Job ID = 8696830 sra ファイルのダウンロード中... Completed: 282836K bytes transferred in 26 seconds (87383K 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 4007 0 4007 0 0 524 0 --:--:-- 0:00:07 --:--:-- 3561 100 27607 0 27607 0 0 3116 0 --:--:-- 0:00:08 --:--:-- 11767 100 31494 0 31494 0 0 3554 0 --:--:-- 0:00:08 --:--:-- 13418 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 25206372 spots for /home/okishinya/chipatlas/results/dm3/SRX110768/SRR388350.sra Written 25206372 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: 00:23:10 25206372 reads; of these: 25206372 (100.00%) were unpaired; of these: 3877523 (15.38%) aligned 0 times 12669352 (50.26%) aligned exactly 1 time 8659497 (34.35%) aligned >1 times 84.62% overall alignment rate Time searching: 00:23:10 Overall time: 00:23:11 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] 13599296 / 21328849 = 0.6376 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 12:27:07: # Command line: callpeak -t SRX110768.bam -f BAM -g dm -n SRX110768.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110768.10 # format = BAM # ChIP-seq file = ['SRX110768.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 12:27:07: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:27:07: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:27:07: # Command line: callpeak -t SRX110768.bam -f BAM -g dm -n SRX110768.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110768.20 # format = BAM # ChIP-seq file = ['SRX110768.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 12:27:07: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:27:07: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:27:07: # Command line: callpeak -t SRX110768.bam -f BAM -g dm -n SRX110768.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110768.05 # format = BAM # ChIP-seq file = ['SRX110768.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 12:27:07: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:27:07: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:27:13: 1000000 INFO @ Fri, 10 Mar 2017 12:27:15: 1000000 INFO @ Fri, 10 Mar 2017 12:27:19: 2000000 INFO @ Fri, 10 Mar 2017 12:27:22: 1000000 INFO @ Fri, 10 Mar 2017 12:27:24: 2000000 INFO @ Fri, 10 Mar 2017 12:27:25: 3000000 INFO @ Fri, 10 Mar 2017 12:27:31: 4000000 INFO @ Fri, 10 Mar 2017 12:27:33: 3000000 INFO @ Fri, 10 Mar 2017 12:27:34: 2000000 INFO @ Fri, 10 Mar 2017 12:27:37: 5000000 INFO @ Fri, 10 Mar 2017 12:27:41: 4000000 INFO @ Fri, 10 Mar 2017 12:27:43: 6000000 INFO @ Fri, 10 Mar 2017 12:27:48: 3000000 INFO @ Fri, 10 Mar 2017 12:27:50: 7000000 INFO @ Fri, 10 Mar 2017 12:27:52: 5000000 INFO @ Fri, 10 Mar 2017 12:27:55: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:27:55: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:27:55: #1 total tags in treatment: 7729553 INFO @ Fri, 10 Mar 2017 12:27:55: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:27:55: #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 12:27:57: #1 tags after filtering in treatment: 7729553 INFO @ Fri, 10 Mar 2017 12:27:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:27:57: #1 finished! INFO @ Fri, 10 Mar 2017 12:27:57: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:27:59: #2 number of paired peaks: 5231 INFO @ Fri, 10 Mar 2017 12:27:59: start model_add_line... INFO @ Fri, 10 Mar 2017 12:28:02: 4000000 INFO @ Fri, 10 Mar 2017 12:28:03: 6000000 INFO @ Fri, 10 Mar 2017 12:28:12: 7000000 INFO @ Fri, 10 Mar 2017 12:28:15: 5000000 INFO @ Fri, 10 Mar 2017 12:28:17: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:28:17: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:28:17: #1 total tags in treatment: 7729553 INFO @ Fri, 10 Mar 2017 12:28:17: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:28:17: #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 12:28:19: #1 tags after filtering in treatment: 7729553 INFO @ Fri, 10 Mar 2017 12:28:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:28:19: #1 