Job ID = 9158631 sra ファイルのダウンロード中... Completed: 834241K bytes transferred in 11 seconds (621207K 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 17779490 spots for /home/okishinya/chipatlas/results/dm3/SRX2011091/SRR4017244.sra Written 17779490 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: 00:14:14 17779490 reads; of these: 17779490 (100.00%) were unpaired; of these: 688046 (3.87%) aligned 0 times 11679871 (65.69%) aligned exactly 1 time 5411573 (30.44%) aligned >1 times 96.13% overall alignment rate Time searching: 00:14:14 Overall time: 00:14:14 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] 1526592 / 17091444 = 0.0893 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 @ Tue, 27 Jun 2017 19:01:23: # Command line: callpeak -t SRX2011091.bam -f BAM -g dm -n SRX2011091.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2011091.20 # format = BAM # ChIP-seq file = ['SRX2011091.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 @ Tue, 27 Jun 2017 19:01:23: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:01:23: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:01:23: # Command line: callpeak -t SRX2011091.bam -f BAM -g dm -n SRX2011091.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2011091.10 # format = BAM # ChIP-seq file = ['SRX2011091.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 @ Tue, 27 Jun 2017 19:01:23: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:01:23: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:01:23: # Command line: callpeak -t SRX2011091.bam -f BAM -g dm -n SRX2011091.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2011091.05 # format = BAM # ChIP-seq file = ['SRX2011091.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 @ Tue, 27 Jun 2017 19:01:23: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:01:23: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:01:30: 1000000 INFO @ Tue, 27 Jun 2017 19:01:31: 1000000 INFO @ Tue, 27 Jun 2017 19:01:31: 1000000 INFO @ Tue, 27 Jun 2017 19:01:38: 2000000 INFO @ Tue, 27 Jun 2017 19:01:39: 2000000 INFO @ Tue, 27 Jun 2017 19:01:39: 2000000 INFO @ Tue, 27 Jun 2017 19:01:45: 3000000 INFO @ Tue, 27 Jun 2017 19:01:46: 3000000 INFO @ Tue, 27 Jun 2017 19:01:46: 3000000 INFO @ Tue, 27 Jun 2017 19:01:52: 4000000 INFO @ Tue, 27 Jun 2017 19:01:54: 4000000 INFO @ Tue, 27 Jun 2017 19:01:54: 4000000 INFO @ Tue, 27 Jun 2017 19:01:59: 5000000 INFO @ Tue, 27 Jun 2017 19:02:02: 5000000 INFO @ Tue, 27 Jun 2017 19:02:02: 5000000 INFO @ Tue, 27 Jun 2017 19:02:07: 6000000 INFO @ Tue, 27 Jun 2017 19:02:10: 6000000 INFO @ Tue, 27 Jun 2017 19:02:10: 6000000 INFO @ Tue, 27 Jun 2017 19:02:15: 7000000 INFO @ Tue, 27 Jun 2017 19:02:18: 7000000 INFO @ Tue, 27 Jun 2017 19:02:18: 7000000 INFO @ Tue, 27 Jun 2017 19:02:22: 8000000 INFO @ Tue, 27 Jun 2017 19:02:25: 8000000 INFO @ Tue, 27 Jun 2017 19:02:25: 8000000 INFO @ Tue, 27 Jun 2017 19:02:29: 9000000 INFO @ Tue, 27 Jun 2017 19:02:33: 9000000 INFO @ Tue, 27 Jun 2017 19:02:33: 9000000 INFO @ Tue, 27 Jun 2017 19:02:37: 10000000 INFO @ Tue, 27 Jun 2017 19:02:41: 10000000 INFO @ Tue, 27 Jun 2017 19:02:41: 10000000 INFO @ Tue, 27 Jun 2017 19:02:44: 11000000 INFO @ Tue, 27 Jun 2017 19:02:49: 11000000 INFO @ Tue, 27 Jun 2017 19:02:49: 11000000 INFO @ Tue, 27 Jun 2017 19:02:52: 12000000 INFO @ Tue, 27 Jun 2017 19:02:57: 12000000 INFO @ Tue, 27 Jun 2017 19:02:57: 12000000 INFO @ Tue, 27 Jun 2017 19:02:59: 13000000 INFO @ Tue, 27 Jun 2017 19:03:05: 13000000 INFO @ Tue, 27 Jun 2017 19:03:05: 13000000 INFO @ Tue, 27 Jun 2017 19:03:07: 14000000 INFO @ Tue, 27 Jun 2017 19:03:13: 14000000 INFO @ Tue, 27 Jun 2017 19:03:13: 14000000 INFO @ Tue, 27 Jun 2017 19:03:14: 15000000 INFO @ Tue, 27 Jun 2017 19:03:18: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 19:03:18: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 19:03:18: #1 total tags in treatment: 15564852 INFO @ Tue, 27 Jun 2017 19:03:18: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:03:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 19:03:19: #1 tags after filtering in treatment: 15564852 INFO @ Tue, 27 Jun 2017 19:03:19: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 19:03:19: #1 finished! INFO @ Tue, 27 Jun 2017 19:03:19: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:03:19: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:03:20: #2 number of paired peaks: 102 WARNING @ Tue, 27 Jun 2017 19:03:20: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 27 Jun 2017 19:03:20: start model_add_line... INFO @ Tue, 27 Jun 2017 19:03:20: start X-correlation... INFO @ Tue, 27 Jun 2017 19:03:20: end of X-cor INFO @ Tue, 27 Jun 2017 19:03:20: #2 finished! INFO @ Tue, 27 Jun 2017 19:03:20: #2 predicted fragment length is 92 bps INFO @ Tue, 27 Jun 2017 19:03:20: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 27 Jun 2017 19:03:20: #2.2 Generate R script for model : SRX2011091.05_model.r WARNING @ Tue, 27 