Job ID = 8696835 sra ファイルのダウンロード中... Completed: 1128138K bytes transferred in 16 seconds (573372K 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 7663 0 7663 0 0 949 0 --:--:-- 0:00:08 --:--:-- 5676 100 29767 0 29767 0 0 3265 0 --:--:-- 0:00:09 --:--:-- 12418 100 31638 0 31638 0 0 3406 0 --:--:-- 0:00:09 --:--:-- 12305 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 41597480 spots for /home/okishinya/chipatlas/results/dm3/SRX110773/SRR388355.sra Written 41597480 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:46 41597480 reads; of these: 41597480 (100.00%) were unpaired; of these: 30663699 (73.72%) aligned 0 times 8123099 (19.53%) aligned exactly 1 time 2810682 (6.76%) aligned >1 times 26.28% overall alignment rate Time searching: 00:14:47 Overall time: 00:14:47 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] 2050868 / 10933781 = 0.1876 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 @ Fri, 10 Mar 2017 12:22:17: # Command line: callpeak -t SRX110773.bam -f BAM -g dm -n SRX110773.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX110773.20 # format = BAM # ChIP-seq file = ['SRX110773.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 @ Fri, 10 Mar 2017 12:22:17: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:22:17: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:22:17: # Command line: callpeak -t SRX110773.bam -f BAM -g dm -n SRX110773.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX110773.10 # format = BAM # ChIP-seq file = ['SRX110773.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 @ Fri, 10 Mar 2017 12:22:17: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:22:17: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:22:17: # Command line: callpeak -t SRX110773.bam -f BAM -g dm -n SRX110773.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX110773.05 # format = BAM # ChIP-seq file = ['SRX110773.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 @ Fri, 10 Mar 2017 12:22:17: #1 read tag files... INFO @ Fri, 10 Mar 2017 12:22:17: #1 read treatment tags... INFO @ Fri, 10 Mar 2017 12:22:25: 1000000 INFO @ Fri, 10 Mar 2017 12:22:27: 1000000 INFO @ Fri, 10 Mar 2017 12:22:27: 1000000 INFO @ Fri, 10 Mar 2017 12:22:32: 2000000 INFO @ Fri, 10 Mar 2017 12:22:34: 2000000 INFO @ Fri, 10 Mar 2017 12:22:38: 2000000 INFO @ Fri, 10 Mar 2017 12:22:40: 3000000 INFO @ Fri, 10 Mar 2017 12:22:42: 3000000 INFO @ Fri, 10 Mar 2017 12:22:49: 4000000 INFO @ Fri, 10 Mar 2017 12:22:49: 4000000 INFO @ Fri, 10 Mar 2017 12:22:52: 3000000 INFO @ Fri, 10 Mar 2017 12:22:57: 5000000 INFO @ Fri, 10 Mar 2017 12:22:58: 5000000 INFO @ Fri, 10 Mar 2017 12:23:04: 4000000 INFO @ Fri, 10 Mar 2017 12:23:07: 6000000 INFO @ Fri, 10 Mar 2017 12:23:12: 6000000 INFO @ Fri, 10 Mar 2017 12:23:15: 5000000 INFO @ Fri, 10 Mar 2017 12:23:15: 7000000 INFO @ Fri, 10 Mar 2017 12:23:22: 8000000 INFO @ Fri, 10 Mar 2017 12:23:26: 6000000 INFO @ Fri, 10 Mar 2017 12:23:26: 7000000 INFO @ Fri, 10 Mar 2017 12:23:29: #1 tag size is determined as 45 bps INFO @ Fri, 10 Mar 2017 12:23:29: #1 tag size = 45 INFO @ Fri, 10 Mar 2017 12:23:29: #1 total tags in treatment: 8882913 INFO @ Fri, 10 Mar 2017 12:23:29: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:23:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:23:31: #1 tags after filtering in treatment: 8879762 INFO @ Fri, 10 Mar 2017 12:23:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:23:31: #1 finished! INFO @ Fri, 10 Mar 2017 12:23:31: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:23:34: #2 number of paired peaks: 2035 INFO @ Fri, 10 Mar 2017 12:23:34: start model_add_line... INFO @ Fri, 10 Mar 2017 12:23:35: 7000000 INFO @ Fri, 10 Mar 2017 12:23:45: 8000000 INFO @ Fri, 10 Mar 2017 12:23:47: 8000000 INFO @ Fri, 10 Mar 2017 12:23:53: start X-correlation... INFO @ Fri, 10 Mar 2017 12:23:53: end of X-cor INFO @ Fri, 10 Mar 2017 12:23:53: #2 finished! INFO @ Fri, 10 Mar 2017 12:23:53: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:23:53: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:23:53: #2.2 Generate R script for model : SRX110773.05_model.r WARNING @ Fri, 10 Mar 2017 12:23:53: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:23:53: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Fri, 10 Mar 2017 