Job ID = 9730450 sra ファイルのダウンロード中... Completed: 1065858K bytes transferred in 22 seconds (383316K 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 32521593 spots for /home/okishinya/chipatlas/results/dm3/SRX2638364/SRR5341690.sra Written 32521593 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: 00:11:03 32521593 reads; of these: 32521593 (100.00%) were unpaired; of these: 21683611 (66.67%) aligned 0 times 3857569 (11.86%) aligned exactly 1 time 6980413 (21.46%) aligned >1 times 33.33% overall alignment rate Time searching: 00:11:03 Overall time: 00:11:03 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] 9247951 / 10837982 = 0.8533 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 01:09:19: # Command line: callpeak -t SRX2638364.bam -f BAM -g dm -n SRX2638364.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2638364.10 # format = BAM # ChIP-seq file = ['SRX2638364.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 01:09:19: # Command line: callpeak -t SRX2638364.bam -f BAM -g dm -n SRX2638364.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2638364.05 # format = BAM # ChIP-seq file = ['SRX2638364.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 01:09:19: # Command line: callpeak -t SRX2638364.bam -f BAM -g dm -n SRX2638364.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2638364.20 # format = BAM # ChIP-seq file = ['SRX2638364.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 01:09:19: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:09:19: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:09:19: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:09:19: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:09:19: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:09:19: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:09:26: 1000000 INFO @ Sun, 03 Sep 2017 01:09:27: 1000000 INFO @ Sun, 03 Sep 2017 01:09:27: 1000000 INFO @ Sun, 03 Sep 2017 01:09:30: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:09:30: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:09:30: #1 total tags in treatment: 1590031 INFO @ Sun, 03 Sep 2017 01:09:30: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:09:30: #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 01:09:30: #1 tags after filtering in treatment: 1590031 INFO @ Sun, 03 Sep 2017 01:09:30: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:09:30: #1 finished! INFO @ Sun, 03 Sep 2017 01:09:30: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:09:30: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:09:31: #2 number of paired peaks: 2909 INFO @ Sun, 03 Sep 2017 01:09:31: start model_add_line... INFO @ Sun, 03 Sep 2017 01:09:31: start X-correlation... INFO @ Sun, 03 Sep 2017 01:09:31: end of X-cor INFO @ Sun, 03 Sep 2017 01:09:31: #2 finished! INFO @ Sun, 03 Sep 2017 01:09:31: #2 predicted fragment length is 68 bps INFO @ Sun, 03 Sep 2017 01:09:31: #2 alternative fragment length(s) may be 68 bps INFO @ Sun, 03 Sep 2017 01:09:31: #2.2 Generate R script for model : SRX2638364.20_model.r WARNING @ Sun, 03 Sep 2017 01:09:31: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:09:31: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sun, 03 Sep 2017 01:09:31: #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 01:09:31: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:09:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:09:32: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:09:32: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:09:32: #1 total tags in treatment: 1590031 INFO @ Sun, 03 Sep 2017 01:09:32: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:09:32: #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 01:09:32: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:09:32: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:09:32: #1 total tags in treatment: 1590031 INFO @ Sun, 03 Sep 2017 01:09:32: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:09:32: #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 01:09:32: #1 tags after filtering in treatment: 1590031 INFO @ Sun, 03 Sep 2017 01:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:09:32: #1 finished! INFO @ Sun, 03 Sep 2017 01:09:32: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:09:32: #1 tags after filtering in treatment: 1590031 INFO @ Sun, 03 Sep 2017 01:09:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:09:32: #1 finished! INFO @ Sun, 03 Sep 2017 01:09:32: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:09:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:09:32: #2 number of paired peaks: 2909 INFO @ Sun, 03 Sep 2017 01:09:32: start model_add_line... INFO @ Sun, 03 Sep 2017 01:09:32: #2 number of paired peaks: 2909 INFO @ Sun, 03 Sep 2017 01:09:32: start model_add_line... INFO @ Sun, 03 Sep 2017 01:09:32: start X-correlation... INFO @ Sun, 03 Sep 2017 01:09:32: start X-correlation... INFO @ Sun, 03 Sep 2017 01:09:32: end of X-cor INFO @ Sun, 03 Sep 2017 01:09:32: #2 finished! INFO @ Sun, 03 Sep 2017 01:09:32: #2 predicted fragment length is 68 bps INFO @ Sun, 03 Sep 2017 01:09:32: #2 alternative fragment length(s) may be 68 bps INFO @ Sun, 03 Sep 2017 01:09:32: #2.2 Generate R script for model : SRX2638364.05_model.r INFO @ Sun, 03 Sep 2017 01:09:32: end of X-cor INFO @ Sun, 03 Sep 2017 01:09:32: #2 finished! INFO @ Sun, 03 Sep 2017 01:09:32: #2 predicted fragment length is 68 bps INFO @ Sun, 03 Sep 2017 01:09:32: #2 alternative fragment length(s) may be 68 bps INFO @ Sun, 03 Sep 2017 01:09:32: #2.2 Generate R script for model : SRX2638364.10_model.r WARNING @ Sun, 03 Sep 2017 01:09:32: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:09:32: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sun, 03 Sep 2017 01:09:32: #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 01:09:32: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:09:32: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 03 Sep 2017 01:09:32: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:09:32: #2 You may need to consider one of the other alternative d(s): 68 WARNING @ Sun, 03 Sep 2017 01:09:32: #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 01:09:32: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:09:36: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:09:36: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:09:37: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:09:38: #4 Write output xls file... SRX2638364.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:09:38: #4 Write peak in narrowPeak format file... SRX2638364.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:09:38: #4 Write summits bed file... SRX2638364.20_summits.bed INFO @ Sun, 03 Sep 2017 01:09:38: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1529 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:09:39: #4 Write output xls file... SRX2638364.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:09:39: #4 Write peak in narrowPeak format file... SRX2638364.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:09:39: #4 Write summits bed file... SRX2638364.05_summits.bed INFO @ Sun, 03 Sep 2017 01:09:39: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3447 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:09:39: #4 Write output xls file... SRX2638364.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:09:39: #4 Write peak in narrowPeak format file... SRX2638364.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:09:39: #4 Write summits bed file... SRX2638364.10_summits.bed INFO @ Sun, 03 Sep 2017 01:09:39: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2327 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。