Job ID = 9029323 sra ファイルのダウンロード中... Completed: 351941K bytes transferred in 5 seconds (488240K 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 20110 0 20110 0 0 2570 0 --:--:-- 0:00:07 --:--:-- 13726 100 49070 0 49070 0 0 5564 0 --:--:-- 0:00:08 --:--:-- 19939 100 69407 0 69407 0 0 7725 0 --:--:-- 0:00:08 --:--:-- 26420 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 11186422 spots for /home/okishinya/chipatlas/results/dm3/SRX1561065/SRR3145067.sra Written 11186422 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: 00:02:44 11186422 reads; of these: 11186422 (100.00%) were unpaired; of these: 5976747 (53.43%) aligned 0 times 4482512 (40.07%) aligned exactly 1 time 727163 (6.50%) aligned >1 times 46.57% overall alignment rate Time searching: 00:02:44 Overall time: 00:02:44 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_rmdupse_core] 1020209 / 5209675 = 0.1958 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 13:17:13: # Command line: callpeak -t SRX1561065.bam -f BAM -g dm -n SRX1561065.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1561065.20 # format = BAM # ChIP-seq file = ['SRX1561065.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 13:17:13: # Command line: callpeak -t SRX1561065.bam -f BAM -g dm -n SRX1561065.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1561065.10 # format = BAM # ChIP-seq file = ['SRX1561065.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 13:17:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:13: # Command line: callpeak -t SRX1561065.bam -f BAM -g dm -n SRX1561065.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1561065.05 # format = BAM # ChIP-seq file = ['SRX1561065.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 13:17:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:17:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:17:20: 1000000 INFO @ Sat, 03 Jun 2017 13:17:20: 1000000 INFO @ Sat, 03 Jun 2017 13:17:20: 1000000 INFO @ Sat, 03 Jun 2017 13:17:28: 2000000 INFO @ Sat, 03 Jun 2017 13:17:28: 2000000 INFO @ Sat, 03 Jun 2017 13:17:28: 2000000 INFO @ Sat, 03 Jun 2017 13:17:35: 3000000 INFO @ Sat, 03 Jun 2017 13:17:35: 3000000 INFO @ Sat, 03 Jun 2017 13:17:35: 3000000 INFO @ Sat, 03 Jun 2017 13:17:43: 4000000 INFO @ Sat, 03 Jun 2017 13:17:43: 4000000 INFO @ Sat, 03 Jun 2017 13:17:43: 4000000 INFO @ Sat, 03 Jun 2017 13:17:44: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:17:44: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:17:44: #1 total tags in treatment: 4189466 INFO @ Sat, 03 Jun 2017 13:17:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:17:44: #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 13:17:44: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:17:44: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:17:44: #1 total tags in treatment: 4189466 INFO @ Sat, 03 Jun 2017 13:17:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:17:44: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:17:44: #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 13:17:44: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:17:44: #1 total tags in treatment: 4189466 INFO @ Sat, 03 Jun 2017 13:17:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:17:44: #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 13:17:45: #1 tags after filtering in treatment: 4188650 INFO @ Sat, 03 Jun 2017 13:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:45: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:45: #1 tags after filtering in treatment: 4188650 INFO @ Sat, 03 Jun 2017 13:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:45: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:45: #1 tags after filtering in treatment: 4188650 INFO @ Sat, 03 Jun 2017 13:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:17:45: #1 finished! INFO @ Sat, 03 Jun 2017 13:17:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:17:46: #2 number of paired peaks: 1815 INFO @ Sat, 03 Jun 2017 13:17:46: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:46: #2 number of paired peaks: 1815 INFO @ Sat, 03 Jun 2017 13:17:46: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:46: #2 number of paired peaks: 1815 INFO @ Sat, 03 Jun 2017 13:17:46: start model_add_line... INFO @ Sat, 03 Jun 2017 13:17:50: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:50: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:50: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:50: #2 predicted fragment length is 202 bps INFO @ Sat, 03 Jun 2017 13:17:50: #2 alternative fragment length(s) may be 4,188,202,227 bps INFO @ Sat, 03 Jun 2017 13:17:50: #2.2 Generate R script for model : SRX1561065.20_model.r INFO @ Sat, 03 Jun 2017 13:17:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:17:51: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:51: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:51: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:51: #2 predicted fragment length is 202 bps INFO @ Sat, 03 Jun 2017 13:17:51: #2 alternative fragment length(s) may be 4,188,202,227 bps INFO @ Sat, 03 Jun 2017 13:17:51: #2.2 Generate R script for model : SRX1561065.10_model.r INFO @ Sat, 03 Jun 2017 13:17:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:17:51: start X-correlation... INFO @ Sat, 03 Jun 2017 13:17:51: end of X-cor INFO @ Sat, 03 Jun 2017 13:17:51: #2 finished! INFO @ Sat, 03 Jun 2017 13:17:51: #2 predicted fragment length is 202 bps INFO @ Sat, 03 Jun 2017 13:17:51: #2 alternative fragment length(s) may be 4,188,202,227 bps INFO @ Sat, 03 Jun 2017 13:17:51: #2.2 Generate R script for model : SRX1561065.05_model.r INFO @ Sat, 03 Jun 2017 13:17:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:17:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:18:15: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:18:34: #4 Write output xls file... SRX1561065.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:18:34: #4 Write peak in narrowPeak format file... SRX1561065.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:18:34: #4 Write summits bed file... SRX1561065.05_summits.bed INFO @ Sat, 03 Jun 2017 13:18:34: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (295 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:18:35: #4 Write output xls file... SRX1561065.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:18:35: #4 Write peak in narrowPeak format file... SRX1561065.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:18:35: #4 Write summits bed file... SRX1561065.20_summits.bed INFO @ Sat, 03 Jun 2017 13:18:35: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (69 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:18:35: #4 Write output xls file... SRX1561065.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:18:35: #4 Write peak in narrowPeak format file... SRX1561065.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:18:35: #4 Write summits bed file... SRX1561065.10_summits.bed INFO @ Sat, 03 Jun 2017 13:18:35: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (145 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。