Job ID = 2236892 sra ファイルのダウンロード中... Completed: 298985K bytes transferred in 8 seconds (279512K 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 --:--:-- --:--:-- --:--:-- 0 100 14928 0 14928 0 0 19619 0 --:--:-- --:--:-- --:--:-- 26189 100 35257 0 35257 0 0 46285 0 --:--:-- --:--:-- --:--:-- 61746 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 16264926 spots for /home/okishinya/chipatlas/results/ce10/SRX059274/SRR190714.sra Written 16264926 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: 00:01:46 16264926 reads; of these: 16264926 (100.00%) were unpaired; of these: 10753192 (66.11%) aligned 0 times 4783113 (29.41%) aligned exactly 1 time 728621 (4.48%) aligned >1 times 33.89% overall alignment rate Time searching: 00:01:46 Overall time: 00:01:46 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 659888 / 5511734 = 0.1197 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 @ Thu, 30 Apr 2015 11:14:57: # Command line: callpeak -t SRX059274.bam -f BAM -g ce -n SRX059274.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX059274.20 # format = BAM # ChIP-seq file = ['SRX059274.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:14:57: # Command line: callpeak -t SRX059274.bam -f BAM -g ce -n SRX059274.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX059274.05 # format = BAM # ChIP-seq file = ['SRX059274.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:14:57: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:14:57: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:14:57: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:14:57: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:14:57: # Command line: callpeak -t SRX059274.bam -f BAM -g ce -n SRX059274.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX059274.10 # format = BAM # ChIP-seq file = ['SRX059274.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Thu, 30 Apr 2015 11:14:57: #1 read tag files... INFO @ Thu, 30 Apr 2015 11:14:57: #1 read treatment tags... INFO @ Thu, 30 Apr 2015 11:15:03: 1000000 INFO @ Thu, 30 Apr 2015 11:15:03: 1000000 INFO @ Thu, 30 Apr 2015 11:15:03: 1000000 INFO @ Thu, 30 Apr 2015 11:15:08: 2000000 INFO @ Thu, 30 Apr 2015 11:15:09: 2000000 INFO @ Thu, 30 Apr 2015 11:15:09: 2000000 INFO @ Thu, 30 Apr 2015 11:15:14: 3000000 INFO @ Thu, 30 Apr 2015 11:15:15: 3000000 INFO @ Thu, 30 Apr 2015 11:15:15: 3000000 INFO @ Thu, 30 Apr 2015 11:15:19: 4000000 INFO @ Thu, 30 Apr 2015 11:15:21: 4000000 INFO @ Thu, 30 Apr 2015 11:15:21: 4000000 INFO @ Thu, 30 Apr 2015 11:15:24: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:15:24: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:15:24: #1 total tags in treatment: 4851846 INFO @ Thu, 30 Apr 2015 11:15:24: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:15:25: #1 tags after filtering in treatment: 4851579 INFO @ Thu, 30 Apr 2015 11:15:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:25: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:25: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:26: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:15:26: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:15:26: #1 total tags in treatment: 4851846 INFO @ Thu, 30 Apr 2015 11:15:26: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:15:26: #1 tag size is determined as 36 bps INFO @ Thu, 30 Apr 2015 11:15:26: #1 tag size = 36 INFO @ Thu, 30 Apr 2015 11:15:26: #1 total tags in treatment: 4851846 INFO @ Thu, 30 Apr 2015 11:15:26: #1 user defined the maximum tags... INFO @ Thu, 30 Apr 2015 11:15:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 30 Apr 2015 11:15:26: #2 number of paired peaks: 2964 INFO @ Thu, 30 Apr 2015 11:15:26: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:27: #1 tags after filtering in treatment: 4851579 INFO @ Thu, 30 Apr 2015 11:15:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:27: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:27: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:27: #1 tags after filtering in treatment: 4851579 INFO @ Thu, 30 Apr 2015 11:15:27: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 30 Apr 2015 11:15:27: #1 finished! INFO @ Thu, 30 Apr 2015 11:15:27: #2 Build Peak Model... INFO @ Thu, 30 Apr 2015 11:15:28: #2 number of paired peaks: 2964 INFO @ Thu, 30 Apr 2015 11:15:28: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:28: #2 number of paired peaks: 2964 INFO @ Thu, 30 Apr 2015 11:15:28: start model_add_line... INFO @ Thu, 30 Apr 2015 11:15:39: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:39: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:39: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:39: #2 predicted fragment length is 243 bps INFO @ Thu, 30 Apr 2015 11:15:39: #2 alternative fragment length(s) may be 243 bps INFO @ Thu, 30 Apr 2015 11:15:39: #2.2 Generate R script for model : SRX059274.10_model.r INFO @ Thu, 30 Apr 2015 11:15:39: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:15:41: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:41: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:41: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:41: #2 predicted fragment length is 243 bps INFO @ Thu, 30 Apr 2015 11:15:41: #2 alternative fragment length(s) may be 243 bps INFO @ Thu, 30 Apr 2015 11:15:41: #2.2 Generate R script for model : SRX059274.05_model.r INFO @ Thu, 30 Apr 2015 11:15:41: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:15:41: start X-correlation... INFO @ Thu, 30 Apr 2015 11:15:41: end of X-cor INFO @ Thu, 30 Apr 2015 11:15:41: #2 finished! INFO @ Thu, 30 Apr 2015 11:15:41: #2 predicted fragment length is 243 bps INFO @ Thu, 30 Apr 2015 11:15:41: #2 alternative fragment length(s) may be 243 bps INFO @ Thu, 30 Apr 2015 11:15:41: #2.2 Generate R script for model : SRX059274.20_model.r INFO @ Thu, 30 Apr 2015 11:15:41: #3 Call peaks... INFO @ Thu, 30 Apr 2015 11:15:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 30 Apr 2015 11:16:09: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:11: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:13: #3 Call peaks for each chromosome... INFO @ Thu, 30 Apr 2015 11:16:34: #4 Write output xls file... SRX059274.10_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:34: #4 Write peak in narrowPeak format file... SRX059274.10_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:35: #4 Write summits bed file... SRX059274.10_summits.bed INFO @ Thu, 30 Apr 2015 11:16:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3115 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:16:35: #4 Write output xls file... SRX059274.20_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:35: #4 Write peak in narrowPeak format file... SRX059274.20_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:35: #4 Write summits bed file... SRX059274.20_summits.bed INFO @ Thu, 30 Apr 2015 11:16:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2166 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 30 Apr 2015 11:16:41: #4 Write output xls file... SRX059274.05_peaks.xls INFO @ Thu, 30 Apr 2015 11:16:41: #4 Write peak in narrowPeak format file... SRX059274.05_peaks.narrowPeak INFO @ Thu, 30 Apr 2015 11:16:41: #4 Write summits bed file... SRX059274.05_summits.bed INFO @ Thu, 30 Apr 2015 11:16:41: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3899 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。