Job ID = 9029579 sra ファイルのダウンロード中... Completed: 664776K bytes transferred in 10 seconds (502757K 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 7663 0 7663 0 0 1082 0 --:--:-- 0:00:07 --:--:-- 10947 100 38933 0 38933 0 0 4819 0 --:--:-- 0:00:08 --:--:-- 22942 100 98k 0 98k 0 0 11368 0 --:--:-- 0:00:08 --:--:-- 40077 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 19949999 spots for /home/okishinya/chipatlas/results/dm3/SRX1848132/SRR3671295.sra Written 19949999 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: 00:06:26 19949999 reads; of these: 19949999 (100.00%) were unpaired; of these: 2953738 (14.81%) aligned 0 times 14112719 (70.74%) aligned exactly 1 time 2883542 (14.45%) aligned >1 times 85.19% overall alignment rate Time searching: 00:06:26 Overall time: 00:06:26 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] 9918570 / 16996261 = 0.5836 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 14:24:03: # Command line: callpeak -t SRX1848132.bam -f BAM -g dm -n SRX1848132.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1848132.20 # format = BAM # ChIP-seq file = ['SRX1848132.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 14:24:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:24:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:24:03: # Command line: callpeak -t SRX1848132.bam -f BAM -g dm -n SRX1848132.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1848132.10 # format = BAM # ChIP-seq file = ['SRX1848132.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 14:24:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:24:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:24:03: # Command line: callpeak -t SRX1848132.bam -f BAM -g dm -n SRX1848132.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1848132.05 # format = BAM # ChIP-seq file = ['SRX1848132.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 14:24:03: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:24:03: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:24:10: 1000000 INFO @ Sat, 03 Jun 2017 14:24:10: 1000000 INFO @ Sat, 03 Jun 2017 14:24:10: 1000000 INFO @ Sat, 03 Jun 2017 14:24:16: 2000000 INFO @ Sat, 03 Jun 2017 14:24:17: 2000000 INFO @ Sat, 03 Jun 2017 14:24:17: 2000000 INFO @ Sat, 03 Jun 2017 14:24:23: 3000000 INFO @ Sat, 03 Jun 2017 14:24:23: 3000000 INFO @ Sat, 03 Jun 2017 14:24:23: 3000000 INFO @ Sat, 03 Jun 2017 14:24:29: 4000000 INFO @ Sat, 03 Jun 2017 14:24:30: 4000000 INFO @ Sat, 03 Jun 2017 14:24:30: 4000000 INFO @ Sat, 03 Jun 2017 14:24:35: 5000000 INFO @ Sat, 03 Jun 2017 14:24:37: 5000000 INFO @ Sat, 03 Jun 2017 14:24:37: 5000000 INFO @ Sat, 03 Jun 2017 14:24:41: 6000000 INFO @ Sat, 03 Jun 2017 14:24:43: 6000000 INFO @ Sat, 03 Jun 2017 14:24:43: 6000000 INFO @ Sat, 03 Jun 2017 14:24:47: 7000000 INFO @ Sat, 03 Jun 2017 14:24:48: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:24:48: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:24:48: #1 total tags in treatment: 7077691 INFO @ Sat, 03 Jun 2017 14:24:48: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:24:48: #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 14:24:49: #1 tags after filtering in treatment: 7072931 INFO @ Sat, 03 Jun 2017 14:24:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:24:49: #1 finished! INFO @ Sat, 03 Jun 2017 14:24:49: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:24:50: 7000000 INFO @ Sat, 03 Jun 2017 14:24:50: 7000000 INFO @ Sat, 03 Jun 2017 14:24:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:24:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:24:51: #1 total tags in treatment: 7077691 INFO @ Sat, 03 Jun 2017 14:24:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:24:51: #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 14:24:51: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:24:51: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:24:51: #1 total tags in treatment: 7077691 INFO @ Sat, 03 Jun 2017 14:24:51: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:24:51: #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 14:24:51: #2 number of paired peaks: 2465 INFO @ Sat, 03 Jun 2017 14:24:51: start model_add_line... INFO @ Sat, 03 Jun 2017 14:24:52: #1 tags after filtering in treatment: 7072931 INFO @ Sat, 03 Jun 2017 14:24:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:24:52: #1 finished! INFO @ Sat, 03 Jun 2017 14:24:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:24:52: #1 tags after filtering in treatment: 7072931 INFO @ Sat, 03 Jun 2017 14:24:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:24:52: #1 finished! INFO @ Sat, 03 Jun 2017 14:24:52: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:24:54: #2 number of paired peaks: 2465 INFO @ Sat, 03 Jun 2017 14:24:54: start model_add_line... INFO @ Sat, 03 Jun 2017 14:24:54: #2 number of paired peaks: 2465 INFO @ Sat, 03 Jun 2017 14:24:54: start model_add_line... INFO @ Sat, 03 Jun 2017 14:25:01: start X-correlation... INFO @ Sat, 03 Jun 2017 14:25:01: end of X-cor INFO @ Sat, 03 Jun 2017 14:25:01: #2 finished! INFO @ Sat, 03 Jun 2017 14:25:01: #2 predicted fragment length is 188 bps INFO @ Sat, 03 Jun 2017 14:25:01: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 03 Jun 2017 14:25:01: #2.2 Generate R script for model : SRX1848132.10_model.r INFO @ Sat, 03 Jun 2017 14:25:01: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:25:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:25:04: start X-correlation... INFO @ Sat, 03 Jun 2017 14:25:04: end of X-cor INFO @ Sat, 03 Jun 2017 14:25:04: #2 finished! INFO @ Sat, 03 Jun 2017 14:25:04: #2 predicted fragment length is 188 bps INFO @ Sat, 03 Jun 2017 14:25:04: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 03 Jun 2017 14:25:04: #2.2 Generate R script for model : SRX1848132.20_model.r INFO @ Sat, 03 Jun 2017 14:25:04: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:25:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:25:04: start X-correlation... INFO @ Sat, 03 Jun 2017 14:25:04: end of X-cor INFO @ Sat, 03 Jun 2017 14:25:04: #2 finished! INFO @ Sat, 03 Jun 2017 14:25:04: #2 predicted fragment length is 188 bps INFO @ Sat, 03 Jun 2017 14:25:04: #2 alternative fragment length(s) may be 188 bps INFO @ Sat, 03 Jun 2017 14:25:04: #2.2 Generate R script for model : SRX1848132.05_model.r INFO @ Sat, 03 Jun 2017 14:25:04: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:25:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:25:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:25:47: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:25:48: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:26:22: #4 Write output xls file... SRX1848132.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:26:22: #4 Write peak in narrowPeak format file... SRX1848132.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:26:22: #4 Write summits bed file... SRX1848132.20_summits.bed INFO @ Sat, 03 Jun 2017 14:26:22: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3732 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:26:27: #4 Write output xls file... SRX1848132.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:26:27: #4 Write peak in narrowPeak format file... SRX1848132.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:26:27: #4 Write summits bed file... SRX1848132.10_summits.bed INFO @ Sat, 03 Jun 2017 14:26:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6931 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:26:31: #4 Write output xls file... SRX1848132.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:26:31: #4 Write peak in narrowPeak format file... SRX1848132.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:26:31: #4 Write summits bed file... SRX1848132.05_summits.bed INFO @ Sat, 03 Jun 2017 14:26:31: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10363 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。