Job ID = 9033334 sra ファイルのダウンロード中... Completed: 474934K bytes transferred in 7 seconds (542209K 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 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 101 5455 0 5455 0 0 621 0 --:--:-- 0:00:08 --:--:-- 2276 100 38318 0 38318 0 0 3920 0 --:--:-- 0:00:09 --:--:-- 11299 100 69565 0 69565 0 0 6772 0 --:--:-- 0:00:10 --:--:-- 17887 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 22516723 spots for /home/okishinya/chipatlas/results/dm3/SRX969923/SRR1931639.sra Written 22516723 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: 00:09:09 22516723 reads; of these: 22516723 (100.00%) were unpaired; of these: 604079 (2.68%) aligned 0 times 16281266 (72.31%) aligned exactly 1 time 5631378 (25.01%) aligned >1 times 97.32% overall alignment rate Time searching: 00:09:09 Overall time: 00:09:09 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] 3942967 / 21912644 = 0.1799 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 SRX969923.bam -f BAM -g dm -n SRX969923.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX969923.10 # format = BAM # ChIP-seq file = ['SRX969923.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 SRX969923.bam -f BAM -g dm -n SRX969923.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX969923.05 # format = BAM # ChIP-seq file = ['SRX969923.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 00:27:12: # Command line: callpeak -t SRX969923.bam -f BAM -g dm -n SRX969923.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX969923.20 # format = BAM # ChIP-seq file = ['SRX969923.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 00:27:18: 1000000 INFO @ Sun, 04 Jun 2017 00:27:18: 1000000 INFO @ Sun, 04 Jun 2017 00:27:18: 1000000 INFO @ Sun, 04 Jun 2017 00:27:23: 2000000 INFO @ Sun, 04 Jun 2017 00:27:24: 2000000 INFO @ Sun, 04 Jun 2017 00:27:24: 2000000 INFO @ Sun, 04 Jun 2017 00:27:28: 3000000 INFO @ Sun, 04 Jun 2017 00:27:29: 3000000 INFO @ Sun, 04 Jun 2017 00:27:29: 3000000 INFO @ Sun, 04 Jun 2017 00:27:33: 4000000 INFO @ Sun, 04 Jun 2017 00:27:35: 4000000 INFO @ Sun, 04 Jun 2017 00:27:35: 4000000 INFO @ Sun, 04 Jun 2017 00:27:39: 5000000 INFO @ Sun, 04 Jun 2017 00:27:40: 5000000 INFO @ Sun, 04 Jun 2017 00:27:40: 5000000 INFO @ Sun, 04 Jun 2017 00:27:44: 6000000 INFO @ Sun, 04 Jun 2017 00:27:46: 6000000 INFO @ Sun, 04 Jun 2017 00:27:46: 6000000 INFO @ Sun, 04 Jun 2017 00:27:49: 7000000 INFO @ Sun, 04 Jun 2017 00:27:51: 7000000 INFO @ Sun, 04 Jun 2017 00:27:51: 7000000 INFO @ Sun, 04 Jun 2017 00:27:54: 8000000 INFO @ Sun, 04 Jun 2017 00:27:57: 8000000 INFO @ Sun, 04 Jun 2017 00:27:57: 8000000 INFO @ Sun, 04 Jun 2017 00:27:59: 9000000 INFO @ Sun, 04 Jun 2017 00:28:02: 9000000 INFO @ Sun, 04 Jun 2017 00:28:02: 9000000 INFO @ Sun, 04 Jun 2017 00:28:04: 10000000 INFO @ Sun, 04 Jun 2017 00:28:08: 10000000 INFO @ Sun, 04 Jun 2017 00:28:08: 10000000 INFO @ Sun, 04 Jun 2017 00:28:09: 11000000 INFO @ Sun, 04 Jun 2017 00:28:13: 11000000 INFO @ Sun, 04 Jun 2017 00:28:13: 11000000 INFO @ Sun, 04 Jun 2017 00:28:14: 12000000 INFO @ Sun, 04 Jun 2017 00:28:19: 12000000 INFO @ Sun, 04 Jun 2017 00:28:19: 12000000 INFO @ Sun, 04 Jun 2017 00:28:19: 13000000 INFO @ Sun, 04 Jun 2017 00:28:24: 14000000 INFO @ Sun, 04 Jun 2017 00:28:24: 13000000 INFO @ Sun, 04 Jun 2017 00:28:25: 13000000 INFO @ Sun, 04 Jun 2017 00:28:29: 15000000 INFO @ Sun, 04 Jun 2017 00:28:30: 14000000 INFO @ Sun, 04 Jun 2017 00:28:30: 14000000 INFO @ Sun, 04 Jun 2017 00:28:34: 16000000 INFO @ Sun, 04 Jun 2017 00:28:36: 15000000 INFO @ Sun, 04 Jun 2017 00:28:36: 15000000 INFO @ Sun, 04 Jun 2017 00:28:39: 17000000 INFO @ Sun, 04 Jun 2017 00:28:42: 16000000 INFO @ Sun, 04 Jun 2017 00:28:42: 16000000 INFO @ Sun, 04 Jun 2017 00:28:44: #1 tag size is determined as 49 bps INFO @ Sun, 04 Jun 2017 00:28:44: #1 tag size = 49 INFO @ Sun, 04 Jun 2017 00:28:44: #1 total tags in treatment: 17969677 INFO @ Sun, 04 Jun 2017 00:28:44: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 00:28:44: #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 00:28:48: 17000000 INFO @ Sun, 04 Jun 2017 00:28:48: #1 tags after filtering in treatment: 17963358 INFO @ Sun, 04 Jun 2017 00:28:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 00:28:48: #1 finished! INFO @ Sun, 04 