Job ID = 2161144 sra ファイルのダウンロード中... Completed: 137525K bytes transferred in 4 seconds (229345K 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 34536 0 34536 0 0 50458 0 --:--:-- --:--:-- --:--:-- 70052 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 6986464 spots for /home/okishinya/chipatlas/results/dm3/SRX013025/SRR030291.sra Written 6986464 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: 00:01:33 6986464 reads; of these: 6986464 (100.00%) were unpaired; of these: 186554 (2.67%) aligned 0 times 6218271 (89.00%) aligned exactly 1 time 581639 (8.33%) aligned >1 times 97.33% overall alignment rate Time searching: 00:01:33 Overall time: 00:01:33 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] 436157 / 6799910 = 0.0641 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 @ Tue, 21 Apr 2015 11:59:53: # Command line: callpeak -t SRX013025.bam -f BAM -g dm -n SRX013025.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013025.05 # format = BAM # ChIP-seq file = ['SRX013025.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 @ Tue, 21 Apr 2015 11:59:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:59:53: # Command line: callpeak -t SRX013025.bam -f BAM -g dm -n SRX013025.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013025.10 # format = BAM # ChIP-seq file = ['SRX013025.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 @ Tue, 21 Apr 2015 11:59:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:59:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:59:53: # Command line: callpeak -t SRX013025.bam -f BAM -g dm -n SRX013025.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013025.20 # format = BAM # ChIP-seq file = ['SRX013025.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 @ Tue, 21 Apr 2015 11:59:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:59:53: #1 read tag files... INFO @ Tue, 21 Apr 2015 11:59:53: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 11:59:58: 1000000 INFO @ Tue, 21 Apr 2015 11:59:58: 1000000 INFO @ Tue, 21 Apr 2015 11:59:58: 1000000 INFO @ Tue, 21 Apr 2015 12:00:04: 2000000 INFO @ Tue, 21 Apr 2015 12:00:04: 2000000 INFO @ Tue, 21 Apr 2015 12:00:04: 2000000 INFO @ Tue, 21 Apr 2015 12:00:09: 3000000 INFO @ Tue, 21 Apr 2015 12:00:10: 3000000 INFO @ Tue, 21 Apr 2015 12:00:10: 3000000 INFO @ Tue, 21 Apr 2015 12:00:15: 4000000 INFO @ Tue, 21 Apr 2015 12:00:15: 4000000 INFO @ Tue, 21 Apr 2015 12:00:16: 4000000 INFO @ Tue, 21 Apr 2015 12:00:21: 5000000 INFO @ Tue, 21 Apr 2015 12:00:21: 5000000 INFO @ Tue, 21 Apr 2015 12:00:22: 5000000 INFO @ Tue, 21 Apr 2015 12:00:27: 6000000 INFO @ Tue, 21 Apr 2015 12:00:27: 6000000 INFO @ Tue, 21 Apr 2015 12:00:28: 6000000 INFO @ Tue, 21 Apr 2015 12:00:29: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:00:29: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:00:29: #1 total tags in treatment: 6363753 INFO @ Tue, 21 Apr 2015 12:00:29: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:00:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:00:29: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:00:29: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:00:29: #1 total tags in treatment: 6363753 INFO @ Tue, 21 Apr 2015 12:00:29: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:00:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:00:30: #1 tags after filtering in treatment: 6363471 INFO @ Tue, 21 Apr 2015 12:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:00:30: #1 finished! INFO @ Tue, 21 Apr 2015 12:00:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:00:30: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:00:30: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:00:30: #1 total tags in treatment: 6363753 INFO @ Tue, 21 Apr 2015 12:00:30: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:00:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:00:31: #1 tags after filtering in treatment: 6363471 INFO @ Tue, 21 Apr 2015 12:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:00:31: #1 finished! INFO @ Tue, 21 Apr 2015 12:00:31: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:00:31: #2 number of paired peaks: 1812 INFO @ Tue, 21 Apr 2015 12:00:31: start model_add_line... INFO @ Tue, 21 Apr 2015 12:00:31: #1 tags after filtering in treatment: 6363471 INFO @ Tue, 21 Apr 2015 12:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:00:31: #1 finished! INFO @ Tue, 21 Apr 2015 12:00:31: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:00:32: #2 number of paired peaks: 1812 INFO @ Tue, 21 Apr 2015 12:00:32: start model_add_line... INFO @ Tue, 21 Apr 2015 12:00:33: #2 number of paired peaks: 1812 INFO @ Tue, 21 Apr 2015 12:00:33: start model_add_line... INFO @ Tue, 21 Apr 2015 12:00:37: start X-correlation... INFO @ Tue, 21 Apr 2015 12:00:37: end of X-cor INFO @ Tue, 21 Apr 2015 12:00:37: #2 finished! INFO @ Tue, 21 Apr 2015 12:00:37: #2 predicted fragment length is 184 bps INFO @ Tue, 21 Apr 2015 12:00:37: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 21 Apr 2015 12:00:37: #2.2 Generate R script for model : SRX013025.20_model.r INFO @ Tue, 21 Apr 2015 12:00:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:00:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:00:38: start X-correlation... INFO @ Tue, 21 Apr 2015 12:00:38: end of X-cor INFO @ Tue, 21 Apr 2015 12:00:38: #2 finished! INFO @ Tue, 21 Apr 2015 12:00:38: #2 predicted fragment length is 184 bps INFO @ Tue, 21 Apr 2015 12:00:38: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 21 Apr 2015 12:00:38: #2.2 Generate R script for model : SRX013025.05_model.r INFO @ Tue, 21 Apr 2015 12:00:38: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:00:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:00:39: start X-correlation... INFO @ Tue, 21 Apr 2015 12:00:39: end of X-cor INFO @ Tue, 21 Apr 2015 12:00:39: #2 finished! INFO @ Tue, 21 Apr 2015 12:00:39: #2 predicted fragment length is 184 bps INFO @ Tue, 21 Apr 2015 12:00:39: #2 alternative fragment length(s) may be 184 bps INFO @ Tue, 21 Apr 2015 12:00:39: #2.2 Generate R script for model : SRX013025.10_model.r INFO @ Tue, 21 Apr 2015 12:00:39: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:00:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:01:13: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:01:14: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:01:16: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:01:42: #4 Write output xls file... SRX013025.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:01:42: #4 Write peak in narrowPeak format file... SRX013025.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:01:42: #4 Write summits bed file... SRX013025.20_summits.bed INFO @ Tue, 21 Apr 2015 12:01:42: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1237 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:01:47: #4 Write output xls file... SRX013025.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:01:47: #4 Write peak in narrowPeak format file... SRX013025.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:01:47: #4 Write summits bed file... SRX013025.10_summits.bed INFO @ Tue, 21 Apr 2015 12:01:47: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (4267 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:01:49: #4 Write output xls file... SRX013025.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:01:49: #4 Write peak in narrowPeak format file... SRX013025.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:01:49: #4 Write summits bed file... SRX013025.05_summits.bed INFO @ Tue, 21 Apr 2015 12:01:49: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (8968 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。