finished! INFO @ Fri, 10 Mar 2017 12:28:19: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:28:21: #2 number of paired peaks: 5231 INFO @ Fri, 10 Mar 2017 12:28:21: start model_add_line... INFO @ Fri, 10 Mar 2017 12:28:25: 6000000 INFO @ Fri, 10 Mar 2017 12:28:32: start X-correlation... INFO @ Fri, 10 Mar 2017 12:28:32: end of X-cor INFO @ Fri, 10 Mar 2017 12:28:32: #2 finished! INFO @ Fri, 10 Mar 2017 12:28:32: #2 predicted fragment length is 75 bps INFO @ Fri, 10 Mar 2017 12:28:32: #2 alternative fragment length(s) may be 75 bps INFO @ Fri, 10 Mar 2017 12:28:32: #2.2 Generate R script for model : SRX110768.20_model.r INFO @ Fri, 10 Mar 2017 12:28:32: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:28:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:28:33: 7000000 INFO @ Fri, 10 Mar 2017 12:28:39: #1 tag size is determined as 18 bps INFO @ Fri, 10 Mar 2017 12:28:39: #1 tag size = 18 INFO @ Fri, 10 Mar 2017 12:28:39: #1 total tags in treatment: 7729553 INFO @ Fri, 10 Mar 2017 12:28:39: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:28:39: #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 12:28:40: #1 tags after filtering in treatment: 7729553 INFO @ Fri, 10 Mar 2017 12:28:40: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:28:40: #1 finished! INFO @ Fri, 10 Mar 2017 12:28:40: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:28:43: #2 number of paired peaks: 5231 INFO @ Fri, 10 Mar 2017 12:28:43: start model_add_line... INFO @ Fri, 10 Mar 2017 12:28:54: start X-correlation... INFO @ Fri, 10 Mar 2017 12:28:54: end of X-cor INFO @ Fri, 10 Mar 2017 12:28:54: #2 finished! INFO @ Fri, 10 Mar 2017 12:28:54: #2 predicted fragment length is 75 bps INFO @ Fri, 10 Mar 2017 12:28:54: #2 alternative fragment length(s) may be 75 bps INFO @ Fri, 10 Mar 2017 12:28:54: #2.2 Generate R script for model : SRX110768.10_model.r INFO @ Fri, 10 Mar 2017 12:28:54: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:28:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:29:25: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:29:26: start X-correlation... INFO @ Fri, 10 Mar 2017 12:29:26: end of X-cor INFO @ Fri, 10 Mar 2017 12:29:26: #2 finished! INFO @ Fri, 10 Mar 2017 12:29:26: #2 predicted fragment length is 75 bps INFO @ Fri, 10 Mar 2017 12:29:26: #2 alternative fragment length(s) may be 75 bps INFO @ Fri, 10 Mar 2017 12:29:26: #2.2 Generate R script for model : SRX110768.05_model.r INFO @ Fri, 10 Mar 2017 12:29:26: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:29:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:29:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:30:05: #4 Write output xls file... SRX110768.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:30:05: #4 Write peak in narrowPeak format file... SRX110768.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:30:05: #4 Write summits bed file... SRX110768.20_summits.bed INFO @ Fri, 10 Mar 2017 12:30:05: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6055 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:30:24: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:30:28: #4 Write output xls file... SRX110768.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:30:28: #4 Write peak in narrowPeak format file... SRX110768.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:30:28: #4 Write summits bed file... SRX110768.10_summits.bed INFO @ Fri, 10 Mar 2017 12:30:28: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8280 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:31:15: #4 Write output xls file... SRX110768.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:31:15: #4 Write peak in narrowPeak format file... SRX110768.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:31:15: #4 Write summits bed file... SRX110768.05_summits.bed INFO @ Fri, 10 Mar 2017 12:31:15: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (10653 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。