Jun 2017 00:28:48: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 00:28:48: 17000000 INFO @ Sun, 04 Jun 2017 00:28:51: #2 number of paired peaks: 336 WARNING @ Sun, 04 Jun 2017 00:28:51: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Sun, 04 Jun 2017 00:28:51: start model_add_line... INFO @ Sun, 04 Jun 2017 00:28:54: #1 tag size is determined as 49 bps INFO @ Sun, 04 Jun 2017 00:28:54: #1 tag size = 49 INFO @ Sun, 04 Jun 2017 00:28:54: #1 total tags in treatment: 17969677 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 00:28:54: #1 tag size is determined as 49 bps INFO @ Sun, 04 Jun 2017 00:28:54: #1 tag size = 49 INFO @ Sun, 04 Jun 2017 00:28:54: #1 total tags in treatment: 17969677 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 00:28:56: start X-correlation... INFO @ Sun, 04 Jun 2017 00:28:56: end of X-cor INFO @ Sun, 04 Jun 2017 00:28:56: #2 finished! INFO @ Sun, 04 Jun 2017 00:28:56: #2 predicted fragment length is 115 bps INFO @ Sun, 04 Jun 2017 00:28:56: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 04 Jun 2017 00:28:56: #2.2 Generate R script for model : SRX969923.20_model.r INFO @ Sun, 04 Jun 2017 00:28:56: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:28:57: #1 tags after filtering in treatment: 17963358 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 00:28:57: #1 tags after filtering in treatment: 17963358 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: #2 number of paired peaks: 336 WARNING @ Sun, 04 Jun 2017 00:29:00: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Sun, 04 Jun 2017 00:29:00: start model_add_line... INFO @ Sun, 04 Jun 2017 00:29:00: #2 number of paired peaks: 336 WARNING @ Sun, 04 Jun 2017 00:29:00: Fewer paired peaks (336) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 336 pairs to build model! INFO @ Sun, 04 Jun 2017 00:29:00: start model_add_line... INFO @ Sun, 04 Jun 2017 00:29:04: start X-correlation... INFO @ Sun, 04 Jun 2017 00:29:04: end of X-cor INFO @ Sun, 04 Jun 2017 00:29:04: #2 finished! INFO @ Sun, 04 Jun 2017 00:29:04: #2 predicted fragment length is 115 bps INFO @ Sun, 04 Jun 2017 00:29:04: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 04 Jun 2017 00:29:04: #2.2 Generate R script for model : SRX969923.05_model.r INFO @ Sun, 04 Jun 2017 00:29:04: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:29:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:29:04: start X-correlation... INFO @ Sun, 04 Jun 2017 00:29:04: end of X-cor INFO @ Sun, 04 Jun 2017 00:29:04: #2 finished! INFO @ Sun, 04 Jun 2017 00:29:04: #2 predicted fragment length is 115 bps INFO @ Sun, 04 Jun 2017 00:29:04: #2 alternative fragment length(s) may be 115 bps INFO @ Sun, 04 Jun 2017 00:29:04: #2.2 Generate R script for model : SRX969923.10_model.r INFO @ Sun, 04 Jun 2017 00:29:04: #3 Call peaks... INFO @ Sun, 04 Jun 2017 00:29:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 00:30:34: #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 00:30:43: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 00:31:42: #4 Write output xls file... SRX969923.20_peaks.xls INFO @ Sun, 04 Jun 2017 00:31:42: #4 Write peak in narrowPeak format file... SRX969923.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:31:42: #4 Write summits bed file... SRX969923.20_summits.bed INFO @ Sun, 04 Jun 2017 00:31:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2667 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:31:50: #4 Write output xls file... SRX969923.05_peaks.xls INFO @ Sun, 04 Jun 2017 00:31:50: #4 Write peak in narrowPeak format file... SRX969923.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:31:50: #4 Write summits bed file... SRX969923.05_summits.bed INFO @ Sun, 04 Jun 2017 00:31:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5747 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 00:31:54: #4 Write output xls file... SRX969923.10_peaks.xls INFO @ Sun, 04 Jun 2017 00:31:54: #4 Write peak in narrowPeak format file... SRX969923.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 00:31:54: #4 Write summits bed file... SRX969923.10_summits.bed INFO @ Sun, 04 Jun 2017 00:31:54: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4131 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。