Job ID = 9157984 sra ファイルのダウンロード中... Completed: 1343362K bytes transferred in 55 seconds (197490K 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 25037552 spots for /home/okishinya/chipatlas/results/dm3/SRX2788643/SRR5515263.sra Written 25037552 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: 00:13:20 25037552 reads; of these: 25037552 (100.00%) were unpaired; of these: 927913 (3.71%) aligned 0 times 19840287 (79.24%) aligned exactly 1 time 4269352 (17.05%) aligned >1 times 96.29% overall alignment rate Time searching: 00:13:20 Overall time: 00:13:20 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 12 files... [bam_rmdupse_core] 10582037 / 24109639 = 0.4389 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 14:43:25: # Command line: callpeak -t SRX2788643.bam -f BAM -g dm -n SRX2788643.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788643.10 # format = BAM # ChIP-seq file = ['SRX2788643.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 14:43:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:43:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:43:25: # Command line: callpeak -t SRX2788643.bam -f BAM -g dm -n SRX2788643.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788643.05 # format = BAM # ChIP-seq file = ['SRX2788643.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 14:43:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:43:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:43:25: # Command line: callpeak -t SRX2788643.bam -f BAM -g dm -n SRX2788643.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788643.20 # format = BAM # ChIP-seq file = ['SRX2788643.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 14:43:25: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:43:25: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:43:35: 1000000 INFO @ Tue, 27 Jun 2017 14:43:35: 1000000 INFO @ Tue, 27 Jun 2017 14:43:35: 1000000 INFO @ Tue, 27 Jun 2017 14:43:45: 2000000 INFO @ Tue, 27 Jun 2017 14:43:45: 2000000 INFO @ Tue, 27 Jun 2017 14:43:46: 2000000 INFO @ Tue, 27 Jun 2017 14:43:56: 3000000 INFO @ Tue, 27 Jun 2017 14:43:56: 3000000 INFO @ Tue, 27 Jun 2017 14:43:56: 3000000 INFO @ Tue, 27 Jun 2017 14:44:06: 4000000 INFO @ Tue, 27 Jun 2017 14:44:06: 4000000 INFO @ Tue, 27 Jun 2017 14:44:06: 4000000 INFO @ Tue, 27 Jun 2017 14:44:16: 5000000 INFO @ Tue, 27 Jun 2017 14:44:16: 5000000 INFO @ Tue, 27 Jun 2017 14:44:16: 5000000 INFO @ Tue, 27 Jun 2017 14:44:25: 6000000 INFO @ Tue, 27 Jun 2017 14:44:25: 6000000 INFO @ Tue, 27 Jun 2017 14:44:26: 6000000 INFO @ Tue, 27 Jun 2017 14:44:35: 7000000 INFO @ Tue, 27 Jun 2017 14:44:35: 7000000 INFO @ Tue, 27 Jun 2017 14:44:36: 7000000 INFO @ Tue, 27 Jun 2017 14:44:46: 8000000 INFO @ Tue, 27 Jun 2017 14:44:46: 8000000 INFO @ Tue, 27 Jun 2017 14:44:46: 8000000 INFO @ Tue, 27 Jun 2017 14:44:56: 9000000 INFO @ Tue, 27 Jun 2017 14:44:56: 9000000 INFO @ Tue, 27 Jun 2017 14:44:57: 9000000 INFO @ Tue, 27 Jun 2017 14:45:07: 10000000 INFO @ Tue, 27 Jun 2017 14:45:07: 10000000 INFO @ Tue, 27 Jun 2017 14:45:08: 10000000 INFO @ Tue, 27 Jun 2017 14:45:17: 11000000 INFO @ Tue, 27 Jun 2017 14:45:17: 11000000 INFO @ Tue, 27 Jun 2017 14:45:19: 11000000 INFO @ Tue, 27 Jun 2017 14:45:28: 12000000 INFO @ Tue, 27 Jun 2017 14:45:28: 12000000 INFO @ Tue, 27 Jun 2017 14:45:30: 12000000 INFO @ Tue, 27 Jun 2017 14:45:38: 13000000 INFO @ Tue, 27 Jun 2017 14:45:38: 13000000 INFO @ Tue, 27 Jun 2017 14:45:41: 13000000 INFO @ Tue, 27 Jun 2017 14:45:43: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 14:45:43: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 14:45:43: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 14:45:43: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 14:45:43: #1 total tags in treatment: 13527602 INFO @ Tue, 27 Jun 2017 14:45:43: #1 total tags in treatment: 13527602 INFO @ Tue, 27 Jun 2017 14:45:43: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:45:43: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:45:43: #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 14:45:43: #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 14:45:44: #1 tags after filtering in treatment: 13527602 INFO @ Tue, 27 Jun 2017 14:45:44: #1 tags after filtering in treatment: 13527602 INFO @ Tue, 27 Jun 2017 14:45:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:45:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:45:44: #1 finished! INFO @ Tue, 27 Jun 2017 14:45:44: #1 finished! INFO @ Tue, 27 Jun 2017 