Job ID = 9157986 sra ファイルのダウンロード中... Completed: 10941133K bytes transferred in 369 seconds (242758K 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 187305317 spots for /home/okishinya/chipatlas/results/dm3/SRX2788644/SRR5515264.sra Written 187305317 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: 01:31:06 187305317 reads; of these: 187305317 (100.00%) were unpaired; of these: 25326280 (13.52%) aligned 0 times 136068205 (72.65%) aligned exactly 1 time 25910832 (13.83%) aligned >1 times 86.48% overall alignment rate Time searching: 01:31:07 Overall time: 01:31:07 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 68 files... [bam_rmdupse_core] 152583732 / 161979037 = 0.9420 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 16:51:20: # Command line: callpeak -t SRX2788644.bam -f BAM -g dm -n SRX2788644.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788644.05 # format = BAM # ChIP-seq file = ['SRX2788644.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 16:51:20: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:51:20: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:51:20: # Command line: callpeak -t SRX2788644.bam -f BAM -g dm -n SRX2788644.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788644.10 # format = BAM # ChIP-seq file = ['SRX2788644.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 16:51:20: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:51:20: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:51:20: # Command line: callpeak -t SRX2788644.bam -f BAM -g dm -n SRX2788644.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788644.20 # format = BAM # ChIP-seq file = ['SRX2788644.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 16:51:20: #1 read tag files... INFO @ Tue, 27 Jun 2017 16:51:20: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 16:51:28: 1000000 INFO @ Tue, 27 Jun 2017 16:51:29: 1000000 INFO @ Tue, 27 Jun 2017 16:51:29: 1000000 INFO @ Tue, 27 Jun 2017 16:51:37: 2000000 INFO @ Tue, 27 Jun 2017 16:51:38: 2000000 INFO @ Tue, 27 Jun 2017 16:51:40: 2000000 INFO @ Tue, 27 Jun 2017 16:51:46: 3000000 INFO @ Tue, 27 Jun 2017 16:51:46: 3000000 INFO @ Tue, 27 Jun 2017 16:51:49: 3000000 INFO @ Tue, 27 Jun 2017 16:51:54: 4000000 INFO @ Tue, 27 Jun 2017 16:51:55: 4000000 INFO @ Tue, 27 Jun 2017 16:51:59: 4000000 INFO @ Tue, 27 Jun 2017 16:52:02: 5000000 INFO @ Tue, 27 Jun 2017 16:52:05: 5000000 INFO @ Tue, 27 Jun 2017 16:52:10: 6000000 INFO @ Tue, 27 Jun 2017 16:52:10: 5000000 INFO @ Tue, 27 Jun 2017 16:52:14: 6000000 INFO @ Tue, 27 Jun 2017 16:52:18: 7000000 INFO @ Tue, 27 Jun 2017 16:52:20: 6000000 INFO @ Tue, 27 Jun 2017 16:52:23: 7000000 INFO @ Tue, 27 Jun 2017 16:52:27: 8000000 INFO @ Tue, 27 Jun 2017 16:52:30: 7000000 INFO @ Tue, 27 Jun 2017 16:52:32: 8000000 INFO @ Tue, 27 Jun 2017 16:52:35: 9000000 INFO @ Tue, 27 Jun 2017 16:52:38: #1 tag size is determined as 96 bps INFO @ Tue, 27 Jun 2017 16:52:38: #1 tag size = 96 INFO @ Tue, 27 Jun 2017 16:52:38: #1 total tags in treatment: 9395305 INFO @ Tue, 27 Jun 2017 16:52:38: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:52:38: #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 16:52:38: #1 tags after filtering in treatment: 9395305 INFO @ Tue, 27 Jun 2017 16:52:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:52:38: #1 finished! INFO @ Tue, 27 Jun 2017 16:52:38: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:52:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:52:39: #2 number of paired peaks: 4514 INFO @ Tue, 27 Jun 2017 16:52:39: start model_add_line... INFO @ Tue, 27 Jun 2017 16:52:39: start X-correlation... INFO @ Tue, 27 Jun 2017 16:52:40: end of X-cor INFO @ Tue, 27 Jun 2017 16:52:40: #2 finished! INFO @ Tue, 27 Jun 2017 16:52:40: #2 predicted fragment length is 97 bps INFO @ Tue, 27 Jun 2017 16:52:40: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 27 Jun 2017 16:52:40: #2.2 Generate R script for model : SRX2788644.05_model.r WARNING @ Tue, 27 Jun 2017 16:52:40: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:52:40: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 27 Jun 2017 16:52:40: #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 16:52:40: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:52:40: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:52:41: 8000000 INFO @ Tue, 27 Jun 2017 