Job ID = 9025631 sra ファイルのダウンロード中... Completed: 585363K bytes transferred in 8 seconds (589483K 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 0 0 0 0 0 0 0 0 --:--:-- 0:00:09 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:10 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:11 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:12 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:13 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:14 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:15 --:--:-- 0 0 0 0 0 0 0 0 0 --:--:-- 0:00:16 --:--:-- 0 100 7663 0 7663 0 0 457 0 --:--:-- 0:00:16 --:--:-- 1852 100 30245 0 30245 0 0 1703 0 --:--:-- 0:00:17 --:--:-- 7321 100 62212 0 62212 0 0 3318 0 --:--:-- 0:00:18 --:--:-- 15081 100 64083 0 64083 0 0 3417 0 --:--:-- 0:00:18 --:--:-- 20513 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 17247211 spots for /home/okishinya/chipatlas/results/ce10/SRX208773/SRR628907.sra Written 17247211 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: 00:07:24 17247211 reads; of these: 17247211 (100.00%) were unpaired; of these: 2385719 (13.83%) aligned 0 times 11695575 (67.81%) aligned exactly 1 time 3165917 (18.36%) aligned >1 times 86.17% overall alignment rate Time searching: 00:07:24 Overall time: 00:07:24 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 11547597 / 14861492 = 0.7770 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 04:55:20: # Command line: callpeak -t SRX208773.bam -f BAM -g ce -n SRX208773.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX208773.05 # format = BAM # ChIP-seq file = ['SRX208773.bam'] # control file = None # effective genome size = 9.00e+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 @ Sat, 03 Jun 2017 04:55:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:55:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:55:20: # Command line: callpeak -t SRX208773.bam -f BAM -g ce -n SRX208773.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX208773.20 # format = BAM # ChIP-seq file = ['SRX208773.bam'] # control file = None # effective genome size = 9.00e+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 @ Sat, 03 Jun 2017 04:55:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:55:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:55:20: # Command line: callpeak -t SRX208773.bam -f BAM -g ce -n SRX208773.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX208773.10 # format = BAM # ChIP-seq file = ['SRX208773.bam'] # control file = None # effective genome size = 9.00e+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 @ Sat, 03 Jun 2017 04:55:20: #1 read tag files... INFO @ Sat, 03 Jun 2017 04:55:20: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 04:55:27: 1000000 INFO @ Sat, 03 Jun 2017 04:55:27: 1000000 INFO @ Sat, 03 Jun 2017 04:55:27: 1000000 INFO @ Sat, 03 Jun 2017 04:55:34: 2000000 INFO @ Sat, 03 Jun 2017 04:55:34: 2000000 INFO @ Sat, 03 Jun 2017 04:55:34: 2000000 INFO @ Sat, 03 Jun 2017 04:55:41: 3000000 INFO @ Sat, 03 Jun 2017 04:55:42: 3000000 INFO @ Sat, 03 Jun 2017 04:55:42: 3000000 INFO @ Sat, 03 Jun 2017 04:55:43: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:55:43: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:55:43: #1 total tags in treatment: 3313895 INFO @ Sat, 03 Jun 2017 04:55:43: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:55:43: #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 04:55:44: #1 tags after filtering in treatment: 3209096 INFO @ Sat, 03 Jun 2017 04:55:44: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 03 Jun 2017 04:55:44: #1 finished! INFO @ Sat, 03 Jun 2017 04:55:44: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:55:44: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:55:44: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 04:55:44: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:55:44: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 04:55:44: #1 total tags in treatment: 3313895 INFO @ Sat, 03 Jun 2017 04:55:44: #1 total tags in treatment: 