14:45:44: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:45:44: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:45:44: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:45:45: #2 number of paired peaks: 2631 INFO @ Tue, 27 Jun 2017 14:45:45: start model_add_line... INFO @ Tue, 27 Jun 2017 14:45:45: #2 number of paired peaks: 2631 INFO @ Tue, 27 Jun 2017 14:45:45: start model_add_line... INFO @ Tue, 27 Jun 2017 14:45:45: start X-correlation... INFO @ Tue, 27 Jun 2017 14:45:45: end of X-cor INFO @ Tue, 27 Jun 2017 14:45:45: #2 finished! INFO @ Tue, 27 Jun 2017 14:45:45: #2 predicted fragment length is 143 bps INFO @ Tue, 27 Jun 2017 14:45:45: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 27 Jun 2017 14:45:45: #2.2 Generate R script for model : SRX2788643.20_model.r WARNING @ Tue, 27 Jun 2017 14:45:45: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:45:45: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 27 Jun 2017 14:45:45: #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 14:45:45: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:45:45: start X-correlation... INFO @ Tue, 27 Jun 2017 14:45:45: end of X-cor INFO @ Tue, 27 Jun 2017 14:45:45: #2 finished! INFO @ Tue, 27 Jun 2017 14:45:45: #2 predicted fragment length is 143 bps INFO @ Tue, 27 Jun 2017 14:45:45: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 27 Jun 2017 14:45:45: #2.2 Generate R script for model : SRX2788643.10_model.r WARNING @ Tue, 27 Jun 2017 14:45:45: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:45:45: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 27 Jun 2017 14:45:45: #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 14:45:45: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:45:47: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 14:45:47: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 14:45:47: #1 total tags in treatment: 13527602 INFO @ Tue, 27 Jun 2017 14:45:47: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:45:47: #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 14:45:47: #1 tags after filtering in treatment: 13527602 INFO @ Tue, 27 Jun 2017 14:45:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:45:47: #1 finished! INFO @ Tue, 27 Jun 2017 14:45:47: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:45:48: #2 number of paired peaks: 2631 INFO @ Tue, 27 Jun 2017 14:45:48: start model_add_line... INFO @ Tue, 27 Jun 2017 14:45:49: start X-correlation... INFO @ Tue, 27 Jun 2017 14:45:49: end of X-cor INFO @ Tue, 27 Jun 2017 14:45:49: #2 finished! INFO @ Tue, 27 Jun 2017 14:45:49: #2 predicted fragment length is 143 bps INFO @ Tue, 27 Jun 2017 14:45:49: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 27 Jun 2017 14:45:49: #2.2 Generate R script for model : SRX2788643.05_model.r WARNING @ Tue, 27 Jun 2017 14:45:49: #2 Since the d (143) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 14:45:49: #2 You may need to consider one of the other alternative d(s): 143 WARNING @ Tue, 27 Jun 2017 14:45:49: #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 14:45:49: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:45:49: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:46:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:46:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:46:24: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:46:36: #4 Write output xls file... SRX2788643.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:46:36: #4 Write peak in narrowPeak format file... SRX2788643.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:46:36: #4 Write summits bed file... SRX2788643.10_summits.bed INFO @ Tue, 27 Jun 2017 14:46:36: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5840 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:46:38: #4 Write output xls file... SRX2788643.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:46:38: #4 Write peak in narrowPeak format file... SRX2788643.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:46:38: #4 Write summits bed file... SRX2788643.20_summits.bed INFO @ Tue, 27 Jun 2017 14:46:38: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3390 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:46:43: #4 Write output xls file... SRX2788643.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:46:43: #4 Write peak in narrowPeak format file... SRX2788643.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:46:43: #4 Write summits bed file... SRX2788643.05_summits.bed INFO @ Tue, 27 Jun 2017 14:46:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8155 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。