16:52:41: 9000000 INFO @ Tue, 27 Jun 2017 16:52:45: #1 tag size is determined as 96 bps INFO @ Tue, 27 Jun 2017 16:52:45: #1 tag size = 96 INFO @ Tue, 27 Jun 2017 16:52:45: #1 total tags in treatment: 9395305 INFO @ Tue, 27 Jun 2017 16:52:45: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:52:45: #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 16:52:45: #1 tags after filtering in treatment: 9395305 INFO @ Tue, 27 Jun 2017 16:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:52:45: #1 finished! INFO @ Tue, 27 Jun 2017 16:52:45: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:52:46: #2 number of paired peaks: 4514 INFO @ Tue, 27 Jun 2017 16:52:46: start model_add_line... INFO @ Tue, 27 Jun 2017 16:52:46: start X-correlation... INFO @ Tue, 27 Jun 2017 16:52:46: end of X-cor INFO @ Tue, 27 Jun 2017 16:52:46: #2 finished! INFO @ Tue, 27 Jun 2017 16:52:46: #2 predicted fragment length is 97 bps INFO @ Tue, 27 Jun 2017 16:52:46: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 27 Jun 2017 16:52:46: #2.2 Generate R script for model : SRX2788644.10_model.r WARNING @ Tue, 27 Jun 2017 16:52:46: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:52:46: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 27 Jun 2017 16:52:46: #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 16:52:46: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:52:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:52:50: 9000000 INFO @ Tue, 27 Jun 2017 16:52:53: #1 tag size is determined as 96 bps INFO @ Tue, 27 Jun 2017 16:52:53: #1 tag size = 96 INFO @ Tue, 27 Jun 2017 16:52:53: #1 total tags in treatment: 9395305 INFO @ Tue, 27 Jun 2017 16:52:53: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 16:52:53: #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 16:52:53: #1 tags after filtering in treatment: 9395305 INFO @ Tue, 27 Jun 2017 16:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 16:52:53: #1 finished! INFO @ Tue, 27 Jun 2017 16:52:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 16:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 16:52:54: #2 number of paired peaks: 4514 INFO @ Tue, 27 Jun 2017 16:52:54: start model_add_line... INFO @ Tue, 27 Jun 2017 16:52:55: start X-correlation... INFO @ Tue, 27 Jun 2017 16:52:55: end of X-cor INFO @ Tue, 27 Jun 2017 16:52:55: #2 finished! INFO @ Tue, 27 Jun 2017 16:52:55: #2 predicted fragment length is 97 bps INFO @ Tue, 27 Jun 2017 16:52:55: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 27 Jun 2017 16:52:55: #2.2 Generate R script for model : SRX2788644.20_model.r WARNING @ Tue, 27 Jun 2017 16:52:55: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 16:52:55: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 27 Jun 2017 16:52:55: #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 16:52:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 16:52:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 16:53:03: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:53:11: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:53:17: #4 Write output xls file... SRX2788644.05_peaks.xls INFO @ Tue, 27 Jun 2017 16:53:17: #4 Write peak in narrowPeak format file... SRX2788644.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:53:17: #4 Write summits bed file... SRX2788644.05_summits.bed INFO @ Tue, 27 Jun 2017 16:53:18: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (16620 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:53:20: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 16:53:24: #4 Write output xls file... SRX2788644.10_peaks.xls INFO @ Tue, 27 Jun 2017 16:53:24: #4 Write peak in narrowPeak format file... SRX2788644.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:53:24: #4 Write summits bed file... SRX2788644.10_summits.bed INFO @ Tue, 27 Jun 2017 16:53:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (11413 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 16:53:32: #4 Write output xls file... SRX2788644.20_peaks.xls INFO @ Tue, 27 Jun 2017 16:53:32: #4 Write peak in narrowPeak format file... SRX2788644.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 16:53:32: #4 Write summits bed file... SRX2788644.20_summits.bed INFO @ Tue, 27 Jun 2017 16:53:32: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6940 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。