Job ID = 9029293 sra ファイルのダウンロード中... Completed: 165363K bytes transferred in 4 seconds (309356K 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 21557 0 21557 0 0 2764 0 --:--:-- 0:00:07 --:--:-- 18268 100 67893 0 67893 0 0 7720 0 --:--:-- 0:00:08 --:--:-- 31215 100 83918 0 83918 0 0 9366 0 --:--:-- 0:00:08 --:--:-- 35847 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 4688873 spots for /home/okishinya/chipatlas/results/dm3/SRX1531769/SRR3102828.sra Written 4688873 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: 00:01:14 4688873 reads; of these: 4688873 (100.00%) were unpaired; of these: 2417510 (51.56%) aligned 0 times 1951355 (41.62%) aligned exactly 1 time 320008 (6.82%) aligned >1 times 48.44% overall alignment rate Time searching: 00:01:14 Overall time: 00:01:14 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] 680551 / 2271363 = 0.2996 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 13:04:18: # Command line: callpeak -t SRX1531769.bam -f BAM -g dm -n SRX1531769.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1531769.20 # format = BAM # ChIP-seq file = ['SRX1531769.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 13:04:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:04:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:04:18: # Command line: callpeak -t SRX1531769.bam -f BAM -g dm -n SRX1531769.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1531769.10 # format = BAM # ChIP-seq file = ['SRX1531769.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 13:04:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:04:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:04:18: # Command line: callpeak -t SRX1531769.bam -f BAM -g dm -n SRX1531769.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1531769.05 # format = BAM # ChIP-seq file = ['SRX1531769.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 13:04:18: #1 read tag files... INFO @ Sat, 03 Jun 2017 13:04:18: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 13:04:25: 1000000 INFO @ Sat, 03 Jun 2017 13:04:26: 1000000 INFO @ Sat, 03 Jun 2017 13:04:26: 1000000 INFO @ Sat, 03 Jun 2017 13:04:29: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:04:29: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:04:29: #1 total tags in treatment: 1590812 INFO @ Sat, 03 Jun 2017 13:04:29: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:04:29: #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 13:04:29: #1 tags after filtering in treatment: 1590413 INFO @ Sat, 03 Jun 2017 13:04:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:04:29: #1 finished! INFO @ Sat, 03 Jun 2017 13:04:29: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:04:30: #2 number of paired peaks: 2199 INFO @ Sat, 03 Jun 2017 13:04:30: start model_add_line... INFO @ Sat, 03 Jun 2017 13:04:30: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:04:30: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:04:30: #1 total tags in treatment: 1590812 INFO @ Sat, 03 Jun 2017 13:04:30: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:04:30: #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 13:04:31: #1 tag size is determined as 51 bps INFO @ Sat, 03 Jun 2017 13:04:31: #1 tag size = 51 INFO @ Sat, 03 Jun 2017 13:04:31: #1 total tags in treatment: 1590812 INFO @ Sat, 03 Jun 2017 13:04:31: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 13:04:31: #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 13:04:31: #1 tags after filtering in treatment: 1590413 INFO @ Sat, 03 Jun 2017 13:04:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:04:31: #1 finished! INFO @ Sat, 03 Jun 2017 13:04:31: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:04:31: #1 tags after filtering in treatment: 1590413 INFO @ Sat, 03 Jun 2017 13:04:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 13:04:31: #1 finished! INFO @ Sat, 03 Jun 2017 13:04:31: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 13:04:31: #2 number of paired peaks: 2199 INFO @ Sat, 03 Jun 2017 13:04:31: start model_add_line... INFO @ Sat, 03 Jun 2017 13:04:31: #2 number of paired peaks: 2199 INFO @ Sat, 03 Jun 2017 13:04:31: start model_add_line... INFO @ Sat, 03 Jun 2017 13:04:32: start X-correlation... INFO @ Sat, 03 Jun 2017 13:04:32: end of X-cor INFO @ Sat, 03 Jun 2017 13:04:32: #2 finished! INFO @ Sat, 03 Jun 2017 13:04:32: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Jun 2017 13:04:32: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Jun 2017 13:04:32: #2.2 Generate R script for model : SRX1531769.20_model.r INFO @ Sat, 03 Jun 2017 13:04:32: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:04:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:04:34: start X-correlation... INFO @ Sat, 03 Jun 2017 13:04:34: end of X-cor INFO @ Sat, 03 Jun 2017 13:04:34: #2 finished! INFO @ Sat, 03 Jun 2017 13:04:34: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Jun 2017 13:04:34: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Jun 2017 13:04:34: #2.2 Generate R script for model : SRX1531769.10_model.r INFO @ Sat, 03 Jun 2017 13:04:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:04:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:04:34: start X-correlation... INFO @ Sat, 03 Jun 2017 13:04:34: end of X-cor INFO @ Sat, 03 Jun 2017 13:04:34: #2 finished! INFO @ Sat, 03 Jun 2017 13:04:34: #2 predicted fragment length is 157 bps INFO @ Sat, 03 Jun 2017 13:04:34: #2 alternative fragment length(s) may be 157 bps INFO @ Sat, 03 Jun 2017 13:04:34: #2.2 Generate R script for model : SRX1531769.05_model.r INFO @ Sat, 03 Jun 2017 13:04:34: #3 Call peaks... INFO @ Sat, 03 Jun 2017 13:04:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 13:04:43: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:04:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:04:45: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 13:04:50: #4 Write output xls file... SRX1531769.20_peaks.xls INFO @ Sat, 03 Jun 2017 13:04:50: #4 Write peak in narrowPeak format file... SRX1531769.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:04:50: #4 Write summits bed file... SRX1531769.20_summits.bed INFO @ Sat, 03 Jun 2017 13:04:50: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (379 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 13:04:53: #4 Write output xls file... SRX1531769.10_peaks.xls INFO @ Sat, 03 Jun 2017 13:04:53: #4 Write peak in narrowPeak format file... SRX1531769.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:04:53: #4 Write summits bed file... SRX1531769.10_summits.bed INFO @ Sat, 03 Jun 2017 13:04:53: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (859 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sat, 03 Jun 2017 13:04:53: #4 Write output xls file... SRX1531769.05_peaks.xls INFO @ Sat, 03 Jun 2017 13:04:53: #4 Write peak in narrowPeak format file... SRX1531769.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 13:04:53: #4 Write summits bed file... SRX1531769.05_summits.bed INFO @ Sat, 03 Jun 2017 13:04:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1861 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。