Job ID = 9036270 sra ファイルのダウンロード中... Completed: 129658K bytes transferred in 4 seconds (239979K 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 12695 0 12695 0 0 1710 0 --:--:-- 0:00:07 --:--:-- 12519 100 37486 0 37486 0 0 4453 0 --:--:-- 0:00:08 --:--:-- 18649 100 62265 0 62265 0 0 6982 0 --:--:-- 0:00:08 --:--:-- 24816 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 5901695 spots for /home/okishinya/chipatlas/results/sacCer3/SRX1738696/SRR3471227.sra Written 5901695 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: 00:01:09 5901695 reads; of these: 5901695 (100.00%) were unpaired; of these: 638581 (10.82%) aligned 0 times 3805090 (64.47%) aligned exactly 1 time 1458024 (24.71%) aligned >1 times 89.18% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 2358717 / 5263114 = 0.4482 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 @ Sun, 04 Jun 2017 02:46:15: # Command line: callpeak -t SRX1738696.bam -f BAM -g 12100000 -n SRX1738696.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1738696.10 # format = BAM # ChIP-seq file = ['SRX1738696.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sun, 04 Jun 2017 02:46:15: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:46:15: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:46:15: # Command line: callpeak -t SRX1738696.bam -f BAM -g 12100000 -n SRX1738696.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1738696.20 # format = BAM # ChIP-seq file = ['SRX1738696.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sun, 04 Jun 2017 02:46:15: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:46:15: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:46:15: # Command line: callpeak -t SRX1738696.bam -f BAM -g 12100000 -n SRX1738696.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1738696.05 # format = BAM # ChIP-seq file = ['SRX1738696.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Sun, 04 Jun 2017 02:46:15: #1 read tag files... INFO @ Sun, 04 Jun 2017 02:46:15: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 02:46:20: 1000000 INFO @ Sun, 04 Jun 2017 02:46:21: 1000000 INFO @ Sun, 04 Jun 2017 02:46:21: 1000000 INFO @ Sun, 04 Jun 2017 02:46:26: 2000000 INFO @ Sun, 04 Jun 2017 02:46:26: 2000000 INFO @ Sun, 04 Jun 2017 02:46:28: 2000000 INFO @ Sun, 04 Jun 2017 02:46:31: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:46:31: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:46:31: #1 total tags in treatment: 2904397 INFO @ Sun, 04 Jun 2017 02:46:31: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:46:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 02:46:32: #1 tags after filtering in treatment: 2897319 INFO @ Sun, 04 Jun 2017 02:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:46:32: #1 finished! INFO @ Sun, 04 Jun 2017 02:46:32: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:46:32: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:46:32: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:46:32: #1 total tags in treatment: 2904397 INFO @ Sun, 04 Jun 2017 02:46:32: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:46:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 02:46:32: #2 number of paired peaks: 147 WARNING @ Sun, 04 Jun 2017 02:46:32: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sun, 04 Jun 2017 02:46:32: start model_add_line... INFO @ Sun, 04 Jun 2017 02:46:32: #1 tags after filtering in treatment: 2897319 INFO @ Sun, 04 Jun 2017 02:46:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:46:32: #1 finished! INFO @ Sun, 04 Jun 2017 02:46:32: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:46:33: #2 number of paired peaks: 147 WARNING @ Sun, 04 Jun 2017 02:46:33: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sun, 04 Jun 2017 02:46:33: start model_add_line... INFO @ Sun, 04 Jun 2017 02:46:33: #1 tag size is determined as 50 bps INFO @ Sun, 04 Jun 2017 02:46:33: #1 tag size = 50 INFO @ Sun, 04 Jun 2017 02:46:33: #1 total tags in treatment: 2904397 INFO @ Sun, 04 Jun 2017 02:46:33: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 02:46:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Jun 2017 02:46:34: #1 tags after filtering in treatment: 2897319 INFO @ Sun, 04 Jun 2017 02:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 02:46:34: #1 finished! INFO @ Sun, 04 Jun 2017 02:46:34: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 02:46:35: #2 number of paired peaks: 147 WARNING @ Sun, 04 Jun 2017 02:46:35: Fewer paired peaks (147) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 147 pairs to build model! INFO @ Sun, 04 Jun 2017 02:46:35: start model_add_line... INFO @ Sun, 04 Jun 2017 02:46:35: start X-correlation... INFO @ Sun, 04 Jun 2017 02:46:35: end of X-cor INFO @ Sun, 04 Jun 2017 02:46:35: #2 finished! INFO @ Sun, 04 Jun 2017 02:46:35: #2 predicted fragment length is 206 bps INFO @ Sun, 04 Jun 2017 02:46:35: #2 alternative fragment length(s) may be 2,206,228 bps INFO @ Sun, 04 Jun 2017 02:46:35: #2.2 Generate R script for model : SRX1738696.20_model.r INFO @ Sun, 04 Jun 2017 02:46:35: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:46:36: start X-correlation... INFO @ Sun, 04 Jun 2017 02:46:36: end of X-cor INFO @ Sun, 04 Jun 2017 02:46:36: #2 finished! INFO @ Sun, 04 Jun 2017 02:46:36: #2 predicted fragment length is 206 bps INFO @ Sun, 04 Jun 2017 02:46:36: #2 alternative fragment length(s) may be 2,206,228 bps INFO @ Sun, 04 Jun 2017 02:46:36: #2.2 Generate R script for model : SRX1738696.05_model.r INFO @ Sun, 04 Jun 2017 02:46:36: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:46:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:46:37: start X-correlation... INFO @ Sun, 04 Jun 2017 02:46:37: end of X-cor INFO @ Sun, 04 Jun 2017 02:46:37: #2 finished! INFO @ Sun, 04 Jun 2017 02:46:37: #2 predicted fragment length is 206 bps INFO @ Sun, 04 Jun 2017 02:46:37: #2 alternative fragment length(s) may be 2,206,228 bps INFO @ Sun, 04 Jun 2017 02:46:37: #2.2 Generate R script for model : SRX1738696.10_model.r INFO @ Sun, 04 Jun 2017 02:46:37: #3 Call peaks... INFO @ Sun, 04 Jun 2017 02:46:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 02:46:50: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:46:51: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:46:53: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 02:46:59: #4 Write output xls file... SRX1738696.20_peaks.xls INFO @ Sun, 04 Jun 2017 02:46:59: #4 Write peak in narrowPeak format file... SRX1738696.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:46:59: #4 Write summits bed file... SRX1738696.20_summits.bed INFO @ Sun, 04 Jun 2017 02:46:59: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (47 records, 4 fields): 44 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:47:01: #4 Write output xls file... SRX1738696.05_peaks.xls INFO @ Sun, 04 Jun 2017 02:47:01: #4 Write peak in narrowPeak format file... SRX1738696.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:47:01: #4 Write summits bed file... SRX1738696.05_summits.bed INFO @ Sun, 04 Jun 2017 02:47:01: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (242 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 02:47:03: #4 Write output xls file... SRX1738696.10_peaks.xls INFO @ Sun, 04 Jun 2017 02:47:03: #4 Write peak in narrowPeak format file... SRX1738696.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 02:47:03: #4 Write summits bed file... SRX1738696.10_summits.bed INFO @ Sun, 04 Jun 2017 02:47:03: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (105 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。