Job ID = 9730452 sra ファイルのダウンロード中... Completed: 841492K bytes transferred in 18 seconds (368890K bits/sec), in 1 file, 2 directories. 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 25053403 spots for /home/okishinya/chipatlas/results/dm3/SRX2638366/SRR5341692.sra Written 25053403 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: 00:00:01 Multiseed full-index search: 00:14:45 25053403 reads; of these: 25053403 (100.00%) were unpaired; of these: 8926419 (35.63%) aligned 0 times 5139589 (20.51%) aligned exactly 1 time 10987395 (43.86%) aligned >1 times 64.37% overall alignment rate Time searching: 00:14:46 Overall time: 00:14:46 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_sort_core] merging from 8 files... [bam_rmdupse_core] 13442437 / 16126984 = 0.8335 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, 03 Sep 2017 01:13:26: # Command line: callpeak -t SRX2638366.bam -f BAM -g dm -n SRX2638366.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2638366.05 # format = BAM # ChIP-seq file = ['SRX2638366.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 # Paired-End mode is off INFO @ Sun, 03 Sep 2017 01:13:26: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:13:26: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:13:26: # Command line: callpeak -t SRX2638366.bam -f BAM -g dm -n SRX2638366.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2638366.10 # format = BAM # ChIP-seq file = ['SRX2638366.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 # Paired-End mode is off INFO @ Sun, 03 Sep 2017 01:13:26: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:13:26: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:13:26: # Command line: callpeak -t SRX2638366.bam -f BAM -g dm -n SRX2638366.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2638366.20 # format = BAM # ChIP-seq file = ['SRX2638366.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 # Paired-End mode is off INFO @ Sun, 03 Sep 2017 01:13:26: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:13:26: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:13:33: 1000000 INFO @ Sun, 03 Sep 2017 01:13:34: 1000000 INFO @ Sun, 03 Sep 2017 01:13:34: 1000000 INFO @ Sun, 03 Sep 2017 01:13:40: 2000000 INFO @ Sun, 03 Sep 2017 01:13:41: 2000000 INFO @ Sun, 03 Sep 2017 01:13:41: 2000000 INFO @ Sun, 03 Sep 2017 01:13:45: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:13:45: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:13:45: #1 total tags in treatment: 2684547 INFO @ Sun, 03 Sep 2017 01:13:45: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:13:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:13:45: #1 tags after filtering in treatment: 2684547 INFO @ Sun, 03 Sep 2017 01:13:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:13:45: #1 finished! INFO @ Sun, 03 Sep 2017 01:13:45: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:13:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:13:45: #2 number of paired peaks: 2655 INFO @ Sun, 03 Sep 2017 01:13:45: start model_add_line... INFO @ Sun, 03 Sep 2017 01:13:45: start X-correlation... INFO @ Sun, 03 Sep 2017 01:13:45: end of X-cor INFO @ Sun, 03 Sep 2017 01:13:45: #2 finished! INFO @ Sun, 03 Sep 2017 01:13:45: #2 predicted fragment length is 59 bps INFO @ Sun, 03 Sep 2017 01:13:45: #2 alternative fragment length(s) may be 59 bps INFO @ Sun, 03 Sep 2017 01:13:45: #2.2 Generate R script for model : SRX2638366.10_model.r WARNING @ Sun, 03 Sep 2017 01:13:45: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:13:45: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sun, 03 Sep 2017 01:13:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:13:45: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:13:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:13:46: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:13:46: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:13:46: #1 total tags in treatment: 2684547 INFO @ Sun, 03 Sep 2017 01:13:46: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:13:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:13:46: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:13:46: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:13:46: #1 total tags in treatment: 2684547 INFO @ Sun, 03 Sep 2017 01:13:46: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:13:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Sep 2017 01:13:46: #1 tags after filtering in treatment: 2684547 INFO @ Sun, 03 Sep 2017 01:13:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:13:46: #1 finished! INFO @ Sun, 03 Sep 2017 01:13:46: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:13:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:13:46: #1 tags after filtering in treatment: 2684547 INFO @ Sun, 03 Sep 2017 01:13:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:13:46: #1 finished! INFO @ Sun, 03 Sep 2017 01:13:46: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:13:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:13:46: #2 number of paired peaks: 2655 INFO @ Sun, 03 Sep 2017 01:13:46: start model_add_line... INFO @ Sun, 03 Sep 2017 01:13:46: #2 number of paired peaks: 2655 INFO @ Sun, 03 Sep 2017 01:13:46: start model_add_line... INFO @ Sun, 03 Sep 2017 01:13:47: start X-correlation... INFO @ Sun, 03 Sep 2017 01:13:47: start X-correlation... INFO @ Sun, 03 Sep 2017 01:13:47: end of X-cor INFO @ Sun, 03 Sep 2017 01:13:47: end of X-cor INFO @ Sun, 03 Sep 2017 01:13:47: #2 finished! INFO @ Sun, 03 Sep 2017 01:13:47: #2 finished! INFO @ Sun, 03 Sep 2017 01:13:47: #2 predicted fragment length is 59 bps INFO @ Sun, 03 Sep 2017 01:13:47: #2 predicted fragment length is 59 bps INFO @ Sun, 03 Sep 2017 01:13:47: #2 alternative fragment length(s) may be 59 bps INFO @ Sun, 03 Sep 2017 01:13:47: #2 alternative fragment length(s) may be 59 bps INFO @ Sun, 03 Sep 2017 01:13:47: #2.2 Generate R script for model : SRX2638366.05_model.r INFO @ Sun, 03 Sep 2017 01:13:47: #2.2 Generate R script for model : SRX2638366.20_model.r WARNING @ Sun, 03 Sep 2017 01:13:47: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:13:47: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sun, 03 Sep 2017 01:13:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:13:47: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:13:47: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 03 Sep 2017 01:13:47: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:13:47: #2 You may need to consider one of the other alternative d(s): 59 WARNING @ Sun, 03 Sep 2017 01:13:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Sep 2017 01:13:47: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:13:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:13:52: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:13:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:13:53: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:13:55: #4 Write output xls file... SRX2638366.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:55: #4 Write peak in narrowPeak format file... SRX2638366.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:56: #4 Write summits bed file... SRX2638366.10_summits.bed INFO @ Sun, 03 Sep 2017 01:13:56: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2576 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:13:57: #4 Write output xls file... SRX2638366.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:57: #4 Write peak in narrowPeak format file... SRX2638366.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:57: #4 Write summits bed file... SRX2638366.20_summits.bed INFO @ Sun, 03 Sep 2017 01:13:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1608 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:13:57: #4 Write output xls file... SRX2638366.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:13:57: #4 Write peak in narrowPeak format file... SRX2638366.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:13:57: #4 Write summits bed file... SRX2638366.05_summits.bed INFO @ Sun, 03 Sep 2017 01:13:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3845 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。