Job ID = 2161292 sra ファイルのダウンロード中... Completed: 166108K bytes transferred in 5 seconds (269977K bits/sec), in 2 files, 3 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 33437 0 33437 0 0 44168 0 --:--:-- --:--:-- --:--:-- 59075 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 3884614 spots for /home/okishinya/chipatlas/results/dm3/SRX016158/SRR034720.sra Written 3884614 spots total Written 4020166 spots for /home/okishinya/chipatlas/results/dm3/SRX016158/SRR034721.sra Written 4020166 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:01:56 7904780 reads; of these: 7904780 (100.00%) were unpaired; of these: 856626 (10.84%) aligned 0 times 5819479 (73.62%) aligned exactly 1 time 1228675 (15.54%) aligned >1 times 89.16% overall alignment rate Time searching: 00:01:57 Overall time: 00:01:57 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] 2174455 / 7048154 = 0.3085 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 12:16:28: # Command line: callpeak -t SRX016158.bam -f BAM -g dm -n SRX016158.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX016158.05 # format = BAM # ChIP-seq file = ['SRX016158.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 12:16:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:28: # Command line: callpeak -t SRX016158.bam -f BAM -g dm -n SRX016158.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX016158.10 # format = BAM # ChIP-seq file = ['SRX016158.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 12:16:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:28: # Command line: callpeak -t SRX016158.bam -f BAM -g dm -n SRX016158.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX016158.20 # format = BAM # ChIP-seq file = ['SRX016158.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 12:16:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:28: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:16:28: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:16:33: 1000000 INFO @ Tue, 21 Apr 2015 12:16:33: 1000000 INFO @ Tue, 21 Apr 2015 12:16:33: 1000000 INFO @ Tue, 21 Apr 2015 12:16:38: 2000000 INFO @ Tue, 21 Apr 2015 12:16:38: 2000000 INFO @ Tue, 21 Apr 2015 12:16:38: 2000000 INFO @ Tue, 21 Apr 2015 12:16:44: 3000000 INFO @ Tue, 21 Apr 2015 12:16:44: 3000000 INFO @ Tue, 21 Apr 2015 12:16:44: 3000000 INFO @ Tue, 21 Apr 2015 12:16:50: 4000000 INFO @ Tue, 21 Apr 2015 12:16:51: 4000000 INFO @ Tue, 21 Apr 2015 12:16:51: 4000000 INFO @ Tue, 21 Apr 2015 12:16:55: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:16:55: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:16:55: #1 total tags in treatment: 4873699 INFO @ Tue, 21 Apr 2015 12:16:55: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:16:55: #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 12:16:55: #1 tags after filtering in treatment: 4873425 INFO @ Tue, 21 Apr 2015 12:16:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:16:55: #1 finished! INFO @ Tue, 21 Apr 2015 12:16:55: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:16:56: #2 number of paired peaks: 1771 INFO @ Tue, 21 Apr 2015 12:16:56: start model_add_line... INFO @ Tue, 21 Apr 2015 12:16:57: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:16:57: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:16:57: #1 total tags in treatment: 4873699 INFO @ Tue, 21 Apr 2015 12:16:57: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:16:57: #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 12:16:57: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:16:57: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:16:57: #1 total tags in treatment: 4873699 INFO @ Tue, 21 Apr 2015 12:16:57: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:16:57: #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 12:16:58: #1 tags after filtering in treatment: 4873425 INFO @ Tue, 21 Apr 2015 12:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:16:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:16:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:16:58: #1 tags after filtering in treatment: 4873425 INFO @ Tue, 21 Apr 2015 12:16:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:16:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:16:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:16:59: #2 number of paired peaks: 1771 INFO @ Tue, 21 Apr 2015 12:16:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:16:59: #2 number of paired peaks: 1771 INFO @ Tue, 21 Apr 2015 12:16:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:17:04: start X-correlation... INFO @ Tue, 21 Apr 2015 12:17:04: end of X-cor INFO @ Tue, 21 Apr 2015 12:17:04: #2 finished! INFO @ Tue, 21 Apr 2015 12:17:04: #2 predicted fragment length is 152 bps INFO @ Tue, 21 Apr 2015 12:17:04: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 21 Apr 2015 12:17:04: #2.2 Generate R script for model : SRX016158.20_model.r INFO @ Tue, 21 Apr 2015 12:17:04: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:17:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:17:06: start X-correlation... INFO @ Tue, 21 Apr 2015 12:17:06: end of X-cor INFO @ Tue, 21 Apr 2015 12:17:06: #2 finished! INFO @ Tue, 21 Apr 2015 12:17:06: #2 predicted fragment length is 152 bps INFO @ Tue, 21 Apr 2015 12:17:06: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 21 Apr 2015 12:17:06: #2.2 Generate R script for model : SRX016158.05_model.r INFO @ Tue, 21 Apr 2015 12:17:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:17:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:17:06: start X-correlation... INFO @ Tue, 21 Apr 2015 12:17:06: end of X-cor INFO @ Tue, 21 Apr 2015 12:17:06: #2 finished! INFO @ Tue, 21 Apr 2015 12:17:06: #2 predicted fragment length is 152 bps INFO @ Tue, 21 Apr 2015 12:17:06: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 21 Apr 2015 12:17:06: #2.2 Generate R script for model : SRX016158.10_model.r INFO @ Tue, 21 Apr 2015 12:17:06: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:17:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:17:34: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:17:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:17:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:17:57: #4 Write output xls file... SRX016158.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:17:57: #4 Write peak in narrowPeak format file... SRX016158.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:17:57: #4 Write summits bed file... SRX016158.20_summits.bed INFO @ Tue, 21 Apr 2015 12:17:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2037 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:17:59: #4 Write output xls file... SRX016158.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:17:59: #4 Write peak in narrowPeak format file... SRX016158.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:17:59: #4 Write summits bed file... SRX016158.10_summits.bed INFO @ Tue, 21 Apr 2015 12:17:59: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3022 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:18:00: #4 Write output xls file... SRX016158.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:18:00: #4 Write peak in narrowPeak format file... SRX016158.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:18:00: #4 Write summits bed file... SRX016158.05_summits.bed INFO @ Tue, 21 Apr 2015 12:18:00: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4304 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。