Job ID = 9029470 sra ファイルのダウンロード中... Completed: 423648K bytes transferred in 6 seconds (524016K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:07 --:--:-- 0 100 30318 0 30318 0 0 3500 0 --:--:-- 0:00:08 --:--:-- 13420 100 54487 0 54487 0 0 5948 0 --:--:-- 0:00:09 --:--:-- 19763 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 12165938 spots for /home/okishinya/chipatlas/results/dm3/SRX1794223/SRR3575258.sra Written 12165938 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: 00:03:56 12165938 reads; of these: 12165938 (100.00%) were unpaired; of these: 459120 (3.77%) aligned 0 times 9929062 (81.61%) aligned exactly 1 time 1777756 (14.61%) aligned >1 times 96.23% overall alignment rate Time searching: 00:03:56 Overall time: 00:03:56 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2697463 / 11706818 = 0.2304 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 13:57:47: # Command line: callpeak -t SRX1794223.bam -f BAM -g dm -n SRX1794223.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794223.20 # format = BAM # ChIP-seq file = ['SRX1794223.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 13:57:47: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:57:47: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:57:47: # Command line: callpeak -t SRX1794223.bam -f BAM -g dm -n SRX1794223.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794223.10 # format = BAM # ChIP-seq file = ['SRX1794223.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 13:57:47: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:57:47: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:57:47: # Command line: callpeak -t SRX1794223.bam -f BAM -g dm -n SRX1794223.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794223.05 # format = BAM # ChIP-seq file = ['SRX1794223.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 13:57:47: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:57:47: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:57:54: 1000000 INFO @ Sat, 03 Jun 2017 13:57:54: 1000000 INFO @ Sat, 03 Jun 2017 13:57:54: 1000000 INFO @ Sat, 03 Jun 2017 13:58:01: 2000000 INFO @ Sat, 03 Jun 2017 13:58:01: 2000000 INFO @ Sat, 03 Jun 2017 13:58:01: 2000000 INFO @ Sat, 03 Jun 2017 13:58:08: 3000000 INFO @ Sat, 03 Jun 2017 13:58:08: 3000000 INFO @ Sat, 03 Jun 2017 13:58:08: 3000000 INFO @ Sat, 03 Jun 2017 13:58:15: 4000000 INFO @ Sat, 03 Jun 2017 13:58:15: 4000000 INFO @ Sat, 03 Jun 2017 13:58:15: 4000000 INFO @ Sat, 03 Jun 2017 13:58:22: 5000000 INFO @ Sat, 03 Jun 2017 13:58:22: 5000000 INFO @ Sat, 03 Jun 2017 13:58:22: 5000000 INFO @ Sat, 03 Jun 2017 13:58:29: 6000000 INFO @ Sat, 03 Jun 2017 13:58:29: 6000000 INFO @ Sat, 03 Jun 2017 13:58:29: 6000000 INFO @ Sat, 03 Jun 2017 13:58:36: 7000000 INFO @ Sat, 03 Jun 2017 13:58:36: 7000000 INFO @ Sat, 03 Jun 2017 13:58:36: 7000000 INFO @ Sat, 03 Jun 2017 13:58:42: 8000000 INFO @ Sat, 03 Jun 2017 13:58:42: 8000000 INFO @ Sat, 03 Jun 2017 13:58:42: 8000000 INFO @ Sat, 03 Jun 2017 13:58:48: 9000000 INFO @ Sat, 03 Jun 2017 13:58:48: 9000000 INFO @ Sat, 03 Jun 2017 13:58:48: 9000000 INFO @ Sat, 03 Jun 2017 13:58:49: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:58:49: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:58:49: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:58:49: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:58:49: #1 total tags in treatment: 9009355 INFO @ Sat, 03 Jun 2017 13:58:49: #1 total tags in treatment: 9009355 INFO @ Sat, 03 Jun 2017 13:58:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:58:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:58:49: #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 13:58:49: #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 13:58:49: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:58:49: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:58:49: #1 total tags in treatment: 9009355 INFO @ Sat, 03 Jun 2017 13:58:49: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:58:49: #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 13:58:50: #1 tags after filtering in