Job ID = 8696838 sra ファイルのダウンロード中... Completed: 774730K bytes transferred in 11 seconds (531342K 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 21815 0 21815 0 0 2652 0 --:--:-- 0:00:08 --:--:-- 14138 100 31432 0 31432 0 0 3742 0 --:--:-- 0:00:08 --:--:-- 18306 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 35884537 spots for /home/okishinya/chipatlas/results/dm3/SRX110776/SRR388358.sra Written 35884537 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: 00:14:23 35884537 reads; of these: 35884537 (100.00%) were unpaired; of these: 14286056 (39.81%) aligned 0 times 17298322 (48.21%) aligned exactly 1 time 4300159 (11.98%) aligned >1 times 60.19% overall alignment rate Time searching: 00:14:23 Overall time: 00:14:23 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] 12488808 / 21598481 = 0.5782 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 @ Fri, 10 Mar 2017 12:27:20: # Command line: callpeak -t SRX110776.bam -f BAM -g dm -n SRX110776.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110776.10 # format = BAM # ChIP-seq file = ['SRX110776.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 @ Fri, 10 Mar 2017 12:27:20: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:27:20: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:27:20: # Command line: callpeak -t SRX110776.bam -f BAM -g dm -n SRX110776.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110776.20 # format = BAM # ChIP-seq file = ['SRX110776.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 @ Fri, 10 Mar 2017 12:27:20: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:27:20: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:27:20: # Command line: callpeak -t SRX110776.bam -f BAM -g dm -n SRX110776.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110776.05 # format = BAM # ChIP-seq file = ['SRX110776.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 @ Fri, 10 Mar 2017 12:27:20: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:27:20: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:27:26: 1000000 INFO @ Fri, 10 Mar 2017 12:27:27: 1000000 INFO @ Fri, 10 Mar 2017 12:27:28: 1000000 INFO @ Fri, 10 Mar 2017 12:27:32: 2000000 INFO @ Fri, 10 Mar 2017 12:27:33: 2000000 INFO @ Fri, 10 Mar 2017 12:27:34: 2000000 INFO @ Fri, 10 Mar 2017 12:27:39: 3000000 INFO @ Fri, 10 Mar 2017 12:27:40: 3000000 INFO @ Fri, 10 Mar 2017 12:27:41: 3000000 INFO @ Fri, 10 Mar 2017 12:27:45: 4000000 INFO @ Fri, 10 Mar 2017 12:27:47: 4000000 INFO @ Fri, 10 Mar 2017 12:27:47: 4000000 INFO @ Fri, 10 Mar 2017 12:27:51: 5000000 INFO @ Fri, 10 Mar 2017 12:27:54: 5000000 INFO @ Fri, 10 Mar 2017 12:27:54: 5000000 INFO @ Fri, 10 Mar 2017 12:27:57: 6000000 INFO @ Fri, 10 Mar 2017 12:28:00: 6000000 INFO @ Fri, 10 Mar 2017 12:28:01: 6000000 INFO @ Fri, 10 Mar 2017 12:28:03: 7000000 INFO @ Fri, 10 Mar 2017 12:28:07: 7000000 INFO @ Fri, 10 Mar 2017 12:28:08: 7000000 INFO @ Fri, 10 Mar 2017 12:28:09: 8000000 INFO @ Fri, 10 Mar 2017 12:28:14: 8000000 INFO @ Fri, 10 Mar 2017 12:28:15: 8000000 INFO @ Fri, 10 Mar 2017 12:28:16: 9000000 INFO @ Fri, 10 Mar 2017 12:28:16: #1 tag size is determined as 36 bps INFO @ Fri, 10 Mar 2017 12:28:16: #1 tag size = 36 INFO @ Fri, 10 Mar 2017 12:28:16: #1 total tags in treatment: 9109673 INFO @ Fri, 10 Mar 2017 12:28:16: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:28:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:28:18: #1 tags after filtering in treatment: 9108292 INFO @ Fri, 10 Mar 2017 12:28:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:28:18: #1 finished! INFO @ Fri, 10 Mar 2017 12:28:18: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:28:21: #2 number of paired peaks: 2937 INFO @ Fri, 10 Mar 2017 12:28:21: start model_add_line... INFO @ Fri, 10 Mar 2017 12:28:21: 9000000 INFO @ Fri, 10 Mar 2017 12:28:22: 9000000 INFO @ Fri, 10 Mar 2017 12:28:22: #1 tag size is determined as 36 bps INFO @ Fri, 10 Mar 2017 12:28:22: #1 tag size = 36 INFO @ Fri, 10 Mar 2017 12:28:22: #1 total tags in treatment: 9109673 INFO @ Fri, 10 Mar 2017 