Job ID = 9029842 sra ファイルのダウンロード中... Completed: 235840K bytes transferred in 4 seconds (391274K 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 --:--:-- 0 100 14323 0 14323 0 0 1804 0 --:--:-- 0:00:07 --:--:-- 9460 100 38317 0 38317 0 0 4289 0 --:--:-- 0:00:08 --:--:-- 15265 100 53405 0 53405 0 0 5763 0 --:--:-- 0:00:09 --:--:-- 18791 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 8394583 spots for /home/okishinya/chipatlas/results/dm3/SRX229429/SRR688261.sra Written 8394583 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: 00:01:12 8394583 reads; of these: 8394583 (100.00%) were unpaired; of these: 4912708 (58.52%) aligned 0 times 2869709 (34.19%) aligned exactly 1 time 612166 (7.29%) aligned >1 times 41.48% overall alignment rate Time searching: 00:01:12 Overall time: 00:01:12 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] 253462 / 3481875 = 0.0728 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 15:29:28: # Command line: callpeak -t SRX229429.bam -f BAM -g dm -n SRX229429.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX229429.05 # format = BAM # ChIP-seq file = ['SRX229429.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 15:29:28: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:29:28: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:29:28: # Command line: callpeak -t SRX229429.bam -f BAM -g dm -n SRX229429.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX229429.20 # format = BAM # ChIP-seq file = ['SRX229429.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 15:29:28: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:29:28: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:29:28: # Command line: callpeak -t SRX229429.bam -f BAM -g dm -n SRX229429.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX229429.10 # format = BAM # ChIP-seq file = ['SRX229429.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 15:29:28: #1 read tag files... INFO @ Sat, 03 Jun 2017 15:29:28: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 15:29:33: 1000000 INFO @ Sat, 03 Jun 2017 15:29:34: 1000000 INFO @ Sat, 03 Jun 2017 15:29:34: 1000000 INFO @ Sat, 03 Jun 2017 15:29:39: 2000000 INFO @ Sat, 03 Jun 2017 15:29:40: 2000000 INFO @ Sat, 03 Jun 2017 15:29:40: 2000000 INFO @ Sat, 03 Jun 2017 15:29:45: 3000000 INFO @ Sat, 03 Jun 2017 15:29:46: 3000000 INFO @ Sat, 03 Jun 2017 15:29:46: 3000000 INFO @ Sat, 03 Jun 2017 15:29:46: #1 tag size is determined as 35 bps INFO @ Sat, 03 Jun 2017 15:29:46: #1 tag size = 35 INFO @ Sat, 03 Jun 2017 15:29:46: #1 total tags in treatment: 3228413 INFO @ Sat, 03 Jun 2017 15:29:46: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:29:46: #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 15:29:47: #1 tags after filtering in treatment: 3227456 INFO @ Sat, 03 Jun 2017 15:29:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:29:47: #1 finished! INFO @ Sat, 03 Jun 2017 15:29:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:29:47: #1 tag size is determined as 35 bps INFO @ Sat, 03 Jun 2017 15:29:47: #1 tag size = 35 INFO @ Sat, 03 Jun 2017 15:29:47: #1 total tags in treatment: 3228413 INFO @ Sat, 03 Jun 2017 15:29:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:29:47: #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 15:29:47: #1 tag size is determined as 35 bps INFO @ Sat, 03 Jun 2017 15:29:47: #1 tag size = 35 INFO @ Sat, 03 Jun 2017 15:29:47: #1 total tags in treatment: 3228413 INFO @ Sat, 03 Jun 2017 15:29:47: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 15:29:47: #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 15:29:47: #2 number of paired peaks: 444 WARNING @ Sat, 03 Jun 2017 15:29:47: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sat, 03 Jun 2017 15:29:47: start model_add_line... INFO @ Sat, 03 Jun 2017 15:29:48: #1 tags after filtering