Jun 2017 19:03:20: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:03:20: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 27 Jun 2017 19:03:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 19:03:20: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:03:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:03:21: 15000000 INFO @ Tue, 27 Jun 2017 19:03:21: 15000000 INFO @ Tue, 27 Jun 2017 19:03:26: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 19:03:26: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 19:03:26: #1 total tags in treatment: 15564852 INFO @ Tue, 27 Jun 2017 19:03:26: #1 tag size is determined as 100 bps INFO @ Tue, 27 Jun 2017 19:03:26: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:03:26: #1 tag size = 100 INFO @ Tue, 27 Jun 2017 19:03:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 19:03:26: #1 total tags in treatment: 15564852 INFO @ Tue, 27 Jun 2017 19:03:26: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:03:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 19:03:26: #1 tags after filtering in treatment: 15564852 INFO @ Tue, 27 Jun 2017 19:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 19:03:26: #1 tags after filtering in treatment: 15564852 INFO @ Tue, 27 Jun 2017 19:03:26: #1 finished! INFO @ Tue, 27 Jun 2017 19:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 19:03:26: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:03:26: #1 finished! INFO @ Tue, 27 Jun 2017 19:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:03:26: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:03:27: #2 number of paired peaks: 102 WARNING @ Tue, 27 Jun 2017 19:03:27: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 27 Jun 2017 19:03:27: start model_add_line... INFO @ Tue, 27 Jun 2017 19:03:27: #2 number of paired peaks: 102 WARNING @ Tue, 27 Jun 2017 19:03:27: Fewer paired peaks (102) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 102 pairs to build model! INFO @ Tue, 27 Jun 2017 19:03:27: start model_add_line... INFO @ Tue, 27 Jun 2017 19:03:27: start X-correlation... INFO @ Tue, 27 Jun 2017 19:03:27: start X-correlation... INFO @ Tue, 27 Jun 2017 19:03:27: end of X-cor INFO @ Tue, 27 Jun 2017 19:03:27: #2 finished! INFO @ Tue, 27 Jun 2017 19:03:27: #2 predicted fragment length is 92 bps INFO @ Tue, 27 Jun 2017 19:03:27: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 27 Jun 2017 19:03:27: #2.2 Generate R script for model : SRX2011091.10_model.r INFO @ Tue, 27 Jun 2017 19:03:27: end of X-cor INFO @ Tue, 27 Jun 2017 19:03:27: #2 finished! INFO @ Tue, 27 Jun 2017 19:03:27: #2 predicted fragment length is 92 bps INFO @ Tue, 27 Jun 2017 19:03:27: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 27 Jun 2017 19:03:27: #2.2 Generate R script for model : SRX2011091.20_model.r WARNING @ Tue, 27 Jun 2017 19:03:27: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:03:27: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 27 Jun 2017 19:03:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 19:03:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:03:27: #3 Pre-compute pvalue-qvalue table... WARNING @ Tue, 27 Jun 2017 19:03:27: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:03:27: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 27 Jun 2017 19:03:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 19:03:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:03:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:03:54: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:04:00: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:04:01: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:04:16: #4 Write output xls file... SRX2011091.05_peaks.xls INFO @ Tue, 27 Jun 2017 19:04:16: #4 Write peak in narrowPeak format file... SRX2011091.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:04:16: #4 Write summits bed file... SRX2011091.05_summits.bed INFO @ Tue, 27 Jun 2017 19:04:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1760 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:04:19: #4 Write output xls file... SRX2011091.10_peaks.xls INFO @ Tue, 27 Jun 2017 19:04:19: #4 Write peak in narrowPeak format file... SRX2011091.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:04:19: #4 Write summits bed file... SRX2011091.10_summits.bed INFO @ Tue, 27 Jun 2017 19:04:19: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1111 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:04:21: #4 Write output xls file... SRX2011091.20_peaks.xls INFO @ Tue, 27 Jun 2017 19:04:21: #4 Write peak in narrowPeak format file... SRX2011091.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:04:21: #4 Write summits bed file... SRX2011091.20_summits.bed INFO @ Tue, 27 Jun 2017 19:04:21: Done! pass1 - making usageList (11 chroms): 0 millis pass2 - checking and writing primary data (711 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。