Job ID = 9730436 sra ファイルのダウンロード中... Completed: 1120976K bytes transferred in 12 seconds (744471K 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 47268691 spots for /home/okishinya/chipatlas/results/dm3/SRX2321783/SRR4841809.sra Written 47268691 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:14:03 47268691 reads; of these: 47268691 (100.00%) were unpaired; of these: 2788241 (5.90%) aligned 0 times 32032415 (67.77%) aligned exactly 1 time 12448035 (26.33%) aligned >1 times 94.10% overall alignment rate Time searching: 00:14:04 Overall time: 00:14:04 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] 29379821 / 44480450 = 0.6605 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 01:19:10: # Command line: callpeak -t SRX2321783.bam -f BAM -g dm -n SRX2321783.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2321783.10 # format = BAM # ChIP-seq file = ['SRX2321783.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 01:19:10: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:19:10: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:19:10: # Command line: callpeak -t SRX2321783.bam -f BAM -g dm -n SRX2321783.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2321783.20 # format = BAM # ChIP-seq file = ['SRX2321783.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 01:19:10: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:19:10: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:19:10: # Command line: callpeak -t SRX2321783.bam -f BAM -g dm -n SRX2321783.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2321783.05 # format = BAM # ChIP-seq file = ['SRX2321783.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 01:19:10: #1 read tag files... INFO @ Sun, 03 Sep 2017 01:19:10: #1 read treatment tags... INFO @ Sun, 03 Sep 2017 01:19:17: 1000000 INFO @ Sun, 03 Sep 2017 01:19:17: 1000000 INFO @ Sun, 03 Sep 2017 01:19:17: 1000000 INFO @ Sun, 03 Sep 2017 01:19:24: 2000000 INFO @ Sun, 03 Sep 2017 01:19:24: 2000000 INFO @ Sun, 03 Sep 2017 01:19:24: 2000000 INFO @ Sun, 03 Sep 2017 01:19:31: 3000000 INFO @ Sun, 03 Sep 2017 01:19:31: 3000000 INFO @ Sun, 03 Sep 2017 01:19:31: 3000000 INFO @ Sun, 03 Sep 2017 01:19:38: 4000000 INFO @ Sun, 03 Sep 2017 01:19:38: 4000000 INFO @ Sun, 03 Sep 2017 01:19:38: 4000000 INFO @ Sun, 03 Sep 2017 01:19:44: 5000000 INFO @ Sun, 03 Sep 2017 01:19:45: 5000000 INFO @ Sun, 03 Sep 2017 01:19:45: 5000000 INFO @ Sun, 03 Sep 2017 01:19:51: 6000000 INFO @ Sun, 03 Sep 2017 01:19:52: 6000000 INFO @ Sun, 03 Sep 2017 01:19:52: 6000000 INFO @ Sun, 03 Sep 2017 01:19:58: 7000000 INFO @ Sun, 03 Sep 2017 01:20:00: 7000000 INFO @ Sun, 03 Sep 2017 01:20:00: 7000000 INFO @ Sun, 03 Sep 2017 01:20:04: 8000000 INFO @ Sun, 03 Sep 2017 01:20:07: 8000000 INFO @ Sun, 03 Sep 2017 01:20:07: 8000000 INFO @ Sun, 03 Sep 2017 01:20:11: 9000000 INFO @ Sun, 03 Sep 2017 01:20:14: 9000000 INFO @ Sun, 03 Sep 2017 01:20:14: 9000000 INFO @ Sun, 03 Sep 2017 01:20:18: 10000000 INFO @ Sun, 03 Sep 2017 01:20:21: 10000000 INFO @ Sun, 03 Sep 2017 01:20:21: 10000000 INFO @ Sun, 03 Sep 2017 01:20:24: 11000000 INFO @ Sun, 03 Sep 2017 01:20:29: 11000000 INFO @ Sun, 03 Sep 2017 01:20:29: 11000000 INFO @ Sun, 03 Sep 2017 01:20:31: 12000000 INFO @ Sun, 03 Sep 2017 01:20:36: 12000000 INFO @ Sun, 03 Sep 2017 01:20:36: 12000000 INFO @ Sun, 03 Sep 2017 01:20:38: 13000000 INFO @ Sun, 03 Sep 2017 01:20:43: 13000000 INFO @ Sun, 03 Sep 2017 01:20:43: 13000000 INFO @ Sun, 03 Sep 2017 01:20:44: 14000000 INFO @ Sun, 03 Sep 2017 01:20:51: 14000000 INFO @ Sun, 03 Sep 2017 01:20:51: 14000000 INFO @ Sun, 03 Sep 2017 01:20:51: 15000000 INFO @ Sun, 03 Sep 2017 01:20:52: #1 tag size is determined as 42 bps INFO @ Sun, 03 Sep 2017 01:20:52: #1 tag size = 42 INFO @ Sun, 03 Sep 2017 01:20:52: #1 total tags in treatment: 15100629 INFO @ Sun, 03 Sep 2017 01:20:52: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:20:52: #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 01:20:52: #1 tags after filtering in treatment: 15100629 INFO @ Sun, 03 Sep 2017 01:20:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:20:52: #1 finished! INFO @ Sun, 03 Sep 2017 01:20:52: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:20:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:20:53: #2 number of paired peaks: 228 WARNING @ Sun, 03 Sep 2017 01:20:53: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 03 Sep 2017 01:20:53: start model_add_line... INFO @ Sun, 03 Sep 2017 01:20:53: start X-correlation... INFO @ Sun, 03 Sep 2017 01:20:53: end of X-cor INFO @ Sun, 03 Sep 2017 01:20:53: #2 finished! INFO @ Sun, 03 Sep 2017 01:20:53: #2 predicted fragment length is 58 bps INFO @ Sun, 03 Sep 2017 01:20:53: #2 alternative fragment length(s) may be 58 bps INFO @ Sun, 03 Sep 2017 01:20:53: #2.2 Generate R script for model : SRX2321783.20_model.r WARNING @ Sun, 03 Sep 2017 