treatment: 9006539 INFO @ Sat, 03 Jun 2017 13:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:58:50: #1 finished! INFO @ Sat, 03 Jun 2017 13:58:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:58:50: #1 tags after filtering in treatment: 9006539 INFO @ Sat, 03 Jun 2017 13:58:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:58:50: #1 finished! INFO @ Sat, 03 Jun 2017 13:58:50: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:58:51: #1 tags after filtering in treatment: 9006539 INFO @ Sat, 03 Jun 2017 13:58:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:58:51: #1 finished! INFO @ Sat, 03 Jun 2017 13:58:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:58:53: #2 number of paired peaks: 10931 INFO @ Sat, 03 Jun 2017 13:58:53: start model_add_line... INFO @ Sat, 03 Jun 2017 13:58:53: #2 number of paired peaks: 10931 INFO @ Sat, 03 Jun 2017 13:58:53: start model_add_line... INFO @ Sat, 03 Jun 2017 13:58:55: #2 number of paired peaks: 10931 INFO @ Sat, 03 Jun 2017 13:58:55: start model_add_line... INFO @ Sat, 03 Jun 2017 14:00:15: start X-correlation... INFO @ Sat, 03 Jun 2017 14:00:15: end of X-cor INFO @ Sat, 03 Jun 2017 14:00:15: #2 finished! INFO @ Sat, 03 Jun 2017 14:00:15: #2 predicted fragment length is 169 bps INFO @ Sat, 03 Jun 2017 14:00:15: #2 alternative fragment length(s) may be 169 bps INFO @ Sat, 03 Jun 2017 14:00:15: #2.2 Generate R script for model : SRX1794223.10_model.r INFO @ Sat, 03 Jun 2017 14:00:15: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:00:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:00:16: start X-correlation... INFO @ Sat, 03 Jun 2017 14:00:16: end of X-cor INFO @ Sat, 03 Jun 2017 14:00:16: #2 finished! INFO @ Sat, 03 Jun 2017 14:00:16: #2 predicted fragment length is 169 bps INFO @ Sat, 03 Jun 2017 14:00:16: #2 alternative fragment length(s) may be 169 bps INFO @ Sat, 03 Jun 2017 14:00:16: #2.2 Generate R script for model : SRX1794223.05_model.r INFO @ Sat, 03 Jun 2017 14:00:16: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:00:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:00:18: start X-correlation... INFO @ Sat, 03 Jun 2017 14:00:18: end of X-cor INFO @ Sat, 03 Jun 2017 14:00:18: #2 finished! INFO @ Sat, 03 Jun 2017 14:00:18: #2 predicted fragment length is 169 bps INFO @ Sat, 03 Jun 2017 14:00:18: #2 alternative fragment length(s) may be 169 bps INFO @ Sat, 03 Jun 2017 14:00:18: #2.2 Generate R script for model : SRX1794223.20_model.r INFO @ Sat, 03 Jun 2017 14:00:18: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:00:18: #3 Pre-compute pvalue-qvalue table... 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 14:01:08: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:01:11: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:01:16: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:02:01: #4 Write output xls file... SRX1794223.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:02:01: #4 Write peak in narrowPeak format file... SRX1794223.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:02:01: #4 Write summits bed file... SRX1794223.10_summits.bed INFO @ Sat, 03 Jun 2017 14:02:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8648 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:02:08: #4 Write output xls file... SRX1794223.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:02:08: #4 Write peak in narrowPeak format file... SRX1794223.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:02:08: #4 Write summits bed file... SRX1794223.20_summits.bed INFO @ Sat, 03 Jun 2017 14:02:08: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7645 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:02:10: #4 Write output xls file... SRX1794223.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:02:10: #4 Write peak in narrowPeak format file... SRX1794223.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:02:10: #4 Write summits bed file... SRX1794223.05_summits.bed INFO @ Sat, 03 Jun 2017 14:02:10: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9287 records, 4 fields): 15 millis CompletedMACS2peakCalling