Job ID = 9033205 sra ファイルのダウンロード中... Completed: 962555K bytes transferred in 15 seconds (510441K 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 1032 0 --:--:-- 0:00:07 --:--:-- 9015 100 30246 0 30246 0 0 3666 0 --:--:-- 0:00:08 --:--:-- 18003 100 65699 0 65699 0 0 7370 0 --:--:-- 0:00:08 --:--:-- 28052 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 27259177 spots for /home/okishinya/chipatlas/results/dm3/SRX969909/SRR1931625.sra Written 27259177 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: 00:12:15 27259177 reads; of these: 27259177 (100.00%) were unpaired; of these: 2526539 (9.27%) aligned 0 times 17076612 (62.65%) aligned exactly 1 time 7656026 (28.09%) aligned >1 times 90.73% overall alignment rate Time searching: 00:12:15 Overall time: 00:12:15 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] 7580166 / 24732638 = 0.3065 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 00:27:12: # Command line: callpeak -t SRX969909.bam -f BAM -g dm -n SRX969909.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX969909.20 # format = BAM # ChIP-seq file = ['SRX969909.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 00:27:12: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:27:12: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:27:12: # Command line: callpeak -t SRX969909.bam -f BAM -g dm -n SRX969909.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX969909.10 # format = BAM # ChIP-seq file = ['SRX969909.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 00:27:12: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:27:12: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:27:12: # Command line: callpeak -t SRX969909.bam -f BAM -g dm -n SRX969909.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX969909.05 # format = BAM # ChIP-seq file = ['SRX969909.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 00:27:12: #1 read tag files... INFO @ Sun, 04 Jun 2017 00:27:12: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 00:27:18: 1000000 INFO @ Sun, 04 Jun 2017 00:27:18: 1000000 INFO @ Sun, 04 Jun 2017 00:27:18: 1000000 INFO @ Sun, 04 Jun 2017 00:27:24: 2000000 INFO @ Sun, 04 Jun 2017 00:27:24: 2000000 INFO @ Sun, 04 Jun 2017 00:27:25: 2000000 INFO @ Sun, 04 Jun 2017 00:27:30: 3000000 INFO @ Sun, 04 Jun 2017 00:27:31: 3000000 INFO @ Sun, 04 Jun 2017 00:27:31: 3000000 INFO @ Sun, 04 Jun 2017 00:27:36: 4000000 INFO @ Sun, 04 Jun 2017 00:27:37: 4000000 INFO @ Sun, 04 Jun 2017 00:27:37: 4000000 INFO @ Sun, 04 Jun 2017 00:27:42: 5000000 INFO @ Sun, 04 Jun 2017 00:27:43: 5000000 INFO @ Sun, 04 Jun 2017 00:27:43: 5000000 INFO @ Sun, 04 Jun 2017 00:27:48: 6000000 INFO @ Sun, 04 Jun 2017 00:27:49: 6000000 INFO @ Sun, 04 Jun 2017 00:27:50: 6000000 INFO @ Sun, 04 Jun 2017 00:27:54: 7000000 INFO @ Sun, 04 Jun 2017 00:27:55: 7000000 INFO @ Sun, 04 Jun 2017 00:27:56: 7000000 INFO @ Sun, 04 Jun 2017 00:28:00: 8000000 INFO @ Sun, 04 Jun 2017 00:28:02: 8000000 INFO @ Sun, 04 Jun 2017 00:28:02: 8000000 INFO @ Sun, 04 Jun 2017 00:28:05: 9000000 INFO @ Sun, 04 Jun 2017 00:28:08: 9000000 INFO @ Sun, 04 Jun 2017 00:28:09: 9000000 INFO @ Sun, 04 Jun 2017 00:28:11: 10000000 INFO @ Sun, 04 Jun 2017 00:28:14: 10000000 INFO @ Sun, 04 Jun 2017 00:28:15: 10000000 INFO @ Sun, 04 Jun 2017 00:28:17: 11000000 INFO @ Sun, 04 Jun 2017 00:28:21: 11000000 INFO @ Sun, 04 Jun 2017 00:28:21: 11000000 INFO @ Sun, 04 Jun 2017 00:28:23: 12000000 INFO @ Sun, 04 Jun 2017 00:28:27: 12000000 INFO @ Sun, 04 Jun 2017 00:28:28: 12000000 INFO @ Sun, 04 Jun 2017 00:28:29: 13000000 INFO @ Sun, 04 Jun 2017 00:28:33: 13000000 INFO @ Sun, 04 Jun 2017 00:28:34: 13000000 INFO @ Sun, 04 Jun 2017 00:28:35: 14000000 INFO @ Sun, 04 Jun 2017 00:28:40: 14000000 INFO @ Sun, 04 Jun 2017 00:28:40: 14000000 INFO @ Sun, 04 Jun 2017 00:28:41: 15000000 INFO @ Sun, 04 Jun 2017 00:28:46: 15000000 INFO @ Sun, 04 Jun 2017 00:28:47: 16000000 INFO @ Sun, 04 Jun 2017 00:28:47: 15000000 INFO @ Sun, 04 Jun 2017 00:28:53: 17000000 INFO @ Sun, 04 Jun 2017 00:28:53: 16000000 INFO @ Sun, 04 Jun 2017 00:28:53: 16000000 INFO @ Sun, 04 Jun 2017 00:28:54: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:28:54: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:28:54: #1 total tags in treatment: 17152472 INFO @ Sun, 04 Jun 2017 00:28:54: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:28:54: #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 00:28:57: #1 tags after filtering in treatment: 17144197 INFO @ Sun, 04 Jun 2017 00:28:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:28:57: #1 finished! INFO @ Sun, 04 Jun 2017 00:28:57: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:29:00: 17000000 INFO @ Sun, 04 Jun 2017 00:29:00: #2 number of paired peaks: 227 WARNING @ Sun, 04 