Job ID = 9157987 sra ファイルのダウンロード中... Completed: 8146645K bytes transferred in 312 seconds (213370K 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 128917535 spots for /home/okishinya/chipatlas/results/dm3/SRX2788645/SRR5515265.sra Written 128917535 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: 00:57:14 128917535 reads; of these: 128917535 (100.00%) were unpaired; of these: 5342613 (4.14%) aligned 0 times 106398118 (82.53%) aligned exactly 1 time 17176804 (13.32%) aligned >1 times 95.86% overall alignment rate Time searching: 00:57:14 Overall time: 00:57:14 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 52 files... [bam_rmdupse_core] 110230526 / 123574922 = 0.8920 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 16:06:23: # Command line: callpeak -t SRX2788645.bam -f BAM -g dm -n SRX2788645.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788645.20 # format = BAM # ChIP-seq file = ['SRX2788645.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 16:06:23: # Command line: callpeak -t SRX2788645.bam -f BAM -g dm -n SRX2788645.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788645.05 # format = BAM # ChIP-seq file = ['SRX2788645.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 16:06:23: # Command line: callpeak -t SRX2788645.bam -f BAM -g dm -n SRX2788645.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788645.10 # format = BAM # ChIP-seq file = ['SRX2788645.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 16:06:23: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:06:23: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:06:23: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:06:23: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:06:23: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:06:23: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:06:30: 1000000 INFO @ Tue, 27 Jun 2017 16:06:30: 1000000 INFO @ Tue, 27 Jun 2017 16:06:30: 1000000 INFO @ Tue, 27 Jun 2017 16:06:38: 2000000 INFO @ Tue, 27 Jun 2017 16:06:38: 2000000 INFO @ Tue, 27 Jun 2017 16:06:38: 2000000 INFO @ Tue, 27 Jun 2017 16:06:46: 3000000 INFO @ Tue, 27 Jun 2017 16:06:46: 3000000 INFO @ Tue, 27 Jun 2017 16:06:46: 3000000 INFO @ Tue, 27 Jun 2017 16:06:53: 4000000 INFO @ Tue, 27 Jun 2017 16:06:54: 4000000 INFO @ Tue, 27 Jun 2017 16:06:55: 4000000 INFO @ Tue, 27 Jun 2017 16:07:01: 5000000 INFO @ Tue, 27 Jun 2017 16:07:02: 5000000 INFO @ Tue, 27 Jun 2017 16:07:03: 5000000 INFO @ Tue, 27 Jun 2017 16:07:08: 6000000 INFO @ Tue, 27 Jun 2017 16:07:10: 6000000 INFO @ Tue, 27 Jun 2017 16:07:12: 6000000 INFO @ Tue, 27 Jun 2017 16:07:16: 7000000 INFO @ Tue, 27 Jun 2017 16:07:18: 7000000 INFO @ Tue, 27 Jun 2017 16:07:20: 7000000 INFO @ Tue, 27 Jun 2017 16:07:23: 8000000 INFO @ Tue, 27 Jun 2017 16:07:26: 8000000 INFO @ Tue, 27 Jun 2017 16:07:28: 8000000 INFO @ Tue, 27 Jun 2017 16:07:31: 9000000 INFO @ Tue, 27 Jun 2017 16:07:35: 9000000 INFO @ Tue, 27 Jun 2017 16:07:37: 9000000 INFO @ Tue, 27 Jun 2017 16:07:38: 10000000 INFO @ Tue, 27 Jun 2017 16:07:43: 10000000 INFO @ Tue, 27 Jun 2017 16:07:45: 10000000 INFO @ Tue, 27 Jun 2017 16:07:46: 11000000 INFO @ Tue, 27 Jun 2017 16:07:51: 11000000 INFO @ Tue, 27 Jun 2017 16:07:54: 11000000 INFO @ Tue, 27 Jun 2017 16:07:54: 12000000 INFO @ Tue, 27 Jun 2017 16:07:59: 12000000 INFO @ Tue, 27 Jun 2017 16:08:01: 13000000 INFO @ Tue, 27 Jun 2017 16:08:02: 12000000 INFO @ Tue, 27 Jun 2017 16:08:04: #1 tag size is determined as 97 bps INFO @ Tue, 27 Jun 2017 16:08:04: #1 tag size = 97 INFO @ Tue, 27 Jun 2017 16:08:04: #1 total tags in treatment: 13344396 INFO @ Tue, 27 Jun 2017 16:08:04: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:08:04: #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 16:08:04: #1 tags after filtering in treatment: 13344396 INFO @ Tue, 27 Jun 2017 16:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:08:04: #1 finished! INFO @ Tue, 27 Jun 2017 16:08:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:08:06: #2 number of paired peaks: 5965 INFO @ Tue, 27 Jun 2017 16:08:06: start model_add_line... INFO @ Tue, 27 Jun 2017 16:08:06: start X-correlation... INFO @ Tue, 27 Jun 2017 16:08:06: end of X-cor INFO @ Tue, 27 Jun 2017 16:08:06: #2 finished! INFO @ Tue, 27 Jun 2017 16:08:06: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 16:08:06: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 27 Jun 2017 16:08:06: #2.2 Generate R script for model : SRX2788645.10_model.r WARNING @ Tue, 27 Jun 2017 16:08:06: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:08:06: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Tue, 27 Jun 2017 16:08:06: #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 16:08:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:08:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:08:07: 13000000 INFO @ Tue, 27 Jun 2017 16:08:10: #1 tag size is determined as 97 bps INFO @ Tue, 27 Jun 2017 16:08:10: #1 tag size = 97 INFO @ Tue, 27 Jun 2017 16:08:10: #1 total tags in treatment: 13344396 INFO @ Tue, 27 Jun 2017 16:08:10: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:08:10: #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 16:08:10: 13000000 INFO @ Tue, 27 Jun 2017 16:08:10: #1 tags after filtering in treatment: 13344396 INFO @ Tue, 27 Jun 2017 16:08:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:08:10: #1 finished! INFO @ Tue, 27 Jun 2017 16:08:10: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:08:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:08:12: #2 number of paired peaks: 5965 INFO @ Tue, 27 Jun 2017 16:08:12: start model_add_line... INFO @ Tue, 27 Jun 2017 16:08:12: start X-correlation... INFO @ Tue, 27 Jun 2017 16:08:12: end of X-cor INFO @ Tue, 27 Jun 2017 16:08:12: #2 finished! INFO @ Tue, 27 Jun 2017 16:08:12: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 16:08:12: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 27 Jun 2017 16:08:12: #2.2 Generate R script for model : SRX2788645.05_model.r WARNING @ Tue, 27 Jun 2017 16:08:12: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:08:12: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Tue, 27 Jun 2017 16:08:12: #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 16:08:12: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:08:12: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:08:13: #1 tag size is determined as 97 bps INFO @ Tue, 27 Jun 2017 16:08:13: #1 tag size = 97 INFO @ Tue, 27 Jun 2017 16:08:13: #1 total tags in treatment: 13344396 INFO @ Tue, 27 Jun 2017 16:08:13: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:08:13: #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 16:08:13: #1 tags after filtering in treatment: 13344396 INFO @ Tue, 27 Jun 2017 16:08:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:08:13: #1 finished! INFO @ Tue, 27 Jun 2017 16:08:13: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:08:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:08:15: #2 number of paired peaks: 5965 INFO @ Tue, 27 Jun 2017 16:08:15: start model_add_line... INFO @ Tue, 27 Jun 2017 16:08:15: start X-correlation... INFO @ Tue, 27 Jun 2017 16:08:15: end of X-cor INFO @ Tue, 27 Jun 2017 16:08:15: #2 finished! INFO @ Tue, 27 Jun 2017 16:08:15: #2 predicted fragment length is 113 bps INFO @ Tue, 27 Jun 2017 16:08:15: #2 alternative fragment length(s) may be 113 bps INFO @ Tue, 27 Jun 2017 16:08:15: #2.2 Generate R script for model : SRX2788645.20_model.r WARNING @ Tue, 27 Jun 2017 16:08:15: #2 Since the d (113) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:08:15: #2 You may need to consider one of the other alternative d(s): 113 WARNING @ Tue, 27 Jun 2017 16:08:15: #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 16:08:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:08:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:08:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:08:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:08:53: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:08:59: #4 Write output xls file... SRX2788645.10_peaks.xls INFO @ Tue, 27 Jun 2017 16:09:00: #4 Write peak in narrowPeak format file... SRX2788645.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:09:00: #4 Write summits bed file... SRX2788645.10_summits.bed INFO @ Tue, 27 Jun 2017 16:09:00: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9502 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:09:08: #4 Write output xls file... SRX2788645.05_peaks.xls INFO @ Tue, 27 Jun 2017 16:09:08: #4 Write peak in narrowPeak format file... SRX2788645.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:09:08: #4 Write summits bed file... SRX2788645.05_summits.bed INFO @ Tue, 27 Jun 2017 16:09:08: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12107 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:09:12: #4 Write output xls file... SRX2788645.20_peaks.xls INFO @ Tue, 27 Jun 2017 16:09:12: #4 Write peak in narrowPeak format file... SRX2788645.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:09:12: #4 Write summits bed file... SRX2788645.20_summits.bed INFO @ Tue, 27 Jun 2017 16:09:12: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7188 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。