Job ID = 9028935 sra ファイルのダウンロード中... Completed: 446501K bytes transferred in 7 seconds (466537K 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 --:--:-- 0:00:07 --:--:-- 0 100 24454 0 24454 0 0 2813 0 --:--:-- 0:00:08 --:--:-- 10907 100 54862 0 54862 0 0 5663 0 --:--:-- 0:00:09 --:--:-- 16948 100 59856 0 59856 0 0 6177 0 --:--:-- 0:00:09 --:--:-- 18485 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 11416796 spots for /home/okishinya/chipatlas/results/dm3/SRX1038031/SRR2039660.sra Written 11416796 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: 00:01:19 11416796 reads; of these: 11416796 (100.00%) were unpaired; of these: 9566258 (83.79%) aligned 0 times 1714969 (15.02%) aligned exactly 1 time 135569 (1.19%) aligned >1 times 16.21% overall alignment rate Time searching: 00:01:19 Overall time: 00:01:19 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] 415264 / 1850538 = 0.2244 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 12:27:48: # Command line: callpeak -t SRX1038031.bam -f BAM -g dm -n SRX1038031.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1038031.05 # format = BAM # ChIP-seq file = ['SRX1038031.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 12:27:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:48: # Command line: callpeak -t SRX1038031.bam -f BAM -g dm -n SRX1038031.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1038031.20 # format = BAM # ChIP-seq file = ['SRX1038031.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 12:27:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:48: # Command line: callpeak -t SRX1038031.bam -f BAM -g dm -n SRX1038031.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1038031.10 # format = BAM # ChIP-seq file = ['SRX1038031.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 12:27:48: #1 read tag files... INFO @ Sat, 03 Jun 2017 12:27:48: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 12:27:54: 1000000 INFO @ Sat, 03 Jun 2017 12:27:55: 1000000 INFO @ Sat, 03 Jun 2017 12:27:55: 1000000 INFO @ Sat, 03 Jun 2017 12:27:57: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:27:57: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:27:57: #1 total tags in treatment: 1435274 INFO @ Sat, 03 Jun 2017 12:27:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:27:57: #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 12:27:57: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:27:57: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:27:57: #1 total tags in treatment: 1435274 INFO @ Sat, 03 Jun 2017 12:27:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:27:57: #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 12:27:57: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 12:27:57: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 12:27:57: #1 total tags in treatment: 1435274 INFO @ Sat, 03 Jun 2017 12:27:57: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 12:27:57: #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 12:27:58: #1 tags after filtering in treatment: 1434622 INFO @ Sat, 03 Jun 2017 12:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:27:58: #1 finished! INFO @ Sat, 03 Jun 2017 12:27:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:27:58: #1 tags after filtering in treatment: 1434622 INFO @ Sat, 03 Jun 2017 12:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:27:58: #1 finished! INFO @ Sat, 03 Jun 2017 12:27:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:27:58: #1 tags after filtering in treatment: 1434622 INFO @ Sat, 03 Jun 2017 12:27:58: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 12:27:58: #1 finished! INFO @ Sat, 03 Jun 2017 12:27:58: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 12:27:58: #2 number of paired peaks: 5123 INFO @ Sat, 03 Jun 2017 12:27:58: start model_add_line... INFO @ Sat, 03 Jun 2017 12:27:59: #2 number of paired peaks: 5123 INFO @ Sat, 03 Jun 2017 12:27:59: start model_add_line... INFO @ Sat, 03 Jun 2017 12:27:59: #2 number of paired peaks: 5123 INFO @ Sat, 03 Jun 2017 12:27:59: start model_add_line... INFO @ Sat, 03 Jun 2017 12:28:07: start X-correlation... INFO @ Sat, 03 Jun 2017 12:28:07: end of X-cor INFO @ Sat, 03 Jun 2017 12:28:07: #2 finished! INFO @ Sat, 03 Jun 2017 12:28:07: #2 predicted fragment length is 152 bps INFO @ Sat, 03 Jun 2017 12:28:07: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 03 Jun 2017 12:28:07: #2.2 Generate R script for model : SRX1038031.20_model.r INFO @ Sat, 03 Jun 2017 12:28:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:28:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:28:07: start X-correlation... INFO @ Sat, 03 Jun 2017 12:28:07: end of X-cor INFO @ Sat, 03 Jun 2017 12:28:07: #2 finished! INFO @ Sat, 03 Jun 2017 12:28:07: #2 predicted fragment length is 152 bps INFO @ Sat, 03 Jun 2017 12:28:07: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 03 Jun 2017 12:28:07: #2.2 Generate R script for model : SRX1038031.05_model.r INFO @ Sat, 03 Jun 2017 12:28:07: start X-correlation... INFO @ Sat, 03 Jun 2017 12:28:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:28:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 12:28:07: end of X-cor INFO @ Sat, 03 Jun 2017 12:28:07: #2 finished! INFO @ Sat, 03 Jun 2017 12:28:07: #2 predicted fragment length is 152 bps INFO @ Sat, 03 Jun 2017 12:28:07: #2 alternative fragment length(s) may be 152 bps INFO @ Sat, 03 Jun 2017 12:28:07: #2.2 Generate R script for model : SRX1038031.10_model.r INFO @ Sat, 03 Jun 2017 12:28:07: #3 Call peaks... INFO @ Sat, 03 Jun 2017 12:28:07: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 12:28:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:28:17: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 12:28:17: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 12:28:23: #4 Write output xls file... SRX1038031.20_peaks.xls INFO @ Sat, 03 Jun 2017 12:28:24: #4 Write peak in narrowPeak format file... SRX1038031.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:28:24: #4 Write summits bed file... SRX1038031.20_summits.bed INFO @ Sat, 03 Jun 2017 12:28:24: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (693 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:28:25: #4 Write output xls file... SRX1038031.10_peaks.xls INFO @ Sat, 03 Jun 2017 12:28:25: #4 Write peak in narrowPeak format file... SRX1038031.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:28:25: #4 Write summits bed file... SRX1038031.10_summits.bed INFO @ Sat, 03 Jun 2017 12:28:25: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1162 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 12:28:25: #4 Write output xls file... SRX1038031.05_peaks.xls INFO @ Sat, 03 Jun 2017 12:28:25: #4 Write peak in narrowPeak format file... SRX1038031.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 12:28:25: #4 Write summits bed file... SRX1038031.05_summits.bed INFO @ Sat, 03 Jun 2017 12:28:25: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1884 records, 4 fields): 5 millis CompletedMACS2peakCalling