Job ID = 2161217 sra ファイルのダウンロード中... Completed: 177266K bytes transferred in 5 seconds (263740K 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 34468 0 34468 0 0 48212 0 --:--:-- --:--:-- --:--:-- 65904 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 7018791 spots for /home/okishinya/chipatlas/results/dm3/SRX013065/SRR030331.sra Written 7018791 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: 00:01:37 7018791 reads; of these: 7018791 (100.00%) were unpaired; of these: 153293 (2.18%) aligned 0 times 6051486 (86.22%) aligned exactly 1 time 814012 (11.60%) aligned >1 times 97.82% overall alignment rate Time searching: 00:01:37 Overall time: 00:01:37 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] 460407 / 6865498 = 0.0671 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 12:07:02: # Command line: callpeak -t SRX013065.bam -f BAM -g dm -n SRX013065.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013065.20 # format = BAM # ChIP-seq file = ['SRX013065.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 12:07:02: # Command line: callpeak -t SRX013065.bam -f BAM -g dm -n SRX013065.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013065.05 # format = BAM # ChIP-seq file = ['SRX013065.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 12:07:02: # Command line: callpeak -t SRX013065.bam -f BAM -g dm -n SRX013065.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013065.10 # format = BAM # ChIP-seq file = ['SRX013065.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 12:07:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:02: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:07:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:02: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:07:09: 1000000 INFO @ Tue, 21 Apr 2015 12:07:09: 1000000 INFO @ Tue, 21 Apr 2015 12:07:09: 1000000 INFO @ Tue, 21 Apr 2015 12:07:15: 2000000 INFO @ Tue, 21 Apr 2015 12:07:15: 2000000 INFO @ Tue, 21 Apr 2015 12:07:17: 2000000 INFO @ Tue, 21 Apr 2015 12:07:21: 3000000 INFO @ Tue, 21 Apr 2015 12:07:21: 3000000 INFO @ Tue, 21 Apr 2015 12:07:24: 3000000 INFO @ Tue, 21 Apr 2015 12:07:27: 4000000 INFO @ Tue, 21 Apr 2015 12:07:27: 4000000 INFO @ Tue, 21 Apr 2015 12:07:32: 4000000 INFO @ Tue, 21 Apr 2015 12:07:33: 5000000 INFO @ Tue, 21 Apr 2015 12:07:33: 5000000 INFO @ Tue, 21 Apr 2015 12:07:39: 6000000 INFO @ Tue, 21 Apr 2015 12:07:39: 6000000 INFO @ Tue, 21 Apr 2015 12:07:39: 5000000 INFO @ Tue, 21 Apr 2015 12:07:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:07:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:07:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:07:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:07:41: #1 total tags in treatment: 6405091 INFO @ Tue, 21 Apr 2015 12:07:41: #1 total tags in treatment: 6405091 INFO @ Tue, 21 Apr 2015 12:07:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:07:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:07:41: #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 12:07:41: #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 12:07:43: #1 tags after filtering in treatment: 6404721 INFO @ Tue, 21 Apr 2015 12:07:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:07:43: #1 tags after filtering in treatment: 6404721 INFO @ Tue, 21 Apr 2015 12:07:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:07:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:07:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:07:43: #1 finished! INFO @ Tue, 21 Apr 2015 12:07:43: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:07:44: #2 number of paired peaks: 2107 INFO @ Tue, 21 Apr 2015 12:07:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:07:44: #2 number of paired peaks: 2107 INFO @ Tue, 21 Apr 2015 12:07:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:07:47: 6000000 INFO @ Tue, 21 Apr 2015 12:07:50: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:07:50: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:07:50: #1 total tags in treatment: 6405091 INFO @ Tue, 21 Apr 2015 12:07:50: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:07:50: #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 12:07:51: #1 tags after filtering in treatment: 6404721 INFO @ Tue, 21 Apr 2015 12:07:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:07:51: #1 finished! INFO @ Tue, 21 Apr 2015 12:07:51: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:07:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:07:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:07:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:07:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:07:51: #2 predicted fragment length is 143 bps INFO @ Tue, 21 Apr 2015 12:07:51: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 21 Apr 2015 12:07:51: #2.2 Generate R script for model : SRX013065.05_model.r INFO @ Tue, 21 Apr 2015 12:07:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:07:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:07:51: #2 predicted fragment length is 143 bps INFO @ Tue, 21 Apr 2015 12:07:51: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 21 Apr 2015 12:07:51: #2.2 Generate R script for model : SRX013065.10_model.r INFO @ Tue, 21 Apr 2015 12:07:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:07:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:07:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:07:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:07:52: #2 number of paired peaks: 2107 INFO @ Tue, 21 Apr 2015 12:07:52: start model_add_line... INFO @ Tue, 21 Apr 2015 12:07:59: start X-correlation... INFO @ Tue, 21 Apr 2015 12:07:59: end of X-cor INFO @ Tue, 21 Apr 2015 12:07:59: #2 finished! INFO @ Tue, 21 Apr 2015 12:07:59: #2 predicted fragment length is 143 bps INFO @ Tue, 21 Apr 2015 12:07:59: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 21 Apr 2015 12:07:59: #2.2 Generate R script for model : SRX013065.20_model.r INFO @ Tue, 21 Apr 2015 12:07:59: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:07:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:08:30: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:08:30: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:08:36: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:09:01: #4 Write output xls file... SRX013065.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:01: #4 Write peak in narrowPeak format file... SRX013065.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:01: #4 Write summits bed file... SRX013065.10_summits.bed INFO @ Tue, 21 Apr 2015 12:09:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4042 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:04: #4 Write output xls file... SRX013065.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:04: #4 Write output xls file... SRX013065.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:09:04: #4 Write peak in narrowPeak format file... SRX013065.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:04: #4 Write peak in narrowPeak format file... SRX013065.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:09:04: #4 Write summits bed file... SRX013065.20_summits.bed INFO @ Tue, 21 Apr 2015 12:09:04: Done! INFO @ Tue, 21 Apr 2015 12:09:04: #4 Write summits bed file... SRX013065.05_summits.bed pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1576 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:09:04: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7166 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。