Job ID = 2161242 sra ファイルのダウンロード中... Completed: 95972K bytes transferred in 4 seconds (165016K 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 14904 0 14904 0 0 20252 0 --:--:-- --:--:-- --:--:-- 27346 100 34637 0 34637 0 0 47014 0 --:--:-- --:--:-- --:--:-- 63437 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 4024334 spots for /home/okishinya/chipatlas/results/dm3/SRX013089/SRR030355.sra Written 4024334 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: 00:01:00 4024334 reads; of these: 4024334 (100.00%) were unpaired; of these: 159579 (3.97%) aligned 0 times 3233333 (80.34%) aligned exactly 1 time 631422 (15.69%) aligned >1 times 96.03% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 209040 / 3864755 = 0.0541 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 12:08:15: # Command line: callpeak -t SRX013089.bam -f BAM -g dm -n SRX013089.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013089.10 # format = BAM # ChIP-seq file = ['SRX013089.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 12:08:15: # Command line: callpeak -t SRX013089.bam -f BAM -g dm -n SRX013089.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013089.20 # format = BAM # ChIP-seq file = ['SRX013089.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 12:08:15: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:15: # Command line: callpeak -t SRX013089.bam -f BAM -g dm -n SRX013089.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013089.05 # format = BAM # ChIP-seq file = ['SRX013089.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 12:08:15: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:15: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:15: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:15: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:15: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:20: 1000000 INFO @ Tue, 21 Apr 2015 12:08:21: 1000000 INFO @ Tue, 21 Apr 2015 12:08:21: 1000000 INFO @ Tue, 21 Apr 2015 12:08:26: 2000000 INFO @ Tue, 21 Apr 2015 12:08:26: 2000000 INFO @ Tue, 21 Apr 2015 12:08:26: 2000000 INFO @ Tue, 21 Apr 2015 12:08:31: 3000000 INFO @ Tue, 21 Apr 2015 12:08:32: 3000000 INFO @ Tue, 21 Apr 2015 12:08:32: 3000000 INFO @ Tue, 21 Apr 2015 12:08:34: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:34: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:34: #1 total tags in treatment: 3655715 INFO @ Tue, 21 Apr 2015 12:08:34: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:34: #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 12:08:35: #1 tags after filtering in treatment: 3655643 INFO @ Tue, 21 Apr 2015 12:08:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:35: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:35: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:35: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:35: #1 total tags in treatment: 3655715 INFO @ Tue, 21 Apr 2015 12:08:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:35: #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 12:08:35: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:08:35: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:08:35: #1 total tags in treatment: 3655715 INFO @ Tue, 21 Apr 2015 12:08:35: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:08:35: #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 12:08:36: #2 number of paired peaks: 2283 INFO @ Tue, 21 Apr 2015 12:08:36: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:36: #1 tags after filtering in treatment: 3655643 INFO @ Tue, 21 Apr 2015 12:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:36: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:36: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:36: #1 tags after filtering in treatment: 3655643 INFO @ Tue, 21 Apr 2015 12:08:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:08:36: #1 finished! INFO @ Tue, 21 Apr 2015 12:08:36: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:08:37: #2 number of paired peaks: 2283 INFO @ Tue, 21 Apr 2015 12:08:37: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:37: #2 number of paired peaks: 2283 INFO @ Tue, 21 Apr 2015 12:08:37: start model_add_line... INFO @ Tue, 21 Apr 2015 12:08:41: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:41: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:41: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:41: #2 predicted fragment length is 167 bps INFO @ Tue, 21 Apr 2015 12:08:41: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 21 Apr 2015 12:08:41: #2.2 Generate R script for model : SRX013089.10_model.r INFO @ Tue, 21 Apr 2015 12:08:41: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:42: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:42: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:42: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:42: #2 predicted fragment length is 167 bps INFO @ Tue, 21 Apr 2015 12:08:42: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 21 Apr 2015 12:08:42: #2.2 Generate R script for model : SRX013089.20_model.r INFO @ Tue, 21 Apr 2015 12:08:42: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:42: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:43: start X-correlation... INFO @ Tue, 21 Apr 2015 12:08:43: end of X-cor INFO @ Tue, 21 Apr 2015 12:08:43: #2 finished! INFO @ Tue, 21 Apr 2015 12:08:43: #2 predicted fragment length is 167 bps INFO @ Tue, 21 Apr 2015 12:08:43: #2 alternative fragment length(s) may be 167 bps INFO @ Tue, 21 Apr 2015 12:08:43: #2.2 Generate R script for model : SRX013089.05_model.r INFO @ Tue, 21 Apr 2015 12:08:43: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:03: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:06: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:19: #4 Write output xls file... SRX013089.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:19: #4 Write peak in narrowPeak format file... SRX013089.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:19: #4 Write summits bed file... SRX013089.10_summits.bed INFO @ Tue, 21 Apr 2015 12:09:19: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (463 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:20: #4 Write output xls file... SRX013089.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:20: #4 Write peak in narrowPeak format file... SRX013089.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:20: #4 Write summits bed file... SRX013089.20_summits.bed INFO @ Tue, 21 Apr 2015 12:09:20: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (138 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:23: #4 Write output xls file... SRX013089.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:23: #4 Write peak in narrowPeak format file... SRX013089.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:23: #4 Write summits bed file... SRX013089.05_summits.bed INFO @ Tue, 21 Apr 2015 12:09:23: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1398 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。