Job ID = 9029482 sra ファイルのダウンロード中... Completed: 205832K bytes transferred in 4 seconds (339557K 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 1068 0 --:--:-- 0:00:07 --:--:-- 10069 100 38318 0 38318 0 0 4790 0 --:--:-- 0:00:07 --:--:-- 24084 100 54557 0 54557 0 0 6548 0 --:--:-- 0:00:08 --:--:-- 28385 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 6589851 spots for /home/okishinya/chipatlas/results/dm3/SRX1794235/SRR3575276.sra Written 6589851 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:25 6589851 reads; of these: 6589851 (100.00%) were unpaired; of these: 360529 (5.47%) aligned 0 times 4904556 (74.43%) aligned exactly 1 time 1324766 (20.10%) aligned >1 times 94.53% overall alignment rate Time searching: 00:02:26 Overall time: 00:02:26 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_rmdupse_core] 732903 / 6229322 = 0.1177 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 13:56:58: # Command line: callpeak -t SRX1794235.bam -f BAM -g dm -n SRX1794235.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1794235.05 # format = BAM # ChIP-seq file = ['SRX1794235.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 13:56:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:56:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:56:58: # Command line: callpeak -t SRX1794235.bam -f BAM -g dm -n SRX1794235.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1794235.10 # format = BAM # ChIP-seq file = ['SRX1794235.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 13:56:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:56:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:56:58: # Command line: callpeak -t SRX1794235.bam -f BAM -g dm -n SRX1794235.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1794235.20 # format = BAM # ChIP-seq file = ['SRX1794235.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 13:56:58: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:56:58: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:57:04: 1000000 INFO @ Sat, 03 Jun 2017 13:57:05: 1000000 INFO @ Sat, 03 Jun 2017 13:57:05: 1000000 INFO @ Sat, 03 Jun 2017 13:57:11: 2000000 INFO @ Sat, 03 Jun 2017 13:57:12: 2000000 INFO @ Sat, 03 Jun 2017 13:57:12: 2000000 INFO @ Sat, 03 Jun 2017 13:57:17: 3000000 INFO @ Sat, 03 Jun 2017 13:57:19: 3000000 INFO @ Sat, 03 Jun 2017 13:57:19: 3000000 INFO @ Sat, 03 Jun 2017 13:57:24: 4000000 INFO @ Sat, 03 Jun 2017 13:57:26: 4000000 INFO @ Sat, 03 Jun 2017 13:57:26: 4000000 INFO @ Sat, 03 Jun 2017 13:57:30: 5000000 INFO @ Sat, 03 Jun 2017 13:57:33: 5000000 INFO @ Sat, 03 Jun 2017 13:57:33: 5000000 INFO @ Sat, 03 Jun 2017 13:57:33: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:57:33: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:57:33: #1 total tags in treatment: 5496419 INFO @ Sat, 03 Jun 2017 13:57:33: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:57:33: #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 13:57:34: #1 tags after filtering in treatment: 5495431 INFO @ Sat, 03 Jun 2017 13:57:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:57:34: #1 finished! INFO @ Sat, 03 Jun 2017 13:57:34: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:57:36: #2 number of paired peaks: 3787 INFO @ Sat, 03 Jun 2017 13:57:36: start model_add_line... INFO @ Sat, 03 Jun 2017 13:57:36: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:57:36: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:57:36: #1 total tags in treatment: 5496419 INFO @ Sat, 03 Jun 2017 13:57:36: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:57:36: #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 13:57:37: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:57:37: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:57:37: #1 total tags in treatment: 5496419 INFO @ Sat, 03 Jun 2017 13:57:37: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:57:37: #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 13:57:38: #1 tags after filtering in treatment: 5495431 INFO @ Sat, 03 Jun 2017 13:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:57:38: #1 finished! INFO @ Sat, 03 Jun 2017 13:57:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:57:38: #1 tags after filtering in treatment: 5495431 INFO @ Sat, 03 Jun 2017 13:57:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:57:38: #1 finished! INFO @ Sat, 03 Jun 2017 13:57:38: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:57:39: #2 number of paired peaks: 3787 INFO @ Sat, 03 Jun 2017 13:57:39: start model_add_line... INFO @ Sat, 03 Jun 2017 13:57:39: #2 number of paired peaks: 3787 INFO @ Sat, 03 Jun 2017 13:57:39: start model_add_line... INFO @ Sat, 03 Jun 2017 13:57:51: start X-correlation... INFO @ Sat, 03 Jun 2017 13:57:51: end of X-cor INFO @ Sat, 03 Jun 2017 13:57:51: #2 finished! INFO @ Sat, 03 Jun 2017 13:57:51: #2 predicted fragment length is 176 bps INFO @ Sat, 03 Jun 2017 13:57:51: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 03 Jun 2017 13:57:51: #2.2 Generate R script for model : SRX1794235.20_model.r INFO @ Sat, 03 Jun 2017 13:57:51: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:57:54: start X-correlation... INFO @ Sat, 03 Jun 2017 13:57:54: end of X-cor INFO @ Sat, 03 Jun 2017 13:57:54: #2 finished! INFO @ Sat, 03 Jun 2017 13:57:54: #2 predicted fragment length is 176 bps INFO @ Sat, 03 Jun 2017 13:57:54: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 03 Jun 2017 13:57:54: #2.2 Generate R script for model : SRX1794235.10_model.r INFO @ Sat, 03 Jun 2017 13:57:54: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:57:55: start X-correlation... INFO @ Sat, 03 Jun 2017 13:57:55: end of X-cor INFO @ Sat, 03 Jun 2017 13:57:55: #2 finished! INFO @ Sat, 03 Jun 2017 13:57:55: #2 predicted fragment length is 176 bps INFO @ Sat, 03 Jun 2017 13:57:55: #2 alternative fragment length(s) may be 176 bps INFO @ Sat, 03 Jun 2017 13:57:55: #2.2 Generate R script for model : SRX1794235.05_model.r INFO @ Sat, 03 Jun 2017 13:57:55: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:57:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:58:25: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:58:29: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:58:31: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:58:53: #4 Write output xls file... SRX1794235.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:58:53: #4 Write peak in narrowPeak format file... SRX1794235.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:58:53: #4 Write summits bed file... SRX1794235.20_summits.bed INFO @ Sat, 03 Jun 2017 13:58:53: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3655 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:59:00: #4 Write output xls file... SRX1794235.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:59:00: #4 Write peak in narrowPeak format file... SRX1794235.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:59:00: #4 Write summits bed file... SRX1794235.10_summits.bed INFO @ Sat, 03 Jun 2017 13:59:00: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5288 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:59:02: #4 Write output xls file... SRX1794235.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:59:02: #4 Write peak in narrowPeak format file... SRX1794235.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:59:02: #4 Write summits bed file... SRX1794235.05_summits.bed INFO @ Sat, 03 Jun 2017 13:59:02: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7214 records, 4 fields): 10 millis CompletedMACS2peakCalling BigWig に変換しました。