12:28:22: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:28:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:28:23: #1 tag size is determined as 36 bps INFO @ Fri, 10 Mar 2017 12:28:23: #1 tag size = 36 INFO @ Fri, 10 Mar 2017 12:28:23: #1 total tags in treatment: 9109673 INFO @ Fri, 10 Mar 2017 12:28:23: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:28:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:28:24: #1 tags after filtering in treatment: 9108292 INFO @ Fri, 10 Mar 2017 12:28:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:28:24: #1 finished! INFO @ Fri, 10 Mar 2017 12:28:24: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:28:25: #1 tags after filtering in treatment: 9108292 INFO @ Fri, 10 Mar 2017 12:28:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:28:25: #1 finished! INFO @ Fri, 10 Mar 2017 12:28:25: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:28:27: #2 number of paired peaks: 2937 INFO @ Fri, 10 Mar 2017 12:28:27: start model_add_line... INFO @ Fri, 10 Mar 2017 12:28:28: #2 number of paired peaks: 2937 INFO @ Fri, 10 Mar 2017 12:28:28: start model_add_line... INFO @ Fri, 10 Mar 2017 12:28:43: start X-correlation... INFO @ Fri, 10 Mar 2017 12:28:43: end of X-cor INFO @ Fri, 10 Mar 2017 12:28:43: #2 finished! INFO @ Fri, 10 Mar 2017 12:28:43: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Mar 2017 12:28:43: #2 alternative fragment length(s) may be 2,76 bps INFO @ Fri, 10 Mar 2017 12:28:43: #2.2 Generate R script for model : SRX110776.10_model.r INFO @ Fri, 10 Mar 2017 12:28:43: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:28:43: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:28:50: start X-correlation... INFO @ Fri, 10 Mar 2017 12:28:50: end of X-cor INFO @ Fri, 10 Mar 2017 12:28:50: #2 finished! INFO @ Fri, 10 Mar 2017 12:28:50: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Mar 2017 12:28:50: #2 alternative fragment length(s) may be 2,76 bps INFO @ Fri, 10 Mar 2017 12:28:50: #2.2 Generate R script for model : SRX110776.20_model.r INFO @ Fri, 10 Mar 2017 12:28:50: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:28:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:28:51: start X-correlation... INFO @ Fri, 10 Mar 2017 12:28:51: end of X-cor INFO @ Fri, 10 Mar 2017 12:28:51: #2 finished! INFO @ Fri, 10 Mar 2017 12:28:51: #2 predicted fragment length is 76 bps INFO @ Fri, 10 Mar 2017 12:28:51: #2 alternative fragment length(s) may be 2,76 bps INFO @ Fri, 10 Mar 2017 12:28:51: #2.2 Generate R script for model : SRX110776.05_model.r INFO @ Fri, 10 Mar 2017 12:28:51: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:29:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:29:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:29:52: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:30:20: #4 Write output xls file... SRX110776.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:30:20: #4 Write peak in narrowPeak format file... SRX110776.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:30:20: #4 Write summits bed file... SRX110776.10_summits.bed INFO @ Fri, 10 Mar 2017 12:30:20: Done! pass1 - making usageList (12 chroms): 3 millis pass2 - checking and writing primary data (1082 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:30:32: #4 Write output xls file... SRX110776.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:30:32: #4 Write peak in narrowPeak format file... SRX110776.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:30:32: #4 Write summits bed file... SRX110776.20_summits.bed INFO @ Fri, 10 Mar 2017 12:30:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (439 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:30:35: #4 Write output xls file... SRX110776.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:30:35: #4 Write peak in narrowPeak format file... SRX110776.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:30:35: #4 Write summits bed file... SRX110776.05_summits.bed INFO @ Fri, 10 Mar 2017 12:30:35: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2027 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。