in treatment: 3227456 INFO @ Sat, 03 Jun 2017 15:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:29:48: #1 finished! INFO @ Sat, 03 Jun 2017 15:29:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:29:48: #1 tags after filtering in treatment: 3227456 INFO @ Sat, 03 Jun 2017 15:29:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 15:29:48: #1 finished! INFO @ Sat, 03 Jun 2017 15:29:48: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 15:29:49: start X-correlation... INFO @ Sat, 03 Jun 2017 15:29:49: end of X-cor INFO @ Sat, 03 Jun 2017 15:29:49: #2 finished! INFO @ Sat, 03 Jun 2017 15:29:49: #2 predicted fragment length is 80 bps INFO @ Sat, 03 Jun 2017 15:29:49: #2 alternative fragment length(s) may be 80 bps INFO @ Sat, 03 Jun 2017 15:29:49: #2.2 Generate R script for model : SRX229429.10_model.r INFO @ Sat, 03 Jun 2017 15:29:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:29:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:29:49: #2 number of paired peaks: 444 WARNING @ Sat, 03 Jun 2017 15:29:49: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sat, 03 Jun 2017 15:29:49: start model_add_line... INFO @ Sat, 03 Jun 2017 15:29:49: #2 number of paired peaks: 444 WARNING @ Sat, 03 Jun 2017 15:29:49: Fewer paired peaks (444) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 444 pairs to build model! INFO @ Sat, 03 Jun 2017 15:29:49: start model_add_line... INFO @ Sat, 03 Jun 2017 15:29:50: start X-correlation... INFO @ Sat, 03 Jun 2017 15:29:50: end of X-cor INFO @ Sat, 03 Jun 2017 15:29:50: #2 finished! INFO @ Sat, 03 Jun 2017 15:29:50: #2 predicted fragment length is 80 bps INFO @ Sat, 03 Jun 2017 15:29:50: #2 alternative fragment length(s) may be 80 bps INFO @ Sat, 03 Jun 2017 15:29:50: #2.2 Generate R script for model : SRX229429.05_model.r INFO @ Sat, 03 Jun 2017 15:29:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:29:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:29:50: start X-correlation... INFO @ Sat, 03 Jun 2017 15:29:50: end of X-cor INFO @ Sat, 03 Jun 2017 15:29:50: #2 finished! INFO @ Sat, 03 Jun 2017 15:29:50: #2 predicted fragment length is 80 bps INFO @ Sat, 03 Jun 2017 15:29:50: #2 alternative fragment length(s) may be 80 bps INFO @ Sat, 03 Jun 2017 15:29:50: #2.2 Generate R script for model : SRX229429.20_model.r INFO @ Sat, 03 Jun 2017 15:29:50: #3 Call peaks... INFO @ Sat, 03 Jun 2017 15:29:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 15:30:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:30:09: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:30:10: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 15:30:22: #4 Write output xls file... SRX229429.10_peaks.xls INFO @ Sat, 03 Jun 2017 15:30:22: #4 Write output xls file... SRX229429.20_peaks.xls INFO @ Sat, 03 Jun 2017 15:30:22: #4 Write peak in narrowPeak format file... SRX229429.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:30:22: #4 Write summits bed file... SRX229429.20_summits.bed INFO @ Sat, 03 Jun 2017 15:30:22: Done! INFO @ Sat, 03 Jun 2017 15:30:22: #4 Write peak in narrowPeak format file... SRX229429.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:30:22: #4 Write summits bed file... SRX229429.10_summits.bed INFO @ Sat, 03 Jun 2017 15:30:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (116 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (1050 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 15:30:24: #4 Write output xls file... SRX229429.05_peaks.xls INFO @ Sat, 03 Jun 2017 15:30:24: #4 Write peak in narrowPeak format file... SRX229429.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 15:30:24: #4 Write summits bed file... SRX229429.05_summits.bed INFO @ Sat, 03 Jun 2017 15:30:24: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3628 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。