Jun 2017 00:29:00: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sun, 04 Jun 2017 00:29:00: start model_add_line... INFO @ Sun, 04 Jun 2017 00:29:00: 17000000 INFO @ Sun, 04 Jun 2017 00:29:01: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:29:01: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:29:01: #1 total tags in treatment: 17152472 INFO @ Sun, 04 Jun 2017 00:29:01: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:29:01: #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 00:29:01: #1 tag size is determined as 51 bps INFO @ Sun, 04 Jun 2017 00:29:01: #1 tag size = 51 INFO @ Sun, 04 Jun 2017 00:29:01: #1 total tags in treatment: 17152472 INFO @ Sun, 04 Jun 2017 00:29:01: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:29:01: #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 00:29:03: start X-correlation... INFO @ Sun, 04 Jun 2017 00:29:03: end of X-cor INFO @ Sun, 04 Jun 2017 00:29:03: #2 finished! INFO @ Sun, 04 Jun 2017 00:29:03: #2 predicted fragment length is 124 bps INFO @ Sun, 04 Jun 2017 00:29:03: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 04 Jun 2017 00:29:03: #2.2 Generate R script for model : SRX969909.20_model.r INFO @ Sun, 04 Jun 2017 00:29:03: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:29:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:29:04: #1 tags after filtering in treatment: 17144197 INFO @ Sun, 04 Jun 2017 00:29:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:29:04: #1 finished! INFO @ Sun, 04 Jun 2017 00:29:04: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:29:05: #1 tags after filtering in treatment: 17144197 INFO @ Sun, 04 Jun 2017 00:29:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:29:05: #1 finished! INFO @ Sun, 04 Jun 2017 00:29:05: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:29:07: #2 number of paired peaks: 227 WARNING @ Sun, 04 Jun 2017 00:29:07: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sun, 04 Jun 2017 00:29:07: start model_add_line... INFO @ Sun, 04 Jun 2017 00:29:08: #2 number of paired peaks: 227 WARNING @ Sun, 04 Jun 2017 00:29:08: Fewer paired peaks (227) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 227 pairs to build model! INFO @ Sun, 04 Jun 2017 00:29:08: start model_add_line... INFO @ Sun, 04 Jun 2017 00:29:11: start X-correlation... INFO @ Sun, 04 Jun 2017 00:29:11: end of X-cor INFO @ Sun, 04 Jun 2017 00:29:11: #2 finished! INFO @ Sun, 04 Jun 2017 00:29:11: #2 predicted fragment length is 124 bps INFO @ Sun, 04 Jun 2017 00:29:11: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 04 Jun 2017 00:29:11: #2.2 Generate R script for model : SRX969909.05_model.r INFO @ Sun, 04 Jun 2017 00:29:11: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:29:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:29:11: start X-correlation... INFO @ Sun, 04 Jun 2017 00:29:11: end of X-cor INFO @ Sun, 04 Jun 2017 00:29:11: #2 finished! INFO @ Sun, 04 Jun 2017 00:29:11: #2 predicted fragment length is 124 bps INFO @ Sun, 04 Jun 2017 00:29:11: #2 alternative fragment length(s) may be 124 bps INFO @ Sun, 04 Jun 2017 00:29:11: #2.2 Generate R script for model : SRX969909.10_model.r INFO @ Sun, 04 Jun 2017 00:29:11: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:29:11: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:30:37: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:30:39: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:30:41: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:31:49: #4 Write output xls file... SRX969909.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:31:49: #4 Write peak in narrowPeak format file... SRX969909.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:31:49: #4 Write summits bed file... SRX969909.10_summits.bed INFO @ Sun, 04 Jun 2017 00:31:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6453 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:31:50: #4 Write output xls file... SRX969909.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:31:50: #4 Write peak in narrowPeak format file... SRX969909.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:31:50: #4 Write summits bed file... SRX969909.20_summits.bed INFO @ Sun, 04 Jun 2017 00:31:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3024 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:31:51: #4 Write output xls file... SRX969909.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:31:51: #4 Write peak in narrowPeak format file... SRX969909.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:31:51: #4 Write summits bed file... SRX969909.05_summits.bed INFO @ Sun, 04 Jun 2017 00:31:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9663 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。