Job ID = 9029287 sra ファイルのダウンロード中... Completed: 28935K bytes transferred in 3 seconds (69490K 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 14324 0 14324 0 0 1890 0 --:--:-- 0:00:07 --:--:-- 12939 100 54318 0 54318 0 0 6462 0 --:--:-- 0:00:08 --:--:-- 28027 100 58276 0 58276 0 0 6900 0 --:--:-- 0:00:08 --:--:-- 29462 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 955550 spots for /home/okishinya/chipatlas/results/dm3/SRX1531763/SRR3102821.sra Written 955550 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: 00:00:17 955550 reads; of these: 955550 (100.00%) were unpaired; of these: 86947 (9.10%) aligned 0 times 764373 (79.99%) aligned exactly 1 time 104230 (10.91%) aligned >1 times 90.90% overall alignment rate Time searching: 00:00:17 Overall time: 00:00:17 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] 106878 / 868603 = 0.1230 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 13:00:09: # Command line: callpeak -t SRX1531763.bam -f BAM -g dm -n SRX1531763.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1531763.05 # format = BAM # ChIP-seq file = ['SRX1531763.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 13:00:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:00:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:00:09: # Command line: callpeak -t SRX1531763.bam -f BAM -g dm -n SRX1531763.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1531763.10 # format = BAM # ChIP-seq file = ['SRX1531763.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 13:00:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:00:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:00:09: # Command line: callpeak -t SRX1531763.bam -f BAM -g dm -n SRX1531763.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1531763.20 # format = BAM # ChIP-seq file = ['SRX1531763.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 13:00:09: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:00:09: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:00:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:00:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:00:14: #1 total tags in treatment: 761725 INFO @ Sat, 03 Jun 2017 13:00:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:00:14: #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 13:00:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:00:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:00:14: #1 total tags in treatment: 761725 INFO @ Sat, 03 Jun 2017 13:00:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:00:14: #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 13:00:14: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:00:14: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:00:14: #1 total tags in treatment: 761725 INFO @ Sat, 03 Jun 2017 13:00:14: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:00:14: #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 13:00:14: #1 tags after filtering in treatment: 761591 INFO @ Sat, 03 Jun 2017 13:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:00:14: #1 finished! INFO @ Sat, 03 Jun 2017 13:00:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:00:14: #1 tags after filtering in treatment: 761591 INFO @ Sat, 03 Jun 2017 13:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:00:14: #1 finished! INFO @ Sat, 03 Jun 2017 13:00:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:00:14: #1 tags after filtering in treatment: 761591 INFO @ Sat, 03 Jun 2017 13:00:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:00:14: #1 finished! INFO @ Sat, 03 Jun 2017 13:00:14: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:00:15: #2 number of paired peaks: 4109 INFO @ Sat, 03 Jun 2017 13:00:15: start model_add_line... INFO @ Sat, 03 Jun 2017 13:00:15: #2 number of paired peaks: 4109 INFO @ Sat, 03 Jun 2017 13:00:15: start model_add_line... INFO @ Sat, 03 Jun 2017 13:00:15: #2 number of paired peaks: 4109 INFO @ Sat, 03 Jun 2017 13:00:15: start model_add_line... INFO @ Sat, 03 Jun 2017 13:00:17: start X-correlation... INFO @ Sat, 03 Jun 2017 13:00:17: end of X-cor INFO @ Sat, 03 Jun 2017 13:00:17: #2 finished! INFO @ Sat, 03 Jun 2017 13:00:17: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Jun 2017 13:00:17: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Jun 2017 13:00:17: #2.2 Generate R script for model : SRX1531763.10_model.r INFO @ Sat, 03 Jun 2017 13:00:17: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:00:17: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:00:18: start X-correlation... INFO @ Sat, 03 Jun 2017 13:00:18: end of X-cor INFO @ Sat, 03 Jun 2017 13:00:18: #2 finished! INFO @ Sat, 03 Jun 2017 13:00:18: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Jun 2017 13:00:18: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Jun 2017 13:00:18: #2.2 Generate R script for model : SRX1531763.20_model.r INFO @ Sat, 03 Jun 2017 13:00:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:00:18: start X-correlation... INFO @ Sat, 03 Jun 2017 13:00:18: end of X-cor INFO @ Sat, 03 Jun 2017 13:00:18: #2 finished! INFO @ Sat, 03 Jun 2017 13:00:18: #2 predicted fragment length is 119 bps INFO @ Sat, 03 Jun 2017 13:00:18: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 03 Jun 2017 13:00:18: #2.2 Generate R script for model : SRX1531763.05_model.r INFO @ Sat, 03 Jun 2017 13:00:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:00:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:00:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:00:22: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:00:26: #4 Write output xls file... SRX1531763.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:00:26: #4 Write peak in narrowPeak format file... SRX1531763.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:00:26: #4 Write summits bed file... SRX1531763.20_summits.bed INFO @ Sat, 03 Jun 2017 13:00:26: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (909 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:00:26: #4 Write output xls file... SRX1531763.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:00:26: #4 Write peak in narrowPeak format file... SRX1531763.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:00:26: #4 Write summits bed file... SRX1531763.10_summits.bed INFO @ Sat, 03 Jun 2017 13:00:26: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1837 records, 4 fields): 3 millis CompletedMACS2peakCalling BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 13:00:27: #4 Write output xls file... SRX1531763.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:00:27: #4 Write peak in narrowPeak format file... SRX1531763.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:00:27: #4 Write summits bed file... SRX1531763.05_summits.bed INFO @ Sat, 03 Jun 2017 13:00:27: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3004 records, 4 fields): 5 millis CompletedMACS2peakCalling