Job ID = 2161268 sra ファイルのダウンロード中... Completed: 156873K bytes transferred in 4 seconds (282181K 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 --:--:-- --:--:-- --:--:-- 0 101 2547 0 2547 0 0 5074 0 --:--:-- --:--:-- --:--:-- 8163 100 34738 0 34738 0 0 24837 0 --:--:-- 0:00:01 --:--:-- 28780 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 7423467 spots for /home/okishinya/chipatlas/results/dm3/SRX013112/SRR030378.sra Written 7423467 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: 00:01:28 7423467 reads; of these: 7423467 (100.00%) were unpaired; of these: 526976 (7.10%) aligned 0 times 6384341 (86.00%) aligned exactly 1 time 512150 (6.90%) aligned >1 times 92.90% overall alignment rate Time searching: 00:01:28 Overall time: 00:01:28 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] 613873 / 6896491 = 0.0890 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 12:13:11: # Command line: callpeak -t SRX013112.bam -f BAM -g dm -n SRX013112.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013112.05 # format = BAM # ChIP-seq file = ['SRX013112.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 12:13:11: # Command line: callpeak -t SRX013112.bam -f BAM -g dm -n SRX013112.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013112.10 # format = BAM # ChIP-seq file = ['SRX013112.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 12:13:11: # Command line: callpeak -t SRX013112.bam -f BAM -g dm -n SRX013112.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013112.20 # format = BAM # ChIP-seq file = ['SRX013112.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 12:13:11: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:13:11: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:13:11: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:13:11: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:13:11: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:13:11: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:13:16: 1000000 INFO @ Tue, 21 Apr 2015 12:13:16: 1000000 INFO @ Tue, 21 Apr 2015 12:13:16: 1000000 INFO @ Tue, 21 Apr 2015 12:13:21: 2000000 INFO @ Tue, 21 Apr 2015 12:13:21: 2000000 INFO @ Tue, 21 Apr 2015 12:13:21: 2000000 INFO @ Tue, 21 Apr 2015 12:13:26: 3000000 INFO @ Tue, 21 Apr 2015 12:13:26: 3000000 INFO @ Tue, 21 Apr 2015 12:13:26: 3000000 INFO @ Tue, 21 Apr 2015 12:13:31: 4000000 INFO @ Tue, 21 Apr 2015 12:13:31: 4000000 INFO @ Tue, 21 Apr 2015 12:13:31: 4000000 INFO @ Tue, 21 Apr 2015 12:13:36: 5000000 INFO @ Tue, 21 Apr 2015 12:13:36: 5000000 INFO @ Tue, 21 Apr 2015 12:13:36: 5000000 INFO @ Tue, 21 Apr 2015 12:13:41: 6000000 INFO @ Tue, 21 Apr 2015 12:13:41: 6000000 INFO @ Tue, 21 Apr 2015 12:13:41: 6000000 INFO @ Tue, 21 Apr 2015 12:13:42: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:13:42: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:13:42: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:13:42: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:13:42: #1 total tags in treatment: 6282618 INFO @ Tue, 21 Apr 2015 12:13:42: #1 total tags in treatment: 6282618 INFO @ Tue, 21 Apr 2015 12:13:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:13:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:13:42: #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 12:13:42: #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 12:13:42: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:13:42: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:13:42: #1 total tags in treatment: 6282618 INFO @ Tue, 21 Apr 2015 12:13:42: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:13:42: #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 12:13:43: #1 tags after filtering in treatment: 6282260 INFO @ Tue, 21 Apr 2015 12:13:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:13:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:13:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:13:44: #1 tags after filtering in treatment: 6282260 INFO @ Tue, 21 Apr 2015 12:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:13:44: #1 finished! INFO @ Tue, 21 Apr 2015 12:13:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:13:44: #1 tags after filtering in treatment: 6282260 INFO @ Tue, 21 Apr 2015 12:13:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:13:44: #1 finished! INFO @ Tue, 21 Apr 2015 12:13:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:13:45: #2 number of paired peaks: 965 WARNING @ Tue, 21 Apr 2015 12:13:45: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Tue, 21 Apr 2015 12:13:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:13:45: #2 number of paired peaks: 965 WARNING @ Tue, 21 Apr 2015 12:13:45: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Tue, 21 Apr 2015 12:13:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:13:45: #2 number of paired peaks: 965 WARNING @ Tue, 21 Apr 2015 12:13:45: Fewer paired peaks (965) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 965 pairs to build model! INFO @ Tue, 21 Apr 2015 12:13:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:13:48: start X-correlation... INFO @ Tue, 21 Apr 2015 12:13:48: end of X-cor INFO @ Tue, 21 Apr 2015 12:13:48: #2 finished! INFO @ Tue, 21 Apr 2015 12:13:48: #2 predicted fragment length is 162 bps INFO @ Tue, 21 Apr 2015 12:13:48: #2 alternative fragment length(s) may be 162,598 bps INFO @ Tue, 21 Apr 2015 12:13:48: #2.2 Generate R script for model : SRX013112.05_model.r INFO @ Tue, 21 Apr 2015 12:13:48: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:13:48: start X-correlation... INFO @ Tue, 21 Apr 2015 12:13:48: end of X-cor INFO @ Tue, 21 Apr 2015 12:13:48: #2 finished! INFO @ Tue, 21 Apr 2015 12:13:48: #2 predicted fragment length is 162 bps INFO @ Tue, 21 Apr 2015 12:13:48: #2 alternative fragment length(s) may be 162,598 bps INFO @ Tue, 21 Apr 2015 12:13:48: #2.2 Generate R script for model : SRX013112.20_model.r INFO @ Tue, 21 Apr 2015 12:13:48: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:13:48: start X-correlation... INFO @ Tue, 21 Apr 2015 12:13:48: end of X-cor INFO @ Tue, 21 Apr 2015 12:13:48: #2 finished! INFO @ Tue, 21 Apr 2015 12:13:48: #2 predicted fragment length is 162 bps INFO @ Tue, 21 Apr 2015 12:13:48: #2 alternative fragment length(s) may be 162,598 bps INFO @ Tue, 21 Apr 2015 12:13:48: #2.2 Generate R script for model : SRX013112.10_model.r INFO @ Tue, 21 Apr 2015 12:13:48: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:13:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:14:24: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:14:25: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:14:27: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:14:51: #4 Write output xls file... SRX013112.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:14:51: #4 Write peak in narrowPeak format file... SRX013112.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:14:51: #4 Write summits bed file... SRX013112.20_summits.bed INFO @ Tue, 21 Apr 2015 12:14:51: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (449 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:14:55: #4 Write output xls file... SRX013112.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:14:55: #4 Write peak in narrowPeak format file... SRX013112.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:14:55: #4 Write summits bed file... SRX013112.05_summits.bed INFO @ Tue, 21 Apr 2015 12:14:55: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5183 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:14:56: #4 Write output xls file... SRX013112.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:14:56: #4 Write peak in narrowPeak format file... SRX013112.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:14:56: #4 Write summits bed file... SRX013112.10_summits.bed INFO @ Tue, 21 Apr 2015 12:14:56: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (2065 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。