12:23:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:23:53: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:23:55: #1 tag size is determined as 45 bps INFO @ Fri, 10 Mar 2017 12:23:55: #1 tag size = 45 INFO @ Fri, 10 Mar 2017 12:23:55: #1 total tags in treatment: 8882913 INFO @ Fri, 10 Mar 2017 12:23:55: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:23:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:23:55: #1 tag size is determined as 45 bps INFO @ Fri, 10 Mar 2017 12:23:55: #1 tag size = 45 INFO @ Fri, 10 Mar 2017 12:23:55: #1 total tags in treatment: 8882913 INFO @ Fri, 10 Mar 2017 12:23:55: #1 user defined the maximum tags... INFO @ Fri, 10 Mar 2017 12:23:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Mar 2017 12:23:57: #1 tags after filtering in treatment: 8879762 INFO @ Fri, 10 Mar 2017 12:23:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:23:57: #1 finished! INFO @ Fri, 10 Mar 2017 12:23:57: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:23:58: #1 tags after filtering in treatment: 8879762 INFO @ Fri, 10 Mar 2017 12:23:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Mar 2017 12:23:58: #1 finished! INFO @ Fri, 10 Mar 2017 12:23:58: #2 Build Peak Model... INFO @ Fri, 10 Mar 2017 12:23:59: #2 number of paired peaks: 2035 INFO @ Fri, 10 Mar 2017 12:23:59: start model_add_line... INFO @ Fri, 10 Mar 2017 12:24:00: #2 number of paired peaks: 2035 INFO @ Fri, 10 Mar 2017 12:24:00: start model_add_line... INFO @ Fri, 10 Mar 2017 12:24:17: start X-correlation... INFO @ Fri, 10 Mar 2017 12:24:17: end of X-cor INFO @ Fri, 10 Mar 2017 12:24:17: #2 finished! INFO @ Fri, 10 Mar 2017 12:24:17: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:24:17: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:24:17: #2.2 Generate R script for model : SRX110773.20_model.r WARNING @ Fri, 10 Mar 2017 12:24:17: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:24:17: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Fri, 10 Mar 2017 12:24:17: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:24:17: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:24:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:24:18: start X-correlation... INFO @ Fri, 10 Mar 2017 12:24:18: end of X-cor INFO @ Fri, 10 Mar 2017 12:24:18: #2 finished! INFO @ Fri, 10 Mar 2017 12:24:18: #2 predicted fragment length is 81 bps INFO @ Fri, 10 Mar 2017 12:24:18: #2 alternative fragment length(s) may be 81 bps INFO @ Fri, 10 Mar 2017 12:24:18: #2.2 Generate R script for model : SRX110773.10_model.r WARNING @ Fri, 10 Mar 2017 12:24:18: #2 Since the d (81) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 10 Mar 2017 12:24:18: #2 You may need to consider one of the other alternative d(s): 81 WARNING @ Fri, 10 Mar 2017 12:24:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 10 Mar 2017 12:24:18: #3 Call peaks... INFO @ Fri, 10 Mar 2017 12:24:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Mar 2017 12:24:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:25:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:25:21: #3 Call peaks for each chromosome... INFO @ Fri, 10 Mar 2017 12:25:44: #4 Write output xls file... SRX110773.05_peaks.xls INFO @ Fri, 10 Mar 2017 12:25:45: #4 Write peak in narrowPeak format file... SRX110773.05_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:25:45: #4 Write summits bed file... SRX110773.05_summits.bed INFO @ Fri, 10 Mar 2017 12:25:45: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6325 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:26:04: #4 Write output xls file... SRX110773.20_peaks.xls INFO @ Fri, 10 Mar 2017 12:26:04: #4 Write peak in narrowPeak format file... SRX110773.20_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:26:04: #4 Write summits bed file... SRX110773.20_summits.bed INFO @ Fri, 10 Mar 2017 12:26:04: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2651 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 10 Mar 2017 12:26:09: #4 Write output xls file... SRX110773.10_peaks.xls INFO @ Fri, 10 Mar 2017 12:26:09: #4 Write peak in narrowPeak format file... SRX110773.10_peaks.narrowPeak INFO @ Fri, 10 Mar 2017 12:26:09: #4 Write summits bed file... SRX110773.10_summits.bed INFO @ Fri, 10 Mar 2017 12:26:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4420 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。