3313895 INFO @ Sat, 03 Jun 2017 04:55:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:55:44: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 04:55:44: #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 04:55:44: #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 04:55:45: #2 number of paired peaks: 1741 INFO @ Sat, 03 Jun 2017 04:55:45: start model_add_line... INFO @ Sat, 03 Jun 2017 04:55:45: #1 tags after filtering in treatment: 3209096 INFO @ Sat, 03 Jun 2017 04:55:45: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 03 Jun 2017 04:55:45: #1 finished! INFO @ Sat, 03 Jun 2017 04:55:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:55:45: #1 tags after filtering in treatment: 3209096 INFO @ Sat, 03 Jun 2017 04:55:45: #1 Redundant rate of treatment: 0.03 INFO @ Sat, 03 Jun 2017 04:55:45: #1 finished! INFO @ Sat, 03 Jun 2017 04:55:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 04:55:45: #2 number of paired peaks: 1741 INFO @ Sat, 03 Jun 2017 04:55:45: start model_add_line... INFO @ Sat, 03 Jun 2017 04:55:45: #2 number of paired peaks: 1741 INFO @ Sat, 03 Jun 2017 04:55:45: start model_add_line... INFO @ Sat, 03 Jun 2017 04:55:52: start X-correlation... INFO @ Sat, 03 Jun 2017 04:55:52: end of X-cor INFO @ Sat, 03 Jun 2017 04:55:52: #2 finished! INFO @ Sat, 03 Jun 2017 04:55:52: #2 predicted fragment length is 277 bps INFO @ Sat, 03 Jun 2017 04:55:52: #2 alternative fragment length(s) may be 277 bps INFO @ Sat, 03 Jun 2017 04:55:52: #2.2 Generate R script for model : SRX208773.05_model.r INFO @ Sat, 03 Jun 2017 04:55:52: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:55:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:55:53: start X-correlation... INFO @ Sat, 03 Jun 2017 04:55:53: end of X-cor INFO @ Sat, 03 Jun 2017 04:55:53: #2 finished! INFO @ Sat, 03 Jun 2017 04:55:53: #2 predicted fragment length is 277 bps INFO @ Sat, 03 Jun 2017 04:55:53: #2 alternative fragment length(s) may be 277 bps INFO @ Sat, 03 Jun 2017 04:55:53: #2.2 Generate R script for model : SRX208773.20_model.r INFO @ Sat, 03 Jun 2017 04:55:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:55:53: start X-correlation... INFO @ Sat, 03 Jun 2017 04:55:53: end of X-cor INFO @ Sat, 03 Jun 2017 04:55:53: #2 finished! INFO @ Sat, 03 Jun 2017 04:55:53: #2 predicted fragment length is 277 bps INFO @ Sat, 03 Jun 2017 04:55:53: #2 alternative fragment length(s) may be 277 bps INFO @ Sat, 03 Jun 2017 04:55:53: #2.2 Generate R script for model : SRX208773.10_model.r INFO @ Sat, 03 Jun 2017 04:55:53: #3 Call peaks... INFO @ Sat, 03 Jun 2017 04:55:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 04:56:12: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:56:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:56:14: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 04:56:28: #4 Write output xls file... SRX208773.05_peaks.xls INFO @ Sat, 03 Jun 2017 04:56:28: #4 Write peak in narrowPeak format file... SRX208773.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:56:28: #4 Write summits bed file... SRX208773.05_summits.bed INFO @ Sat, 03 Jun 2017 04:56:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1640 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:56:30: #4 Write output xls file... SRX208773.20_peaks.xls INFO @ Sat, 03 Jun 2017 04:56:30: #4 Write peak in narrowPeak format file... SRX208773.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:56:30: #4 Write summits bed file... SRX208773.20_summits.bed INFO @ Sat, 03 Jun 2017 04:56:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1108 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 04:56:32: #4 Write output xls file... SRX208773.10_peaks.xls INFO @ Sat, 03 Jun 2017 04:56:32: #4 Write peak in narrowPeak format file... SRX208773.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 04:56:32: #4 Write summits bed file... SRX208773.10_summits.bed INFO @ Sat, 03 Jun 2017 04:56:32: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1398 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。