Job ID = 9029478 sra ファイルのダウンロード中... Completed: 165113K bytes transferred in 4 seconds (292664K 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 13455 0 13455 0 0 1808 0 --:--:-- 0:00:07 --:--:-- 13282 100 53414 0 53414 0 0 6332 0 --:--:-- 0:00:08 --:--:-- 26587 100 56683 0 56683 0 0 6719 0 --:--:-- 0:00:08 --:--:-- 28200 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 5277536 spots for /home/okishinya/chipatlas/results/dm3/SRX1794231/SRR3575270.sra Written 5277536 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: 00:02:01 5277536 reads; of these: 5277536 (100.00%) were unpaired; of these: 237685 (4.50%) aligned 0 times 3824216 (72.46%) aligned exactly 1 time 1215635 (23.03%) aligned >1 times 95.50% overall alignment rate Time searching: 00:02:01 Overall time: 00:02:01 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] 390212 / 5039851 = 0.0774 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 13:55:27: # Command line: callpeak -t SRX1794231.bam -f BAM -g dm -n SRX1794231.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794231.10 # format = BAM # ChIP-seq file = ['SRX1794231.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 13:55:27: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:27: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:27: # Command line: callpeak -t SRX1794231.bam -f BAM -g dm -n SRX1794231.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794231.05 # format = BAM # ChIP-seq file = ['SRX1794231.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 13:55:27: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:27: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:27: # Command line: callpeak -t SRX1794231.bam -f BAM -g dm -n SRX1794231.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794231.20 # format = BAM # ChIP-seq file = ['SRX1794231.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 13:55:27: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:55:27: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:55:33: 1000000 INFO @ Sat, 03 Jun 2017 13:55:33: 1000000 INFO @ Sat, 03 Jun 2017 13:55:35: 1000000 INFO @ Sat, 03 Jun 2017 13:55:40: 2000000 INFO @ Sat, 03 Jun 2017 13:55:40: 2000000 INFO @ Sat, 03 Jun 2017 13:55:43: 2000000 INFO @ Sat, 03 Jun 2017 13:55:46: 3000000 INFO @ Sat, 03 Jun 2017 13:55:46: 3000000 INFO @ Sat, 03 Jun 2017 13:55:49: 3000000 INFO @ Sat, 03 Jun 2017 13:55:52: 4000000 INFO @ Sat, 03 Jun 2017 13:55:52: 4000000 INFO @ Sat, 03 Jun 2017 13:55:55: 4000000 INFO @ Sat, 03 Jun 2017 13:55:56: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:55:56: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:55:56: #1 total tags in treatment: 4649639 INFO @ Sat, 03 Jun 2017 13:55:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:55:56: #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 13:55:56: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:55:56: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:55:56: #1 total tags in treatment: 4649639 INFO @ Sat, 03 Jun 2017 13:55:56: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:55:56: #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 13:55:57: #1 tags after filtering in treatment: 4648836 INFO @ Sat, 03 Jun 2017 13:55:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:55:57: #1 finished! INFO @ Sat, 03 Jun 2017 13:55:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:55:57: #1 tags after filtering in treatment: 4648836 INFO @ Sat, 03 Jun 2017 13:55:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:55:57: #1 finished! INFO @ Sat, 03 Jun 2017 13:55:57: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:55:58: #2 number of paired peaks: 2086 INFO @ Sat, 03 Jun 2017 13:55:58: start model_add_line... INFO @ Sat, 03 Jun 2017 13:55:58: #2 number of paired peaks: 2086 INFO @ Sat, 03 Jun 2017 13:55:58: start model_add_line... INFO @ Sat, 03 Jun 2017 13:55:58: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:55:58: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:55:58: #1 total tags in treatment: 4649639 INFO @ Sat, 03 Jun 2017 13:55:58: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:55:58: #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 13:55:59: #1 tags after filtering in treatment: 4648836 INFO @ Sat, 03 Jun 2017 13:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:55:59: #1 finished! INFO @ Sat, 03 Jun 2017 13:55:59: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:56:01: #2 number of paired peaks: 2086 INFO @ Sat, 03 Jun 2017 13:56:01: start model_add_line... INFO @ Sat, 03 Jun 2017 13:56:06: start X-correlation... INFO @ Sat, 03 Jun 2017 13:56:06: end of X-cor INFO @ Sat, 03 Jun 2017 13:56:06: #2 finished! INFO @ Sat, 03 Jun 2017 13:56:06: #2 predicted fragment length is 163 bps INFO @ Sat, 03 Jun 2017 13:56:06: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 03 Jun 2017 13:56:06: #2.2 Generate R script for model : SRX1794231.20_model.r INFO @ Sat, 03 Jun 2017 13:56:06: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:56:06: start X-correlation... INFO @ Sat, 03 Jun 2017 13:56:06: end of X-cor INFO @ Sat, 03 Jun 2017 13:56:06: #2 finished! INFO @ Sat, 03 Jun 2017 13:56:06: #2 predicted fragment length is 163 bps INFO @ Sat, 03 Jun 2017 13:56:06: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 03 Jun 2017 13:56:06: #2.2 Generate R script for model : SRX1794231.10_model.r INFO @ Sat, 03 Jun 2017 13:56:06: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:56:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:56:08: start X-correlation... INFO @ Sat, 03 Jun 2017 13:56:08: end of X-cor INFO @ Sat, 03 Jun 2017 13:56:08: #2 finished! INFO @ Sat, 03 Jun 2017 13:56:08: #2 predicted fragment length is 163 bps INFO @ Sat, 03 Jun 2017 13:56:08: #2 alternative fragment length(s) may be 163 bps INFO @ Sat, 03 Jun 2017 13:56:08: #2.2 Generate R script for model : SRX1794231.05_model.r INFO @ Sat, 03 Jun 2017 13:56:08: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:56:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:56:37: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:56:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:56:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:57:00: #4 Write output xls file... SRX1794231.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:57:00: #4 Write peak in narrowPeak format file... SRX1794231.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:57:00: #4 Write summits bed file... SRX1794231.20_summits.bed INFO @ Sat, 03 Jun 2017 13:57:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1361 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:57:02: #4 Write output xls file... SRX1794231.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:57:02: #4 Write peak in narrowPeak format file... SRX1794231.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:57:02: #4 Write summits bed file... SRX1794231.10_summits.bed INFO @ Sat, 03 Jun 2017 13:57:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2699 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:57:04: #4 Write output xls file... SRX1794231.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:57:04: #4 Write peak in narrowPeak format file... SRX1794231.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:57:04: #4 Write summits bed file... SRX1794231.05_summits.bed INFO @ Sat, 03 Jun 2017 13:57:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4423 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。