Job ID = 9157980 sra ファイルのダウンロード中... Completed: 5214591K bytes transferred in 225 seconds (189810K 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 83490159 spots for /home/okishinya/chipatlas/results/dm3/SRX2788641/SRR5515261.sra Written 83490159 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: 00:30:31 83490159 reads; of these: 83490159 (100.00%) were unpaired; of these: 42659850 (51.10%) aligned 0 times 35193466 (42.15%) aligned exactly 1 time 5636843 (6.75%) aligned >1 times 48.90% overall alignment rate Time searching: 00:30:31 Overall time: 00:30:31 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 20 files... [bam_rmdupse_core] 36626727 / 40830309 = 0.8970 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 @ Tue, 27 Jun 2017 15:09:22: # Command line: callpeak -t SRX2788641.bam -f BAM -g dm -n SRX2788641.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788641.20 # format = BAM # ChIP-seq file = ['SRX2788641.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 @ Tue, 27 Jun 2017 15:09:22: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:09:22: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:09:22: # Command line: callpeak -t SRX2788641.bam -f BAM -g dm -n SRX2788641.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788641.10 # format = BAM # ChIP-seq file = ['SRX2788641.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 @ Tue, 27 Jun 2017 15:09:22: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:09:22: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:09:22: # Command line: callpeak -t SRX2788641.bam -f BAM -g dm -n SRX2788641.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788641.05 # format = BAM # ChIP-seq file = ['SRX2788641.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 @ Tue, 27 Jun 2017 15:09:22: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:09:22: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:09:32: 1000000 INFO @ Tue, 27 Jun 2017 15:09:32: 1000000 INFO @ Tue, 27 Jun 2017 15:09:33: 1000000 INFO @ Tue, 27 Jun 2017 15:09:42: 2000000 INFO @ Tue, 27 Jun 2017 15:09:42: 2000000 INFO @ Tue, 27 Jun 2017 15:09:43: 2000000 INFO @ Tue, 27 Jun 2017 15:09:52: 3000000 INFO @ Tue, 27 Jun 2017 15:09:52: 3000000 INFO @ Tue, 27 Jun 2017 15:09:53: 3000000 INFO @ Tue, 27 Jun 2017 15:10:02: 4000000 INFO @ Tue, 27 Jun 2017 15:10:03: 4000000 INFO @ Tue, 27 Jun 2017 15:10:03: 4000000 INFO @ Tue, 27 Jun 2017 15:10:04: #1 tag size is determined as 101 bps INFO @ Tue, 27 Jun 2017 15:10:04: #1 tag size = 101 INFO @ Tue, 27 Jun 2017 15:10:04: #1 total tags in treatment: 4203582 INFO @ Tue, 27 Jun 2017 15:10:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:10:04: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:10:04: #1 tags after filtering in treatment: 4203582 INFO @ Tue, 27 Jun 2017 15:10:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:10:04: #1 finished! INFO @ Tue, 27 Jun 2017 15:10:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:10:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:10:04: #2 number of paired peaks: 1570 INFO @ Tue, 27 Jun 2017 15:10:04: start model_add_line... INFO @ Tue, 27 Jun 2017 15:10:04: start X-correlation... INFO @ Tue, 27 Jun 2017 15:10:04: end of X-cor INFO @ Tue, 27 Jun 2017 15:10:04: #2 finished! INFO @ Tue, 27 Jun 2017 15:10:04: #2 predicted fragment length is 128 bps INFO @ Tue, 27 Jun 2017 15:10:04: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 27 Jun 2017 15:10:04: #2.2 Generate R script for model : SRX2788641.10_model.r WARNING @ Tue, 27 Jun 2017 15:10:04: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:10:04: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Tue, 27 Jun 2017 15:10:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 15:10:04: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:10:05: #1 tag size is determined as 101 bps INFO @ Tue, 27 Jun 2017 15:10:05: #1 tag size = 101 INFO @ Tue, 27 Jun 2017 15:10:05: #1 total tags in treatment: 4203582 INFO @ Tue, 27 Jun 2017 15:10:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:10:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:10:05: #1 tags after filtering in treatment: 4203582 INFO @ Tue, 27 Jun 2017 15:10:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:10:05: #1 finished! INFO @ Tue, 27 Jun 2017 15:10:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:10:05: #1 tag size is determined as 101 bps INFO @ Tue, 27 Jun 2017 15:10:05: #1 tag size = 101 INFO @ Tue, 27 Jun 2017 15:10:05: #1 total tags in treatment: 4203582 INFO @ Tue, 27 Jun 2017 15:10:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:10:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:10:05: #1 tags after filtering in treatment: 4203582 INFO @ Tue, 27 Jun 2017 15:10:05: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:10:05: #1 finished! INFO @ Tue, 27 Jun 2017 15:10:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:10:05: #2 number of paired peaks: 1570 INFO @ Tue, 27 Jun 2017 15:10:05: start model_add_line... INFO @ Tue, 27 Jun 2017 15:10:05: start X-correlation... INFO @ Tue, 27 Jun 2017 15:10:05: end of X-cor INFO @ Tue, 27 Jun 2017 15:10:05: #2 finished! INFO @ Tue, 27 Jun 2017 15:10:05: #2 predicted fragment length is 128 bps INFO @ Tue, 27 Jun 2017 15:10:05: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 27 Jun 2017 15:10:05: #2.2 Generate R script for model : SRX2788641.05_model.r WARNING @ Tue, 27 Jun 2017 15:10:05: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:10:05: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Tue, 27 Jun 2017 15:10:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 15:10:05: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:10:05: #2 number of paired peaks: 1570 INFO @ Tue, 27 Jun 2017 15:10:05: start model_add_line... INFO @ Tue, 27 Jun 2017 15:10:05: start X-correlation... INFO @ Tue, 27 Jun 2017 15:10:05: end of X-cor INFO @ Tue, 27 Jun 2017 15:10:05: #2 finished! INFO @ Tue, 27 Jun 2017 15:10:05: #2 predicted fragment length is 128 bps INFO @ Tue, 27 Jun 2017 15:10:05: #2 alternative fragment length(s) may be 128 bps INFO @ Tue, 27 Jun 2017 15:10:05: #2.2 Generate R script for model : SRX2788641.20_model.r WARNING @ Tue, 27 Jun 2017 15:10:05: #2 Since the d (128) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:10:05: #2 You may need to consider one of the other alternative d(s): 128 WARNING @ Tue, 27 Jun 2017 15:10:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 15:10:05: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:10:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:10:14: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:10:16: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:10:17: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:10:20: #4 Write output xls file... SRX2788641.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:10:20: #4 Write peak in narrowPeak format file... SRX2788641.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:10:20: #4 Write summits bed file... SRX2788641.10_summits.bed INFO @ Tue, 27 Jun 2017 15:10:20: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1435 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:10:22: #4 Write output xls file... SRX2788641.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:10:22: #4 Write peak in narrowPeak format file... SRX2788641.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:10:22: #4 Write summits bed file... SRX2788641.05_summits.bed INFO @ Tue, 27 Jun 2017 15:10:22: Done! INFO @ Tue, 27 Jun 2017 15:10:22: #4 Write output xls file... SRX2788641.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:10:22: #4 Write peak in narrowPeak format file... SRX2788641.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:10:22: #4 Write summits bed file... SRX2788641.20_summits.bed INFO @ Tue, 27 Jun 2017 15:10:22: Done! pass1 - making usageList (10 chroms): 1 millis pass1 - making usageList (15 chroms)pass2 - checking and writing primary data (497 records, 4 fields): 1 millis : 2 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (4519 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。