Job ID = 11371347 sra ファイルのダウンロード中... Completed: 402871K bytes transferred in 9 seconds (364951K bits/sec), in 1 file. 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... Read 10451179 spots for /home/okishinya/chipatlas/results/dm3/SRX4580643/SRR7724136.sra Written 10451179 spots for /home/okishinya/chipatlas/results/dm3/SRX4580643/SRR7724136.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:04:04 10451179 reads; of these: 10451179 (100.00%) were unpaired; of these: 2749797 (26.31%) aligned 0 times 3407336 (32.60%) aligned exactly 1 time 4294046 (41.09%) aligned >1 times 73.69% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:05 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] 898123 / 7701382 = 0.1166 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 @ Thu, 06 Dec 2018 02:53:26: # Command line: callpeak -t SRX4580643.bam -f BAM -g dm -n SRX4580643.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4580643.10 # format = BAM # ChIP-seq file = ['SRX4580643.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 @ Thu, 06 Dec 2018 02:53:26: # Command line: callpeak -t SRX4580643.bam -f BAM -g dm -n SRX4580643.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4580643.20 # format = BAM # ChIP-seq file = ['SRX4580643.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 @ Thu, 06 Dec 2018 02:53:26: # Command line: callpeak -t SRX4580643.bam -f BAM -g dm -n SRX4580643.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4580643.05 # format = BAM # ChIP-seq file = ['SRX4580643.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 @ Thu, 06 Dec 2018 02:53:26: #1 read tag files... INFO @ Thu, 06 Dec 2018 02:53:26: #1 read tag files... INFO @ Thu, 06 Dec 2018 02:53:26: #1 read tag files... INFO @ Thu, 06 Dec 2018 02:53:26: #1 read treatment tags... INFO @ Thu, 06 Dec 2018 02:53:26: #1 read treatment tags... INFO @ Thu, 06 Dec 2018 02:53:26: #1 read treatment tags... INFO @ Thu, 06 Dec 2018 02:53:33: 1000000 INFO @ Thu, 06 Dec 2018 02:53:34: 1000000 INFO @ Thu, 06 Dec 2018 02:53:34: 1000000 INFO @ Thu, 06 Dec 2018 02:53:40: 2000000 INFO @ Thu, 06 Dec 2018 02:53:41: 2000000 INFO @ Thu, 06 Dec 2018 02:53:41: 2000000 INFO @ Thu, 06 Dec 2018 02:53:47: 3000000 INFO @ Thu, 06 Dec 2018 02:53:48: 3000000 INFO @ Thu, 06 Dec 2018 02:53:48: 3000000 INFO @ Thu, 06 Dec 2018 02:53:54: 4000000 INFO @ Thu, 06 Dec 2018 02:53:56: 4000000 INFO @ Thu, 06 Dec 2018 02:53:56: 4000000 INFO @ Thu, 06 Dec 2018 02:54:01: 5000000 INFO @ Thu, 06 Dec 2018 02:54:03: 5000000 INFO @ Thu, 06 Dec 2018 02:54:04: 5000000 INFO @ Thu, 06 Dec 2018 02:54:08: 6000000 INFO @ Thu, 06 Dec 2018 02:54:11: 6000000 INFO @ Thu, 06 Dec 2018 02:54:12: 6000000 INFO @ Thu, 06 Dec 2018 02:54:13: #1 tag size is determined as 50 bps INFO @ Thu, 06 Dec 2018 02:54:13: #1 tag size = 50 INFO @ Thu, 06 Dec 2018 02:54:13: #1 total tags in treatment: 6803259 INFO @ Thu, 06 Dec 2018 02:54:13: #1 user defined the maximum tags... INFO @ Thu, 06 Dec 2018 02:54:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 06 Dec 2018 02:54:14: #1 tags after filtering in treatment: 6803259 INFO @ Thu, 06 Dec 2018 02:54:14: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 06 Dec 2018 02:54:14: #1 finished! INFO @ Thu, 06 Dec 2018 02:54:14: #2 Build Peak Model... INFO @ Thu, 06 Dec 2018 02:54:14: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 06 Dec 2018 02:54:14: #2 number of paired peaks: 1386 INFO @ Thu, 06 Dec 2018 02:54:14: start model_add_line... INFO @ Thu, 06 Dec 2018 02:54:14: start X-correlation... INFO @ Thu, 06 Dec 2018 02:54:15: end of X-cor INFO @ Thu, 06 Dec 2018 02:54:15: #2 finished! INFO @ Thu, 06 Dec 2018 02:54:15: #2 predicted fragment length is 77 bps INFO @ Thu, 06 Dec 2018 02:54:15: #2 alternative fragment length(s) may be 77,598 bps INFO @ Thu, 06 Dec 2018 02:54:15: #2.2 Generate R script for model : SRX4580643.10_model.r WARNING @ Thu, 06 Dec 2018 02:54:15: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 06 Dec 2018 02:54:15: #2 You may need to consider one of the other alternative d(s): 77,598 WARNING @ Thu, 06 Dec 2018 02:54:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 06 Dec 2018 02:54:15: #3 Call peaks... INFO @ Thu, 06 Dec 2018 02:54:15: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 06 Dec 2018 02:54:17: #1 tag size is determined as 50 bps INFO @ Thu, 06 Dec 2018 02:54:17: #1 tag size = 50 INFO @ Thu, 06 Dec 2018 02:54:17: #1 total tags in treatment: 6803259 INFO @ Thu, 06 Dec 