Job ID = 10175225 sra ファイルのダウンロード中... Completed: 591914K bytes transferred in 9 seconds (533768K 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... Written 19642448 spots for /home/okishinya/chipatlas/results/dm3/SRX2458928/SRR5140277.sra Written 19642448 spots total 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: 00:07:49 19642448 reads; of these: 19642448 (100.00%) were unpaired; of these: 1399048 (7.12%) aligned 0 times 12396104 (63.11%) aligned exactly 1 time 5847296 (29.77%) aligned >1 times 92.88% overall alignment rate Time searching: 00:07:49 Overall time: 00:07:49 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] 2806308 / 18243400 = 0.1538 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, 06 Nov 2017 11:55:05: # Command line: callpeak -t SRX2458928.bam -f BAM -g dm -n SRX2458928.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2458928.10 # format = BAM # ChIP-seq file = ['SRX2458928.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, 06 Nov 2017 11:55:05: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:55:05: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:55:05: # Command line: callpeak -t SRX2458928.bam -f BAM -g dm -n SRX2458928.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2458928.20 # format = BAM # ChIP-seq file = ['SRX2458928.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, 06 Nov 2017 11:55:05: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:55:05: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:55:05: # Command line: callpeak -t SRX2458928.bam -f BAM -g dm -n SRX2458928.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2458928.05 # format = BAM # ChIP-seq file = ['SRX2458928.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, 06 Nov 2017 11:55:05: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:55:05: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:55:12: 1000000 INFO @ Mon, 06 Nov 2017 11:55:12: 1000000 INFO @ Mon, 06 Nov 2017 11:55:12: 1000000 INFO @ Mon, 06 Nov 2017 11:55:19: 2000000 INFO @ Mon, 06 Nov 2017 11:55:20: 2000000 INFO @ Mon, 06 Nov 2017 11:55:20: 2000000 INFO @ Mon, 06 Nov 2017 11:55:26: 3000000 INFO @ Mon, 06 Nov 2017 11:55:27: 3000000 INFO @ Mon, 06 Nov 2017 11:55:27: 3000000 INFO @ Mon, 06 Nov 2017 11:55:33: 4000000 INFO @ Mon, 06 Nov 2017 11:55:34: 4000000 INFO @ Mon, 06 Nov 2017 11:55:35: 4000000 INFO @ Mon, 06 Nov 2017 11:55:40: 5000000 INFO @ Mon, 06 Nov 2017 11:55:42: 5000000 INFO @ Mon, 06 Nov 2017 11:55:42: 5000000 INFO @ Mon, 06 Nov 2017 11:55:47: 6000000 INFO @ Mon, 06 Nov 2017 11:55:49: 6000000 INFO @ Mon, 06 Nov 2017 11:55:49: 6000000 INFO @ Mon, 06 Nov 2017 11:55:54: 7000000 INFO @ Mon, 06 Nov 2017 11:55:55: 7000000 INFO @ Mon, 06 Nov 2017 11:55:56: 7000000 INFO @ Mon, 06 Nov 2017 11:56:01: 8000000 INFO @ Mon, 06 Nov 2017 11:56:01: 8000000 INFO @ Mon, 06 Nov 2017 11:56:02: 8000000 INFO @ Mon, 06 Nov 2017 11:56:07: 9000000 INFO @ Mon, 06 Nov 2017 11:56:08: 9000000 INFO @ Mon, 06 Nov 2017 11:56:09: 9000000 INFO @ Mon, 06 Nov 2017 11:56:14: 10000000 INFO @ Mon, 06 Nov 2017 11:56:14: 10000000 INFO @ Mon, 06 Nov 2017 11:56:16: 10000000 INFO @ Mon, 06 Nov 2017 11:56:20: 11000000 INFO @ Mon, 06 Nov 2017 11:56:20: 11000000 INFO @ Mon, 06 Nov 2017 11:56:23: 11000000 INFO @ Mon, 06 Nov 2017 11:56:26: 12000000 INFO @ Mon, 06 Nov 2017 11:56:27: 12000000 INFO @ Mon, 06 Nov 2017 11:56:30: 12000000 INFO @ Mon, 06 Nov 2017 11:56:32: 13000000 INFO @ Mon, 06 Nov 2017 11:56:33: 13000000 INFO @ Mon, 06 Nov 2017 11:56:37: 13000000 INFO @ Mon, 06 Nov 2017 11:56:38: 14000000 INFO @ Mon, 06 Nov 2017 11:56:40: 14000000 INFO @ Mon, 06 Nov 2017 11:56:44: 14000000 INFO @ Mon, 06 Nov 2017 11:56:44: 15000000 INFO @ Mon, 06 Nov 2017 11:56:47: 15000000 INFO @ Mon, 06 Nov 2017 11:56:47: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:56:47: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:56:47: #1 total tags in treatment: 15437092 INFO @ Mon, 06 Nov 2017 11:56:47: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:56:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:56:47: #1 tags after filtering in treatment: 15437092 INFO @ Mon, 06 Nov 2017 11:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:56:47: #1 finished! INFO @ Mon, 06 Nov 2017 11:56:47: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:56:48: #2 number of paired peaks: 746 WARNING @ Mon, 06 Nov 2017 11:56:48: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Mon, 06 Nov 2017 11:56:48: start model_add_line... INFO @ Mon, 06 Nov 2017 11:56:48: start X-correlation... INFO @ Mon, 06 Nov 2017 11:56:49: end of X-cor INFO @ Mon, 06 Nov 2017 11:56:49: #2 finished! INFO @ Mon, 06 Nov 2017 11:56:49: #2 predicted fragment length is 56 bps INFO @ Mon, 06 Nov 2017 11:56:49: #2 alternative fragment length(s) may be 2,56,73 bps INFO @ Mon, 06 Nov 2017 11:56:49: #2.2 Generate R script for model : SRX2458928.05_model.r WARNING @ Mon, 06 Nov 2017 