01:20:53: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:20:53: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sun, 03 Sep 2017 01:20:53: #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 01:20:53: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:20:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:20:58: 15000000 INFO @ Sun, 03 Sep 2017 01:20:58: 15000000 INFO @ Sun, 03 Sep 2017 01:20:59: #1 tag size is determined as 42 bps INFO @ Sun, 03 Sep 2017 01:20:59: #1 tag size = 42 INFO @ Sun, 03 Sep 2017 01:20:59: #1 total tags in treatment: 15100629 INFO @ Sun, 03 Sep 2017 01:20:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:20:59: #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 01:20:59: #1 tag size is determined as 42 bps INFO @ Sun, 03 Sep 2017 01:20:59: #1 tag size = 42 INFO @ Sun, 03 Sep 2017 01:20:59: #1 total tags in treatment: 15100629 INFO @ Sun, 03 Sep 2017 01:20:59: #1 user defined the maximum tags... INFO @ Sun, 03 Sep 2017 01:20:59: #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 01:20:59: #1 tags after filtering in treatment: 15100629 INFO @ Sun, 03 Sep 2017 01:20:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:20:59: #1 finished! INFO @ Sun, 03 Sep 2017 01:20:59: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:20:59: #1 tags after filtering in treatment: 15100629 INFO @ Sun, 03 Sep 2017 01:20:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Sep 2017 01:20:59: #1 finished! INFO @ Sun, 03 Sep 2017 01:20:59: #2 Build Peak Model... INFO @ Sun, 03 Sep 2017 01:20:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Sep 2017 01:21:00: #2 number of paired peaks: 228 WARNING @ Sun, 03 Sep 2017 01:21:00: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 03 Sep 2017 01:21:00: start model_add_line... INFO @ Sun, 03 Sep 2017 01:21:00: #2 number of paired peaks: 228 WARNING @ Sun, 03 Sep 2017 01:21:00: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 03 Sep 2017 01:21:00: start model_add_line... INFO @ Sun, 03 Sep 2017 01:21:00: start X-correlation... INFO @ Sun, 03 Sep 2017 01:21:00: end of X-cor INFO @ Sun, 03 Sep 2017 01:21:00: #2 finished! INFO @ Sun, 03 Sep 2017 01:21:00: #2 predicted fragment length is 58 bps INFO @ Sun, 03 Sep 2017 01:21:00: #2 alternative fragment length(s) may be 58 bps INFO @ Sun, 03 Sep 2017 01:21:00: #2.2 Generate R script for model : SRX2321783.05_model.r WARNING @ Sun, 03 Sep 2017 01:21:00: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:21:00: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sun, 03 Sep 2017 01:21:00: #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 01:21:00: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:21:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:21:00: start X-correlation... INFO @ Sun, 03 Sep 2017 01:21:00: end of X-cor INFO @ Sun, 03 Sep 2017 01:21:00: #2 finished! INFO @ Sun, 03 Sep 2017 01:21:00: #2 predicted fragment length is 58 bps INFO @ Sun, 03 Sep 2017 01:21:00: #2 alternative fragment length(s) may be 58 bps INFO @ Sun, 03 Sep 2017 01:21:00: #2.2 Generate R script for model : SRX2321783.10_model.r WARNING @ Sun, 03 Sep 2017 01:21:00: #2 Since the d (58) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Sep 2017 01:21:00: #2 You may need to consider one of the other alternative d(s): 58 WARNING @ Sun, 03 Sep 2017 01:21:00: #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 01:21:00: #3 Call peaks... INFO @ Sun, 03 Sep 2017 01:21:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Sep 2017 01:21:26: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:21:30: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:21:34: #3 Call peaks for each chromosome... INFO @ Sun, 03 Sep 2017 01:21:43: #4 Write output xls file... SRX2321783.20_peaks.xls INFO @ Sun, 03 Sep 2017 01:21:43: #4 Write peak in narrowPeak format file... SRX2321783.20_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:21:43: #4 Write summits bed file... SRX2321783.20_summits.bed INFO @ Sun, 03 Sep 2017 01:21:43: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (820 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:21:49: #4 Write output xls file... SRX2321783.05_peaks.xls INFO @ Sun, 03 Sep 2017 01:21:49: #4 Write peak in narrowPeak format file... SRX2321783.05_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:21:49: #4 Write summits bed file... SRX2321783.05_summits.bed INFO @ Sun, 03 Sep 2017 01:21:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5856 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Sep 2017 01:21:51: #4 Write output xls file... SRX2321783.10_peaks.xls INFO @ Sun, 03 Sep 2017 01:21:52: #4 Write peak in narrowPeak format file... SRX2321783.10_peaks.narrowPeak INFO @ Sun, 03 Sep 2017 01:21:52: #4 Write summits bed file... SRX2321783.10_summits.bed INFO @ Sun, 03 Sep 2017 01:21:52: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1922 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。