Job ID = 10609600 sra ファイルのダウンロード中... Completed: 538954K bytes transferred in 15 seconds (278959K 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 18911306 spots for /home/okishinya/chipatlas/results/dm3/SRX3011246/SRR5834723.sra Written 18911306 spots for /home/okishinya/chipatlas/results/dm3/SRX3011246/SRR5834723.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:42 18911306 reads; of these: 18911306 (100.00%) were unpaired; of these: 599346 (3.17%) aligned 0 times 14619082 (77.30%) aligned exactly 1 time 3692878 (19.53%) aligned >1 times 96.83% overall alignment rate Time searching: 00:07:43 Overall time: 00:07:43 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 8 files... [bam_rmdupse_core] 6270262 / 18311960 = 0.3424 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 @ Mon, 07 May 2018 12:59:01: # Command line: callpeak -t SRX3011246.bam -f BAM -g dm -n SRX3011246.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011246.10 # format = BAM # ChIP-seq file = ['SRX3011246.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 @ Mon, 07 May 2018 12:59:01: #1 read tag files... INFO @ Mon, 07 May 2018 12:59:01: #1 read treatment tags... INFO @ Mon, 07 May 2018 12:59:01: # Command line: callpeak -t SRX3011246.bam -f BAM -g dm -n SRX3011246.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011246.20 # format = BAM # ChIP-seq file = ['SRX3011246.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 @ Mon, 07 May 2018 12:59:01: #1 read tag files... INFO @ Mon, 07 May 2018 12:59:01: #1 read treatment tags... INFO @ Mon, 07 May 2018 12:59:01: # Command line: callpeak -t SRX3011246.bam -f BAM -g dm -n SRX3011246.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011246.05 # format = BAM # ChIP-seq file = ['SRX3011246.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 @ Mon, 07 May 2018 12:59:01: #1 read tag files... INFO @ Mon, 07 May 2018 12:59:01: #1 read treatment tags... INFO @ Mon, 07 May 2018 12:59:08: 1000000 INFO @ Mon, 07 May 2018 12:59:10: 1000000 INFO @ Mon, 07 May 2018 12:59:10: 1000000 INFO @ Mon, 07 May 2018 12:59:15: 2000000 INFO @ Mon, 07 May 2018 12:59:19: 2000000 INFO @ Mon, 07 May 2018 12:59:19: 2000000 INFO @ Mon, 07 May 2018 12:59:21: 3000000 INFO @ Mon, 07 May 2018 12:59:28: 3000000 INFO @ Mon, 07 May 2018 12:59:28: 4000000 INFO @ Mon, 07 May 2018 12:59:28: 3000000 INFO @ Mon, 07 May 2018 12:59:35: 5000000 INFO @ Mon, 07 May 2018 12:59:37: 4000000 INFO @ Mon, 07 May 2018 12:59:38: 4000000 INFO @ Mon, 07 May 2018 12:59:41: 6000000 INFO @ Mon, 07 May 2018 12:59:46: 5000000 INFO @ Mon, 07 May 2018 12:59:47: 5000000 INFO @ Mon, 07 May 2018 12:59:48: 7000000 INFO @ Mon, 07 May 2018 12:59:55: 8000000 INFO @ Mon, 07 May 2018 12:59:56: 6000000 INFO @ Mon, 07 May 2018 12:59:57: 6000000 INFO @ Mon, 07 May 2018 13:00:01: 9000000 INFO @ Mon, 07 May 2018 13:00:04: 7000000 INFO @ Mon, 07 May 2018 13:00:06: 7000000 INFO @ Mon, 07 May 2018 13:00:08: 10000000 INFO @ Mon, 07 May 2018 13:00:13: 8000000 INFO @ Mon, 07 May 2018 13:00:15: 11000000 INFO @ Mon, 07 May 2018 13:00:15: 8000000 INFO @ Mon, 07 May 2018 13:00:22: 12000000 INFO @ Mon, 07 May 2018 13:00:22: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 13:00:22: #1 tag size = 80 INFO @ Mon, 07 May 2018 13:00:22: #1 total tags in treatment: 12041698 INFO @ Mon, 07 May 2018 13:00:22: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 13:00:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 13:00:22: #1 tags after filtering in treatment: 12041698 INFO @ Mon, 07 May 2018 13:00:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 13:00:22: #1 finished! INFO @ Mon, 07 May 2018 13:00:22: #2 Build Peak Model... INFO @ Mon, 07 May 2018 13:00:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 13:00:22: 9000000 INFO @ Mon, 07 May 2018 13:00:23: #2 number of paired peaks: 1811 INFO @ Mon, 07 May 2018 13:00:23: start model_add_line... INFO @ Mon, 07 May 2018 13:00:23: start X-correlation... INFO @ Mon, 07 May 2018 13:00:23: end of X-cor INFO @ Mon, 07 May 2018 13:00:23: #2 finished! INFO @ Mon, 07 May 2018 13:00:23: #2 predicted fragment length is 148 bps INFO @ Mon, 07 May 2018 13:00:23: #2 alternative fragment length(s) may be 148 bps INFO @ Mon, 07 May 2018 13:00:23: #2.2 Generate R script for model : SRX3011246.10_model.r WARNING @ Mon, 07 May 2018 13:00:23: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 13:00:23: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Mon, 07 May 2018 13:00:23: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 13:00:23: #3 Call peaks... INFO @ Mon, 07 May 2018 13:00:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 13:00:24: 9000000 INFO @ Mon, 07 May 2018 13:00:31: 10000000 INFO @ Mon, 07 May 2018 13:00:33: 10000000 INFO @ Mon, 07 May 2018 13:00:40: 11000000 INFO @ Mon, 07 May 2018 13:00:42: 11000000 INFO @ Mon, 07 May 2018 13:00:50: 12000000 INFO @ Mon, 07 May 2018 13:00:50: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 13:00:50: #1 tag size = 80 INFO @ Mon, 07 May 2018 13:00:50: #1 total tags in treatment: 12041698 INFO @ Mon, 07 May 2018 13:00:50: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 13:00:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 13:00:50: #1 tags after filtering in treatment: 12041698 INFO @ Mon, 07 May 2018 13:00:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 13:00:50: #1 finished! INFO @ Mon, 07 May 2018 13:00:50: #2 Build Peak Model... INFO @ Mon, 07 May 2018 13:00:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 13:00:51: 12000000 INFO @ Mon, 07 May 2018 13:00:51: #1 tag size is determined as 80 bps INFO @ Mon, 07 May 2018 13:00:51: #1 tag size = 80 INFO @ Mon, 07 May 2018 13:00:51: #1 total tags in treatment: 12041698 INFO @ Mon, 07 May 2018 13:00:51: #1 user defined the maximum tags... INFO @ Mon, 07 May 2018 13:00:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 07 May 2018 13:00:51: #1 tags after filtering in treatment: 12041698 INFO @ Mon, 07 May 2018 13:00:51: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 07 May 2018 13:00:51: #1 finished! INFO @ Mon, 07 May 2018 13:00:51: #2 Build Peak Model... INFO @ Mon, 07 May 2018 13:00:51: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 07 May 2018 13:00:51: #2 number of paired peaks: 1811 INFO @ Mon, 07 May 2018 13:00:51: start model_add_line... INFO @ Mon, 07 May 2018 13:00:51: start X-correlation... INFO @ Mon, 07 May 2018 13:00:51: end of X-cor INFO @ Mon, 07 May 2018 13:00:51: #2 finished! INFO @ Mon, 07 May 2018 13:00:51: #2 predicted fragment length is 148 bps INFO @ Mon, 07 May 2018 13:00:51: #2 alternative fragment length(s) may be 148 bps INFO @ Mon, 07 May 2018 13:00:51: #2.2 Generate R script for model : SRX3011246.20_model.r WARNING @ Mon, 07 May 2018 13:00:51: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 13:00:51: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Mon, 07 May 2018 13:00:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 13:00:51: #3 Call peaks... INFO @ Mon, 07 May 2018 13:00:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 13:00:52: #2 number of paired peaks: 1811 INFO @ Mon, 07 May 2018 13:00:52: start model_add_line... INFO @ Mon, 07 May 2018 13:00:52: start X-correlation... INFO @ Mon, 07 May 2018 13:00:52: end of X-cor INFO @ Mon, 07 May 2018 13:00:52: #2 finished! INFO @ Mon, 07 May 2018 13:00:52: #2 predicted fragment length is 148 bps INFO @ Mon, 07 May 2018 13:00:52: #2 alternative fragment length(s) may be 148 bps INFO @ Mon, 07 May 2018 13:00:52: #2.2 Generate R script for model : SRX3011246.05_model.r WARNING @ Mon, 07 May 2018 13:00:52: #2 Since the d (148) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 07 May 2018 13:00:52: #2 You may need to consider one of the other alternative d(s): 148 WARNING @ Mon, 07 May 2018 13:00:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 07 May 2018 13:00:52: #3 Call peaks... INFO @ Mon, 07 May 2018 13:00:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 07 May 2018 13:00:55: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 13:01:10: #4 Write output xls file... SRX3011246.10_peaks.xls INFO @ Mon, 07 May 2018 13:01:10: #4 Write peak in narrowPeak format file... SRX3011246.10_peaks.narrowPeak INFO @ Mon, 07 May 2018 13:01:11: #4 Write summits bed file... SRX3011246.10_summits.bed INFO @ Mon, 07 May 2018 13:01:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6305 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 13:01:23: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 13:01:24: #3 Call peaks for each chromosome... INFO @ Mon, 07 May 2018 13:01:41: #4 Write output xls file... SRX3011246.20_peaks.xls INFO @ Mon, 07 May 2018 13:01:41: #4 Write peak in narrowPeak format file... SRX3011246.20_peaks.narrowPeak INFO @ Mon, 07 May 2018 13:01:41: #4 Write summits bed file... SRX3011246.20_summits.bed INFO @ Mon, 07 May 2018 13:01:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3040 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 07 May 2018 13:01:42: #4 Write output xls file... SRX3011246.05_peaks.xls INFO @ Mon, 07 May 2018 13:01:42: #4 Write peak in narrowPeak format file... SRX3011246.05_peaks.narrowPeak INFO @ Mon, 07 May 2018 13:01:42: #4 Write summits bed file... SRX3011246.05_summits.bed INFO @ Mon, 07 May 2018 13:01:42: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10397 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。