Job ID = 9029497 sra ファイルのダウンロード中... Completed: 330953K bytes transferred in 5 seconds (483862K 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 --:--:-- 0:00:06 --:--:-- 0 100 14324 0 14324 0 0 1937 0 --:--:-- 0:00:07 --:--:-- 14381 100 38318 0 38318 0 0 4567 0 --:--:-- 0:00:08 --:--:-- 19235 100 54975 0 54975 0 0 6185 0 --:--:-- 0:00:08 --:--:-- 22087 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 9505267 spots for /home/okishinya/chipatlas/results/dm3/SRX1794251/SRR3575295.sra Written 9505267 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: 00:03:00 9505267 reads; of these: 9505267 (100.00%) were unpaired; of these: 488537 (5.14%) aligned 0 times 7391967 (77.77%) aligned exactly 1 time 1624763 (17.09%) aligned >1 times 94.86% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 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] 900342 / 9016730 = 0.0999 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 @ Sat, 03 Jun 2017 14:01:13: # Command line: callpeak -t SRX1794251.bam -f BAM -g dm -n SRX1794251.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794251.05 # format = BAM # ChIP-seq file = ['SRX1794251.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 @ Sat, 03 Jun 2017 14:01:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:01:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:13: # Command line: callpeak -t SRX1794251.bam -f BAM -g dm -n SRX1794251.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794251.20 # format = BAM # ChIP-seq file = ['SRX1794251.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 @ Sat, 03 Jun 2017 14:01:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:01:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:13: # Command line: callpeak -t SRX1794251.bam -f BAM -g dm -n SRX1794251.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794251.10 # format = BAM # ChIP-seq file = ['SRX1794251.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 @ Sat, 03 Jun 2017 14:01:13: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:01:13: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:18: 1000000 INFO @ Sat, 03 Jun 2017 14:01:19: 1000000 INFO @ Sat, 03 Jun 2017 14:01:19: 1000000 INFO @ Sat, 03 Jun 2017 14:01:24: 2000000 INFO @ Sat, 03 Jun 2017 14:01:25: 2000000 INFO @ Sat, 03 Jun 2017 14:01:25: 2000000 INFO @ Sat, 03 Jun 2017 14:01:31: 3000000 INFO @ Sat, 03 Jun 2017 14:01:32: 3000000 INFO @ Sat, 03 Jun 2017 14:01:32: 3000000 INFO @ Sat, 03 Jun 2017 14:01:37: 4000000 INFO @ Sat, 03 Jun 2017 14:01:38: 4000000 INFO @ Sat, 03 Jun 2017 14:01:38: 4000000 INFO @ Sat, 03 Jun 2017 14:01:45: 5000000 INFO @ Sat, 03 Jun 2017 14:01:45: 5000000 INFO @ Sat, 03 Jun 2017 14:01:45: 5000000 INFO @ Sat, 03 Jun 2017 14:01:51: 6000000 INFO @ Sat, 03 Jun 2017 14:01:51: 6000000 INFO @ Sat, 03 Jun 2017 14:01:52: 6000000 INFO @ Sat, 03 Jun 2017 14:01:58: 7000000 INFO @ Sat, 03 Jun 2017 14:01:58: 7000000 INFO @ Sat, 03 Jun 2017 14:01:59: 7000000 INFO @ Sat, 03 Jun 2017 14:02:05: 8000000 INFO @ Sat, 03 Jun 2017 14:02:05: 8000000 INFO @ Sat, 03 Jun 2017 14:02:06: 8000000 INFO @ Sat, 03 Jun 2017 14:02:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:02:06: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:02:06: #1 total tags in treatment: 8116388 INFO @ Sat, 03 Jun 2017 14:02:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:02:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:02:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:02:06: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:02:06: #1 total tags in treatment: 8116388 INFO @ Sat, 03 Jun 2017 14:02:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:02:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:02:06: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:02:06: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:02:06: #1 total tags in treatment: 8116388 INFO @ Sat, 03 Jun 2017 14:02:06: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:02:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 14:02:07: #1 tags after filtering in treatment: 8114851 INFO @ Sat, 03 Jun 2017 14:02:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:02:07: #1 finished! INFO @ Sat, 03 Jun 2017 14:02:07: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:02:08: #1 tags after filtering in treatment: 8114851 INFO @ Sat, 03 Jun 2017 14:02:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:02:08: #1 finished! INFO @ Sat, 03 Jun 2017 14:02:08: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:02:08: #1 tags after filtering in treatment: 8114851 INFO @ Sat, 03 Jun 2017 14:02:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:02:08: #1 finished! INFO @ Sat, 03 Jun 2017 14:02:08: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:02:10: #2 number of paired peaks: 8866 INFO @ Sat, 03 Jun 2017 14:02:10: start model_add_line... INFO @ Sat, 03 Jun 2017 14:02:10: #2 number of paired peaks: 8866 INFO @ Sat, 03 Jun 2017 14:02:10: start model_add_line... INFO @ Sat, 03 Jun 2017 14:02:10: #2 number of paired peaks: 8866 INFO @ Sat, 03 Jun 2017 14:02:10: start model_add_line... INFO @ Sat, 03 Jun 2017 14:02:58: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:58: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:58: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:58: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 14:02:58: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 03 Jun 2017 14:02:58: #2.2 Generate R script for model : SRX1794251.05_model.r INFO @ Sat, 03 Jun 2017 14:02:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:59: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:59: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:59: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:59: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 14:02:59: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 03 Jun 2017 14:02:59: #2.2 Generate R script for model : SRX1794251.20_model.r INFO @ Sat, 03 Jun 2017 14:02:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:59: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:59: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:59: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:59: #2 predicted fragment length is 171 bps INFO @ Sat, 03 Jun 2017 14:02:59: #2 alternative fragment length(s) may be 171 bps INFO @ Sat, 03 Jun 2017 14:02:59: #2.2 Generate R script for model : SRX1794251.10_model.r INFO @ Sat, 03 Jun 2017 14:02:59: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:03:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:50: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:51: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 14:04:31: #4 Write output xls file... SRX1794251.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:31: #4 Write peak in narrowPeak format file... SRX1794251.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:31: #4 Write summits bed file... SRX1794251.10_summits.bed INFO @ Sat, 03 Jun 2017 14:04:31: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7726 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:31: #4 Write output xls file... SRX1794251.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:31: #4 Write peak in narrowPeak format file... SRX1794251.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:31: #4 Write summits bed file... SRX1794251.20_summits.bed INFO @ Sat, 03 Jun 2017 14:04:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4198 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:40: #4 Write output xls file... SRX1794251.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:40: #4 Write peak in narrowPeak format file... SRX1794251.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:40: #4 Write summits bed file... SRX1794251.05_summits.bed INFO @ Sat, 03 Jun 2017 14:04:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9990 records, 4 fields): 13 millis CompletedMACS2peakCalling