Job ID = 9730448 sra ファイルのダウンロード中... Completed: 1054047K bytes transferred in 22 seconds (387174K 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 32660686 spots for /home/okishinya/chipatlas/results/dm3/SRX2638362/SRR5341687.sra Written 32660686 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: 00:06:01 32660686 reads; of these: 32660686 (100.00%) were unpaired; of these: 28815632 (88.23%) aligned 0 times 1455439 (4.46%) aligned exactly 1 time 2389615 (7.32%) aligned >1 times 11.77% overall alignment rate Time searching: 00:06:01 Overall time: 00:06:01 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_rmdupse_core] 2974814 / 3845054 = 0.7737 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 01:03:03: # Command line: callpeak -t SRX2638362.bam -f BAM -g dm -n SRX2638362.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2638362.05 # format = BAM # ChIP-seq file = ['SRX2638362.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 01:03:03: # Command line: callpeak -t SRX2638362.bam -f BAM -g dm -n SRX2638362.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2638362.10 # format = BAM # ChIP-seq file = ['SRX2638362.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 01:03:03: # Command line: callpeak -t SRX2638362.bam -f BAM -g dm -n SRX2638362.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2638362.20 # format = BAM # ChIP-seq file = ['SRX2638362.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 01:03:03: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:03:03: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:03:03: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:03:03: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:03:03: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:03:03: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:03:09: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:03:09: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:03:09: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:03:09: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:03:09: #1 total tags in treatment: 870240 INFO @ Sun, 03 Sep 2017 01:03:09: #1 total tags in treatment: 870240 INFO @ Sun, 03 Sep 2017 01:03:09: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:03:09: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:03:09: #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 01:03:09: #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 01:03:09: #1 tags after filtering in treatment: 870240 INFO @ Sun, 03 Sep 2017 01:03:09: #1 tags after filtering in treatment: 870240 INFO @ Sun, 03 Sep 2017 01:03:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:03:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:03:09: #1 finished! INFO @ Sun, 03 Sep 2017 01:03:09: #1 finished! INFO @ Sun, 03 Sep 2017 01:03:09: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:03:09: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:03:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:03:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:03:09: #1 tag size is determined as 51 bps INFO @ Sun, 03 Sep 2017 01:03:09: #1 tag size = 51 INFO @ Sun, 03 Sep 2017 01:03:09: #1 total tags in treatment: 870240 INFO @ Sun, 03 Sep 2017 01:03:09: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:03:09: #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 01:03:09: #1 tags after filtering in treatment: 870240 INFO @ Sun, 03 Sep 2017 01:03:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:03:09: #1 finished! INFO @ Sun, 03 Sep 2017 01:03:09: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:03:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:03:10: #2 number of paired peaks: 1985 INFO @ Sun, 03 Sep 2017 01:03:10: #2 number of paired peaks: 1985 INFO @ Sun, 03 Sep 2017 01:03:10: start model_add_line... INFO @ Sun, 03 Sep 2017 01:03:10: start model_add_line... INFO @ Sun, 03 Sep 2017 01:03:10: start X-correlation... INFO @ Sun, 03 Sep 2017 01:03:10: start X-correlation... INFO @ Sun, 03 Sep 2017 01:03:10: #2 number of paired peaks: 1985 INFO @ Sun, 03 Sep 2017 01:03:10: start model_add_line... INFO @ Sun, 03 Sep 2017 01:03:10: start X-correlation... INFO @ Sun, 03 Sep 2017 01:03:10: end of X-cor INFO @ Sun, 03 Sep 2017 01:03:10: end of X-cor INFO @ Sun, 03 Sep 2017 01:03:10: end of X-cor INFO @ Sun, 03 Sep 2017 01:03:10: #2 finished! INFO @ Sun, 03 Sep 2017 01:03:10: #2 finished! INFO @ Sun, 03 Sep 2017 01:03:10: #2 finished! INFO @ Sun, 03 Sep 2017 01:03:10: #2 predicted fragment length is 53 bps INFO @ Sun, 03 Sep 2017 01:03:10: #2 predicted fragment length is 53 bps INFO @ Sun, 03 Sep 2017 01:03:10: #2 predicted fragment length is 53 bps INFO @ Sun, 03 Sep 2017 01:03:10: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 03 Sep 2017 01:03:10: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 03 Sep 2017 01:03:10: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 03 Sep 2017 01:03:10: #2.2 Generate R script for model : SRX2638362.05_model.r INFO @ Sun, 03 Sep 2017 01:03:10: #2.2 Generate R script for model : SRX2638362.20_model.r INFO @ Sun, 03 Sep 2017 01:03:10: #2.2 Generate R script for model : SRX2638362.10_model.r WARNING @ Sun, 03 Sep 2017 01:03:10: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:03:10: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:03:10: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 03 Sep 2017 01:03:10: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 03 Sep 2017 01:03:10: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Sun, 03 Sep 2017 01:03:10: #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 01:03:10: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:03:10: #3 Call peaks... WARNING @ Sun, 03 Sep 2017 01:03:10: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:03:10: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 03 Sep 2017 01:03:10: #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 01:03:10: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:03:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:03:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:03:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:03:12: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:03:13: #4 Write output xls file... SRX2638362.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:03:13: #4 Write peak in narrowPeak format file... SRX2638362.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:03:13: #4 Write summits bed file... SRX2638362.10_summits.bed INFO @ Sun, 03 Sep 2017 01:03:13: Done! INFO @ Sun, 03 Sep 2017 01:03:13: #4 Write output xls file... SRX2638362.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:03:13: #4 Write peak in narrowPeak format file... SRX2638362.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:03:13: #4 Write summits bed file... SRX2638362.05_summits.bed INFO @ Sun, 03 Sep 2017 01:03:13: Done! INFO @ Sun, 03 Sep 2017 01:03:13: #4 Write output xls file... SRX2638362.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:03:13: #4 Write peak in narrowPeak format file... SRX2638362.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:03:13: #4 Write summits bed file... SRX2638362.20_summits.bed INFO @ Sun, 03 Sep 2017 01:03:13: Done! pass1 - making usageList (12 chroms)pass1 - making usageList (15 chroms): 1 millis pass1 - making usageList (14 chroms): 1 millis : 1 millis pass2 - checking and writing primary data (1143 records, 4 fields): 7 millis pass2 - checking and writing primary data (1610 records, 4 fields): 8 millis pass2 - checking and writing primary data (2214 records, 4 fields): 9 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。