2017 12:49:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:49:29: #1 finished! INFO @ Fri, 10 Mar 2017 12:49:29: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:49:32: 16000000 INFO @ Fri, 10 Mar 2017 12:49:32: 15000000 INFO @ Fri, 10 Mar 2017 12:49:35: #2 number of paired peaks: 2596 INFO @ Fri, 10 Mar 2017 12:49:35: start model_add_line... INFO @ Fri, 10 Mar 2017 12:49:38: 17000000 INFO @ Fri, 10 Mar 2017 12:49:39: 16000000 INFO @ Fri, 10 Mar 2017 12:49:44: 18000000 INFO @ Fri, 10 Mar 2017 12:49:46: 17000000 INFO @ Fri, 10 Mar 2017 12:49:50: 19000000 INFO @ Fri, 10 Mar 2017 12:49:53: 18000000 INFO @ Fri, 10 Mar 2017 12:49:57: 20000000 INFO @ Fri, 10 Mar 2017 12:50:00: 19000000 INFO @ Fri, 10 Mar 2017 12:50:03: 21000000 INFO @ Fri, 10 Mar 2017 12:50:07: 20000000 INFO @ Fri, 10 Mar 2017 12:50:10: 22000000 INFO @ Fri, 10 Mar 2017 12:50:14: 21000000 INFO @ Fri, 10 Mar 2017 12:50:16: 23000000 INFO @ Fri, 10 Mar 2017 12:50:17: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:50:17: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:50:17: #1 total tags in treatment: 23045039 INFO @ Fri, 10 Mar 2017 12:50:17: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:50:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:50:18: start X-correlation... INFO @ Fri, 10 Mar 2017 12:50:18: end of X-cor INFO @ Fri, 10 Mar 2017 12:50:18: #2 finished! INFO @ Fri, 10 Mar 2017 12:50:18: #2 predicted fragment length is 325 bps INFO @ Fri, 10 Mar 2017 12:50:18: #2 alternative fragment length(s) may be 325 bps INFO @ Fri, 10 Mar 2017 12:50:18: #2.2 Generate R script for model : SRX110774.10_model.r INFO @ Fri, 10 Mar 2017 12:50:18: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:50:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:50:21: 22000000 INFO @ Fri, 10 Mar 2017 12:50:22: #1 tags after filtering in treatment: 23045039 INFO @ Fri, 10 Mar 2017 12:50:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:50:22: #1 finished! INFO @ Fri, 10 Mar 2017 12:50:22: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:50:27: 23000000 INFO @ Fri, 10 Mar 2017 12:50:27: #2 number of paired peaks: 2596 INFO @ Fri, 10 Mar 2017 12:50:27: start model_add_line... INFO @ Fri, 10 Mar 2017 12:50:28: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:50:28: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:50:28: #1 total tags in treatment: 23045039 INFO @ Fri, 10 Mar 2017 12:50:28: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:50:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:50:33: #1 tags after filtering in treatment: 23045039 INFO @ Fri, 10 Mar 2017 12:50:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:50:33: #1 finished! INFO @ Fri, 10 Mar 2017 12:50:33: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:50:39: #2 number of paired peaks: 2596 INFO @ Fri, 10 Mar 2017 12:50:39: start model_add_line... INFO @ Fri, 10 Mar 2017 12:51:13: start X-correlation... INFO @ Fri, 10 Mar 2017 12:51:13: end of X-cor INFO @ Fri, 10 Mar 2017 12:51:13: #2 finished! INFO @ Fri, 10 Mar 2017 12:51:13: #2 predicted fragment length is 325 bps INFO @ Fri, 10 Mar 2017 12:51:13: #2 alternative fragment length(s) may be 325 bps INFO @ Fri, 10 Mar 2017 12:51:13: #2.2 Generate R script for model : SRX110774.20_model.r INFO @ Fri, 10 Mar 2017 12:51:13: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:51:13: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:51:24: start X-correlation... INFO @ Fri, 10 Mar 2017 12:51:24: end of X-cor INFO @ Fri, 10 Mar 2017 12:51:24: #2 finished! INFO @ Fri, 10 Mar 2017 12:51:24: #2 predicted fragment length is 325 bps INFO @ Fri, 10 Mar 2017 12:51:24: #2 alternative fragment length(s) may be 325 bps INFO @ Fri, 10 Mar 2017 12:51:24: #2.2 Generate R script for model : SRX110774.05_model.r INFO @ Fri, 10 Mar 2017 12:51:24: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:51:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:53:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:54:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:54:27: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:55:33: #4 Write output xls file... SRX110774.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:55:33: #4 Write peak in narrowPeak format file... SRX110774.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:55:33: #4 Write summits bed file... SRX110774.10_summits.bed INFO @ Fri, 10 Mar 2017 12:55:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5545 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:56:08: #4 Write output xls file... SRX110774.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:56:08: #4 Write peak in narrowPeak format file... SRX110774.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:56:09: #4 Write summits bed file... SRX110774.20_summits.bed INFO @ Fri, 10 Mar 2017 12:56:09: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4064 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:56:40: #4 Write output xls file... SRX110774.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:56:40: #4 Write peak in narrowPeak format file... SRX110774.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:56:40: #4 Write summits bed file... SRX110774.05_summits.bed INFO @ Fri, 10 Mar 2017 12:56:41: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7026 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。