Job ID = 9029491 sra ファイルのダウンロード中... Completed: 270534K bytes transferred in 5 seconds (407657K 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 --:--:-- 0:00:06 --:--:-- 0 100 30318 0 30318 0 0 3845 0 --:--:-- 0:00:07 --:--:-- 20388 100 55794 0 55794 0 0 6656 0 --:--:-- 0:00:08 --:--:-- 28107 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 10580602 spots for /home/okishinya/chipatlas/results/dm3/SRX1794245/SRR3575289.sra Written 10580602 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: 00:03:23 10580602 reads; of these: 10580602 (100.00%) were unpaired; of these: 290350 (2.74%) aligned 0 times 8777630 (82.96%) aligned exactly 1 time 1512622 (14.30%) aligned >1 times 97.26% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 2432635 / 10290252 = 0.2364 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 14:00:53: # Command line: callpeak -t SRX1794245.bam -f BAM -g dm -n SRX1794245.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794245.20 # format = BAM # ChIP-seq file = ['SRX1794245.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 14:00:53: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:53: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:53: # Command line: callpeak -t SRX1794245.bam -f BAM -g dm -n SRX1794245.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794245.10 # format = BAM # ChIP-seq file = ['SRX1794245.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 14:00:53: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:53: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:00:53: # Command line: callpeak -t SRX1794245.bam -f BAM -g dm -n SRX1794245.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794245.05 # format = BAM # ChIP-seq file = ['SRX1794245.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 14:00:53: #1 read tag files... INFO @ Sat, 03 Jun 2017 14:00:53: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 14:01:00: 1000000 INFO @ Sat, 03 Jun 2017 14:01:00: 1000000 INFO @ Sat, 03 Jun 2017 14:01:00: 1000000 INFO @ Sat, 03 Jun 2017 14:01:06: 2000000 INFO @ Sat, 03 Jun 2017 14:01:06: 2000000 INFO @ Sat, 03 Jun 2017 14:01:06: 2000000 INFO @ Sat, 03 Jun 2017 14:01:12: 3000000 INFO @ Sat, 03 Jun 2017 14:01:12: 3000000 INFO @ Sat, 03 Jun 2017 14:01:12: 3000000 INFO @ Sat, 03 Jun 2017 14:01:18: 4000000 INFO @ Sat, 03 Jun 2017 14:01:18: 4000000 INFO @ Sat, 03 Jun 2017 14:01:19: 4000000 INFO @ Sat, 03 Jun 2017 14:01:25: 5000000 INFO @ Sat, 03 Jun 2017 14:01:25: 5000000 INFO @ Sat, 03 Jun 2017 14:01:25: 5000000 INFO @ Sat, 03 Jun 2017 14:01:31: 6000000 INFO @ Sat, 03 Jun 2017 14:01:31: 6000000 INFO @ Sat, 03 Jun 2017 14:01:31: 6000000 INFO @ Sat, 03 Jun 2017 14:01:37: 7000000 INFO @ Sat, 03 Jun 2017 14:01:37: 7000000 INFO @ Sat, 03 Jun 2017 14:01:38: 7000000 INFO @ Sat, 03 Jun 2017 14:01:43: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:43: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:43: #1 total tags in treatment: 7857617 INFO @ Sat, 03 Jun 2017 14:01:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:43: #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 14:01:43: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:43: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:43: #1 total tags in treatment: 7857617 INFO @ Sat, 03 Jun 2017 14:01:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:43: #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 14:01:43: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 14:01:43: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 14:01:43: #1 total tags in treatment: 7857617 INFO @ Sat, 03 Jun 2017 14:01:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 14:01:43: #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 14:01:44: #1 tags after filtering in treatment: 7855271 INFO @ Sat, 03 Jun 2017 14:01:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:44: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:44: #1 tags after filtering in treatment: 7855271 INFO @ Sat, 03 Jun 2017 14:01:44: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:44: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:45: #1 tags after filtering in treatment: 7855271 INFO @ Sat, 03 Jun 2017 14:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 14:01:45: #1 finished! INFO @ Sat, 03 Jun 2017 14:01:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 14:01:47: #2 number of paired peaks: 10251 INFO @ Sat, 03 Jun 2017 14:01:47: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:47: #2 number of paired peaks: 10251 INFO @ Sat, 03 Jun 2017 14:01:47: start model_add_line... INFO @ Sat, 03 Jun 2017 14:01:47: #2 number of paired peaks: 10251 INFO @ Sat, 03 Jun 2017 14:01:47: start model_add_line... INFO @ Sat, 03 Jun 2017 14:02:56: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:56: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:56: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:56: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Jun 2017 14:02:56: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Jun 2017 14:02:56: #2.2 Generate R script for model : SRX1794245.20_model.r INFO @ Sat, 03 Jun 2017 14:02:56: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:57: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:57: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:57: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:57: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Jun 2017 14:02:57: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Jun 2017 14:02:57: #2.2 Generate R script for model : SRX1794245.10_model.r INFO @ Sat, 03 Jun 2017 14:02:57: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 14:02:58: start X-correlation... INFO @ Sat, 03 Jun 2017 14:02:58: end of X-cor INFO @ Sat, 03 Jun 2017 14:02:58: #2 finished! INFO @ Sat, 03 Jun 2017 14:02:58: #2 predicted fragment length is 146 bps INFO @ Sat, 03 Jun 2017 14:02:58: #2 alternative fragment length(s) may be 146 bps INFO @ Sat, 03 Jun 2017 14:02:58: #2.2 Generate R script for model : SRX1794245.05_model.r INFO @ Sat, 03 Jun 2017 14:02:58: #3 Call peaks... INFO @ Sat, 03 Jun 2017 14:02:58: #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 14:03:44: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:03:46: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 14:04:28: #4 Write output xls file... SRX1794245.20_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:28: #4 Write peak in narrowPeak format file... SRX1794245.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:28: #4 Write summits bed file... SRX1794245.20_summits.bed INFO @ Sat, 03 Jun 2017 14:04:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7436 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:33: #4 Write output xls file... SRX1794245.10_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:33: #4 Write peak in narrowPeak format file... SRX1794245.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:33: #4 Write summits bed file... SRX1794245.10_summits.bed INFO @ Sat, 03 Jun 2017 14:04:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8545 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 14:04:34: #4 Write output xls file... SRX1794245.05_peaks.xls INFO @ Sat, 03 Jun 2017 14:04:34: #4 Write peak in narrowPeak format file... SRX1794245.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 14:04:34: #4 Write summits bed file... SRX1794245.05_summits.bed INFO @ Sat, 03 Jun 2017 14:04:34: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9300 records, 4 fields): 13 millis CompletedMACS2peakCalling