11:56:49: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:56:49: #2 You may need to consider one of the other alternative d(s): 2,56,73 WARNING @ Mon, 06 Nov 2017 11:56:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:56:49: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:56:49: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:56:49: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:56:49: #1 total tags in treatment: 15437092 INFO @ Mon, 06 Nov 2017 11:56:49: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:56:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:56:50: #1 tags after filtering in treatment: 15437092 INFO @ Mon, 06 Nov 2017 11:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:56:50: #1 finished! INFO @ Mon, 06 Nov 2017 11:56:50: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:56:50: 15000000 INFO @ Mon, 06 Nov 2017 11:56:51: #2 number of paired peaks: 746 WARNING @ Mon, 06 Nov 2017 11:56:51: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Mon, 06 Nov 2017 11:56:51: start model_add_line... INFO @ Mon, 06 Nov 2017 11:56:51: start X-correlation... INFO @ Mon, 06 Nov 2017 11:56:51: end of X-cor INFO @ Mon, 06 Nov 2017 11:56:51: #2 finished! INFO @ Mon, 06 Nov 2017 11:56:51: #2 predicted fragment length is 56 bps INFO @ Mon, 06 Nov 2017 11:56:51: #2 alternative fragment length(s) may be 2,56,73 bps INFO @ Mon, 06 Nov 2017 11:56:51: #2.2 Generate R script for model : SRX2458928.20_model.r WARNING @ Mon, 06 Nov 2017 11:56:51: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:56:51: #2 You may need to consider one of the other alternative d(s): 2,56,73 WARNING @ Mon, 06 Nov 2017 11:56:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:56:51: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:56:53: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:56:53: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:56:53: #1 total tags in treatment: 15437092 INFO @ Mon, 06 Nov 2017 11:56:53: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:56:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 11:56:53: #1 tags after filtering in treatment: 15437092 INFO @ Mon, 06 Nov 2017 11:56:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:56:53: #1 finished! INFO @ Mon, 06 Nov 2017 11:56:53: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:56:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:56:55: #2 number of paired peaks: 746 WARNING @ Mon, 06 Nov 2017 11:56:55: Fewer paired peaks (746) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 746 pairs to build model! INFO @ Mon, 06 Nov 2017 11:56:55: start model_add_line... INFO @ Mon, 06 Nov 2017 11:56:55: start X-correlation... INFO @ Mon, 06 Nov 2017 11:56:55: end of X-cor INFO @ Mon, 06 Nov 2017 11:56:55: #2 finished! INFO @ Mon, 06 Nov 2017 11:56:55: #2 predicted fragment length is 56 bps INFO @ Mon, 06 Nov 2017 11:56:55: #2 alternative fragment length(s) may be 2,56,73 bps INFO @ Mon, 06 Nov 2017 11:56:55: #2.2 Generate R script for model : SRX2458928.10_model.r WARNING @ Mon, 06 Nov 2017 11:56:55: #2 Since the d (56) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 06 Nov 2017 11:56:55: #2 You may need to consider one of the other alternative d(s): 2,56,73 WARNING @ Mon, 06 Nov 2017 11:56:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 06 Nov 2017 11:56:55: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:56:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:57:22: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:57:24: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:57:26: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:57:39: #4 Write output xls file... SRX2458928.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:57:40: #4 Write peak in narrowPeak format file... SRX2458928.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:57:40: #4 Write summits bed file... SRX2458928.20_summits.bed INFO @ Mon, 06 Nov 2017 11:57:40: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (613 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:57:42: #4 Write output xls file... SRX2458928.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:57:42: #4 Write peak in narrowPeak format file... SRX2458928.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:57:42: #4 Write summits bed file... SRX2458928.05_summits.bed INFO @ Mon, 06 Nov 2017 11:57:42: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2637 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:57:44: #4 Write output xls file... SRX2458928.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:57:44: #4 Write peak in narrowPeak format file... SRX2458928.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:57:44: #4 Write summits bed file... SRX2458928.10_summits.bed INFO @ Mon, 06 Nov 2017 11:57:44: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1552 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。