Job ID = 9029486 sra ファイルのダウンロード中... Completed: 268767K bytes transferred in 5 seconds (438575K 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 10559 0 10559 0 0 1466 0 --:--:-- 0:00:07 --:--:-- 13035 100 33902 0 33902 0 0 4135 0 --:--:-- 0:00:08 --:--:-- 18771 100 54120 0 54120 0 0 6222 0 --:--:-- 0:00:08 --:--:-- 23489 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 10472735 spots for /home/okishinya/chipatlas/results/dm3/SRX1794239/SRR3575282.sra Written 10472735 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: 00:03:30 10472735 reads; of these: 10472735 (100.00%) were unpaired; of these: 276407 (2.64%) aligned 0 times 8388178 (80.10%) aligned exactly 1 time 1808150 (17.27%) aligned >1 times 97.36% overall alignment rate Time searching: 00:03:30 Overall time: 00:03:30 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] 1238074 / 10196328 = 0.1214 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 14:00:41: # Command line: callpeak -t SRX1794239.bam -f BAM -g dm -n SRX1794239.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794239.10 # format = BAM # ChIP-seq file = ['SRX1794239.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 14:00:41: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:41: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:41: # Command line: callpeak -t SRX1794239.bam -f BAM -g dm -n SRX1794239.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794239.05 # format = BAM # ChIP-seq file = ['SRX1794239.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 14:00:41: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:41: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:41: # Command line: callpeak -t SRX1794239.bam -f BAM -g dm -n SRX1794239.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794239.20 # format = BAM # ChIP-seq file = ['SRX1794239.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 14:00:41: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:41: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:48: 1000000 INFO @ Sat, 03 Jun 2017 14:00:49: 1000000 INFO @ Sat, 03 Jun 2017 14:00:49: 1000000 INFO @ Sat, 03 Jun 2017 14:00:55: 2000000 INFO @ Sat, 03 Jun 2017 14:00:56: 2000000 INFO @ Sat, 03 Jun 2017 14:00:57: 2000000 INFO @ Sat, 03 Jun 2017 14:01:01: 3000000 INFO @ Sat, 03 Jun 2017 14:01:04: 3000000 INFO @ Sat, 03 Jun 2017 14:01:04: 3000000 INFO @ Sat, 03 Jun 2017 14:01:07: 4000000 INFO @ Sat, 03 Jun 2017 14:01:12: 4000000 INFO @ Sat, 03 Jun 2017 14:01:12: 4000000 INFO @ Sat, 03 Jun 2017 14:01:14: 5000000 INFO @ Sat, 03 Jun 2017 14:01:20: 5000000 INFO @ Sat, 03 Jun 2017 14:01:20: 5000000 INFO @ Sat, 03 Jun 2017 14:01:21: 6000000 INFO @ Sat, 03 Jun 2017 14:01:27: 6000000 INFO @ Sat, 03 Jun 2017 14:01:27: 6000000 INFO @ Sat, 03 Jun 2017 14:01:28: 7000000 INFO @ Sat, 03 Jun 2017 14:01:34: 8000000 INFO @ Sat, 03 Jun 2017 14:01:34: 7000000 INFO @ Sat, 03 Jun 2017 14:01:35: 7000000 INFO @ Sat, 03 Jun 2017 14:01:40: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:40: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:40: #1 total tags in treatment: 8958254 INFO @ Sat, 03 Jun 2017 14:01:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:40: #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 14:01:42: #1 tags after filtering in treatment: 8956572 INFO @ Sat, 03 Jun 2017 14:01:42: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:42: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:42: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:42: 8000000 INFO @ Sat, 03 Jun 2017 14:01:42: 8000000 INFO @ Sat, 03 Jun 2017 14:01:45: #2 number of paired peaks: 9374 INFO @ Sat, 03 Jun 2017 14:01:45: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:50: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:50: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:50: #1 total tags in treatment: 8958254 INFO @ Sat, 03 Jun 2017 14:01:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:50: #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 14:01:50: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:50: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:50: #1 total tags in treatment: 8958254 INFO @ Sat, 03 Jun 2017 14:01:50: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:50: #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 14:01:51: #1 tags after filtering in treatment: 8956572 INFO @ Sat, 03 Jun 2017 14:01:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:51: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:51: #1 tags after filtering in treatment: 8956572 INFO @ Sat, 03 Jun 2017 14:01:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:51: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:51: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:54: #2 number of paired peaks: 9374 INFO @ Sat, 03 Jun 2017 14:01:54: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:54: #2 number of paired peaks: 9374 INFO @ Sat, 03 Jun 2017 14:01:54: start model_add_line... INFO @ Sat, 03 Jun 2017 14:02:43: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:43: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:43: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:43: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Jun 2017 14:02:43: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 03 Jun 2017 14:02:43: #2.2 Generate R script for model : SRX1794239.10_model.r INFO @ Sat, 03 Jun 2017 14:02:43: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:50: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:50: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:50: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:50: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Jun 2017 14:02:50: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 03 Jun 2017 14:02:50: #2.2 Generate R script for model : SRX1794239.05_model.r INFO @ Sat, 03 Jun 2017 14:02:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:52: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:52: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:52: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:52: #2 predicted fragment length is 154 bps INFO @ Sat, 03 Jun 2017 14:02:52: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 03 Jun 2017 14:02:52: #2.2 Generate R script for model : SRX1794239.20_model.r INFO @ Sat, 03 Jun 2017 14:02:52: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:03:35: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 14:03:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:47: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sat, 03 Jun 2017 14:04:24: #4 Write output xls file... SRX1794239.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:24: #4 Write peak in narrowPeak format file... SRX1794239.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:24: #4 Write summits bed file... SRX1794239.10_summits.bed INFO @ Sat, 03 Jun 2017 14:04:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8331 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:30: #4 Write output xls file... SRX1794239.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:30: #4 Write peak in narrowPeak format file... SRX1794239.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:31: #4 Write summits bed file... SRX1794239.20_summits.bed INFO @ Sat, 03 Jun 2017 14:04:31: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5631 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:40: #4 Write output xls file... SRX1794239.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:40: #4 Write peak in narrowPeak format file... SRX1794239.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:40: #4 Write summits bed file... SRX1794239.05_summits.bed INFO @ Sat, 03 Jun 2017 14:04:41: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10132 records, 4 fields): 14 millis CompletedMACS2peakCalling