Job ID = 9037308 sra ファイルのダウンロード中... Completed: 659131K bytes transferred in 8 seconds (631126K 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 --:--:-- 0:00:07 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:08 --:--:-- 0 100 13455 0 13455 0 0 1449 0 --:--:-- 0:00:09 --:--:-- 4957 100 41902 0 41902 0 0 4059 0 --:--:-- 0:00:10 --:--:-- 11170 100 55207 0 55207 0 0 5202 0 --:--:-- 0:00:10 --:--:-- 13658 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 29220683 spots for /home/okishinya/chipatlas/results/sacCer3/SRX707477/SRR1582480.sra Written 29220683 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: 00:02:51 29220683 reads; of these: 29220683 (100.00%) were unpaired; of these: 462832 (1.58%) aligned 0 times 5793242 (19.83%) aligned exactly 1 time 22964609 (78.59%) aligned >1 times 98.42% overall alignment rate Time searching: 00:02:51 Overall time: 00:02:51 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_sort_core] merging from 8 files... [bam_rmdupse_core] 25987792 / 28757851 = 0.9037 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 04:38:08: # Command line: callpeak -t SRX707477.bam -f BAM -g 12100000 -n SRX707477.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX707477.05 # format = BAM # ChIP-seq file = ['SRX707477.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 04:38:08: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:38:08: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:38:08: # Command line: callpeak -t SRX707477.bam -f BAM -g 12100000 -n SRX707477.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX707477.10 # format = BAM # ChIP-seq file = ['SRX707477.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 04:38:08: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:38:08: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:38:08: # Command line: callpeak -t SRX707477.bam -f BAM -g 12100000 -n SRX707477.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX707477.20 # format = BAM # ChIP-seq file = ['SRX707477.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 04:38:08: #1 read tag files... INFO @ Sun, 04 Jun 2017 04:38:08: #1 read treatment tags... INFO @ Sun, 04 Jun 2017 04:38:12: 1000000 INFO @ Sun, 04 Jun 2017 04:38:13: 1000000 INFO @ Sun, 04 Jun 2017 04:38:13: 1000000 INFO @ Sun, 04 Jun 2017 04:38:17: 2000000 INFO @ Sun, 04 Jun 2017 04:38:18: 2000000 INFO @ Sun, 04 Jun 2017 04:38:18: 2000000 INFO @ Sun, 04 Jun 2017 04:38:21: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:38:21: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:38:21: #1 total tags in treatment: 2770059 INFO @ Sun, 04 Jun 2017 04:38:21: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:38:21: #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 04:38:22: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:38:22: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:38:22: #1 total tags in treatment: 2770059 INFO @ Sun, 04 Jun 2017 04:38:22: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:38:22: #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 04:38:22: #1 tags after filtering in treatment: 2769399 INFO @ Sun, 04 Jun 2017 04:38:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:38:22: #1 finished! INFO @ Sun, 04 Jun 2017 04:38:22: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:38:22: #1 tag size is determined as 40 bps INFO @ Sun, 04 Jun 2017 04:38:22: #1 tag size = 40 INFO @ Sun, 04 Jun 2017 04:38:22: #1 total tags in treatment: 2770059 INFO @ Sun, 04 Jun 2017 04:38:22: #1 user defined the maximum tags... INFO @ Sun, 04 Jun 2017 04:38:22: #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 04:38:22: #2 number of paired peaks: 174 WARNING @ Sun, 04 Jun 2017 04:38:22: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sun, 04 Jun 2017 04:38:22: start model_add_line... INFO @ Sun, 04 Jun 2017 04:38:22: #1 tags after filtering in treatment: 2769399 INFO @ Sun, 04 Jun 2017 04:38:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:38:22: #1 finished! INFO @ Sun, 04 Jun 2017 04:38:22: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:38:23: #1 tags after filtering in treatment: 2769399 INFO @ Sun, 04 Jun 2017 04:38:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Jun 2017 04:38:23: #1 finished! INFO @ Sun, 04 Jun 2017 04:38:23: #2 Build Peak Model... INFO @ Sun, 04 Jun 2017 04:38:23: #2 number of paired peaks: 174 WARNING @ Sun, 04 Jun 2017 04:38:23: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sun, 04 Jun 2017 04:38:23: start model_add_line... INFO @ Sun, 04 Jun 2017 04:38:23: #2 number of paired peaks: 174 WARNING @ Sun, 04 Jun 2017 04:38:23: Fewer paired peaks (174) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 174 pairs to build model! INFO @ Sun, 04 Jun 2017 04:38:23: start model_add_line... INFO @ Sun, 04 Jun 2017 04:38:25: start X-correlation... INFO @ Sun, 04 Jun 2017 04:38:25: end of X-cor INFO @ Sun, 04 Jun 2017 04:38:25: #2 finished! INFO @ Sun, 04 Jun 2017 04:38:25: #2 predicted fragment length is 141 bps INFO @ Sun, 04 Jun 2017 04:38:25: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 04 Jun 2017 04:38:25: #2.2 Generate R script for model : SRX707477.10_model.r INFO @ Sun, 04 Jun 2017 04:38:25: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:38:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:38:26: start X-correlation... INFO @ Sun, 04 Jun 2017 04:38:26: end of X-cor INFO @ Sun, 04 Jun 2017 04:38:26: #2 finished! INFO @ Sun, 04 Jun 2017 04:38:26: #2 predicted fragment length is 141 bps INFO @ Sun, 04 Jun 2017 04:38:26: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 04 Jun 2017 04:38:26: #2.2 Generate R script for model : SRX707477.20_model.r INFO @ Sun, 04 Jun 2017 04:38:26: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:38:26: start X-correlation... INFO @ Sun, 04 Jun 2017 04:38:26: end of X-cor INFO @ Sun, 04 Jun 2017 04:38:26: #2 finished! INFO @ Sun, 04 Jun 2017 04:38:26: #2 predicted fragment length is 141 bps INFO @ Sun, 04 Jun 2017 04:38:26: #2 alternative fragment length(s) may be 141 bps INFO @ Sun, 04 Jun 2017 04:38:26: #2.2 Generate R script for model : SRX707477.05_model.r INFO @ Sun, 04 Jun 2017 04:38:26: #3 Call peaks... INFO @ Sun, 04 Jun 2017 04:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Jun 2017 04:38:40: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:38:41: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:38:41: #3 Call peaks for each chromosome... INFO @ Sun, 04 Jun 2017 04:38:51: #4 Write output xls file... SRX707477.10_peaks.xls INFO @ Sun, 04 Jun 2017 04:38:51: #4 Write peak in narrowPeak format file... SRX707477.10_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:38:51: #4 Write summits bed file... SRX707477.10_summits.bed INFO @ Sun, 04 Jun 2017 04:38:51: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (1223 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:38:51: #4 Write output xls file... SRX707477.20_peaks.xls INFO @ Sun, 04 Jun 2017 04:38:51: #4 Write peak in narrowPeak format file... SRX707477.20_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:38:51: #4 Write summits bed file... SRX707477.20_summits.bed INFO @ Sun, 04 Jun 2017 04:38:51: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (830 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Jun 2017 04:38:53: #4 Write output xls file... SRX707477.05_peaks.xls INFO @ Sun, 04 Jun 2017 04:38:53: #4 Write peak in narrowPeak format file... SRX707477.05_peaks.narrowPeak INFO @ Sun, 04 Jun 2017 04:38:53: #4 Write summits bed file... SRX707477.05_summits.bed INFO @ Sun, 04 Jun 2017 04:38:53: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1736 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。