2018 02:54:17: #1 user defined the maximum tags... INFO @ Thu, 06 Dec 2018 02:54:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 06 Dec 2018 02:54:17: #1 tags after filtering in treatment: 6803259 INFO @ Thu, 06 Dec 2018 02:54:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 06 Dec 2018 02:54:17: #1 finished! INFO @ Thu, 06 Dec 2018 02:54:17: #2 Build Peak Model... INFO @ Thu, 06 Dec 2018 02:54:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 06 Dec 2018 02:54:18: #2 number of paired peaks: 1386 INFO @ Thu, 06 Dec 2018 02:54:18: start model_add_line... INFO @ Thu, 06 Dec 2018 02:54:18: #1 tag size is determined as 50 bps INFO @ Thu, 06 Dec 2018 02:54:18: #1 tag size = 50 INFO @ Thu, 06 Dec 2018 02:54:18: #1 total tags in treatment: 6803259 INFO @ Thu, 06 Dec 2018 02:54:18: #1 user defined the maximum tags... INFO @ Thu, 06 Dec 2018 02:54:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 06 Dec 2018 02:54:18: start X-correlation... INFO @ Thu, 06 Dec 2018 02:54:18: end of X-cor INFO @ Thu, 06 Dec 2018 02:54:18: #2 finished! INFO @ Thu, 06 Dec 2018 02:54:18: #2 predicted fragment length is 77 bps INFO @ Thu, 06 Dec 2018 02:54:18: #2 alternative fragment length(s) may be 77,598 bps INFO @ Thu, 06 Dec 2018 02:54:18: #2.2 Generate R script for model : SRX4580643.05_model.r WARNING @ Thu, 06 Dec 2018 02:54:18: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 06 Dec 2018 02:54:18: #2 You may need to consider one of the other alternative d(s): 77,598 WARNING @ Thu, 06 Dec 2018 02:54:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 06 Dec 2018 02:54:18: #3 Call peaks... INFO @ Thu, 06 Dec 2018 02:54:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 06 Dec 2018 02:54:18: #1 tags after filtering in treatment: 6803259 INFO @ Thu, 06 Dec 2018 02:54:18: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 06 Dec 2018 02:54:18: #1 finished! INFO @ Thu, 06 Dec 2018 02:54:18: #2 Build Peak Model... INFO @ Thu, 06 Dec 2018 02:54:18: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 06 Dec 2018 02:54:19: #2 number of paired peaks: 1386 INFO @ Thu, 06 Dec 2018 02:54:19: start model_add_line... INFO @ Thu, 06 Dec 2018 02:54:19: start X-correlation... INFO @ Thu, 06 Dec 2018 02:54:19: end of X-cor INFO @ Thu, 06 Dec 2018 02:54:19: #2 finished! INFO @ Thu, 06 Dec 2018 02:54:19: #2 predicted fragment length is 77 bps INFO @ Thu, 06 Dec 2018 02:54:19: #2 alternative fragment length(s) may be 77,598 bps INFO @ Thu, 06 Dec 2018 02:54:19: #2.2 Generate R script for model : SRX4580643.20_model.r WARNING @ Thu, 06 Dec 2018 02:54:19: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 06 Dec 2018 02:54:19: #2 You may need to consider one of the other alternative d(s): 77,598 WARNING @ Thu, 06 Dec 2018 02:54:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 06 Dec 2018 02:54:19: #3 Call peaks... INFO @ Thu, 06 Dec 2018 02:54:19: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 06 Dec 2018 02:54:30: #3 Call peaks for each chromosome... INFO @ Thu, 06 Dec 2018 02:54:34: #3 Call peaks for each chromosome... INFO @ Thu, 06 Dec 2018 02:54:35: #3 Call peaks for each chromosome... INFO @ Thu, 06 Dec 2018 02:54:39: #4 Write output xls file... SRX4580643.10_peaks.xls INFO @ Thu, 06 Dec 2018 02:54:39: #4 Write peak in narrowPeak format file... SRX4580643.10_peaks.narrowPeak INFO @ Thu, 06 Dec 2018 02:54:39: #4 Write summits bed file... SRX4580643.10_summits.bed INFO @ Thu, 06 Dec 2018 02:54:39: Done! pass1 - making usageList (15 chroms): 11 millis pass2 - checking and writing primary data (1557 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Thu, 06 Dec 2018 02:54:43: #4 Write output xls file... SRX4580643.05_peaks.xls INFO @ Thu, 06 Dec 2018 02:54:43: #4 Write peak in narrowPeak format file... SRX4580643.05_peaks.narrowPeak INFO @ Thu, 06 Dec 2018 02:54:43: #4 Write summits bed file... SRX4580643.05_summits.bed INFO @ Thu, 06 Dec 2018 02:54:43: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3034 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 06 Dec 2018 02:54:44: #4 Write output xls file... SRX4580643.20_peaks.xls INFO @ Thu, 06 Dec 2018 02:54:44: #4 Write peak in narrowPeak format file... SRX4580643.20_peaks.narrowPeak INFO @ Thu, 06 Dec 2018 02:54:44: #4 Write summits bed file... SRX4580643.20_summits.bed INFO @ Thu, 06 Dec 2018 02:54:44: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (651 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。