Job ID = 2161231 sra ファイルのダウンロード中... Completed: 201838K bytes transferred in 5 seconds (323477K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 34451 0 34451 0 0 49362 0 --:--:-- --:--:-- --:--:-- 68084 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 7908091 spots for /home/okishinya/chipatlas/results/dm3/SRX013079/SRR030345.sra Written 7908091 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: 00:02:17 7908091 reads; of these: 7908091 (100.00%) were unpaired; of these: 302500 (3.83%) aligned 0 times 6019596 (76.12%) aligned exactly 1 time 1585995 (20.06%) aligned >1 times 96.17% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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] 295599 / 7605591 = 0.0389 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, 21 Apr 2015 12:08:57: # Command line: callpeak -t SRX013079.bam -f BAM -g dm -n SRX013079.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013079.05 # format = BAM # ChIP-seq file = ['SRX013079.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 INFO @ Tue, 21 Apr 2015 12:08:57: # Command line: callpeak -t SRX013079.bam -f BAM -g dm -n SRX013079.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013079.20 # format = BAM # ChIP-seq file = ['SRX013079.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 INFO @ Tue, 21 Apr 2015 12:08:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:57: # Command line: callpeak -t SRX013079.bam -f BAM -g dm -n SRX013079.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013079.10 # format = BAM # ChIP-seq file = ['SRX013079.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 INFO @ Tue, 21 Apr 2015 12:08:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:57: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:08:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:08:57: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:09:02: 1000000 INFO @ Tue, 21 Apr 2015 12:09:02: 1000000 INFO @ Tue, 21 Apr 2015 12:09:03: 1000000 INFO @ Tue, 21 Apr 2015 12:09:08: 2000000 INFO @ Tue, 21 Apr 2015 12:09:09: 2000000 INFO @ Tue, 21 Apr 2015 12:09:10: 2000000 INFO @ Tue, 21 Apr 2015 12:09:14: 3000000 INFO @ Tue, 21 Apr 2015 12:09:15: 3000000 INFO @ Tue, 21 Apr 2015 12:09:17: 3000000 INFO @ Tue, 21 Apr 2015 12:09:20: 4000000 INFO @ Tue, 21 Apr 2015 12:09:21: 4000000 INFO @ Tue, 21 Apr 2015 12:09:25: 4000000 INFO @ Tue, 21 Apr 2015 12:09:27: 5000000 INFO @ Tue, 21 Apr 2015 12:09:28: 5000000 INFO @ Tue, 21 Apr 2015 12:09:32: 5000000 INFO @ Tue, 21 Apr 2015 12:09:33: 6000000 INFO @ Tue, 21 Apr 2015 12:09:34: 6000000 INFO @ Tue, 21 Apr 2015 12:09:39: 7000000 INFO @ Tue, 21 Apr 2015 12:09:39: 6000000 INFO @ Tue, 21 Apr 2015 12:09:41: 7000000 INFO @ Tue, 21 Apr 2015 12:09:41: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:41: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:41: #1 total tags in treatment: 7309992 INFO @ Tue, 21 Apr 2015 12:09:41: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:09:42: #1 tags after filtering in treatment: 7309302 INFO @ Tue, 21 Apr 2015 12:09:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:42: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:42: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:43: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:43: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:43: #1 total tags in treatment: 7309992 INFO @ Tue, 21 Apr 2015 12:09:43: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:09:44: #2 number of paired peaks: 114 WARNING @ Tue, 21 Apr 2015 12:09:44: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 21 Apr 2015 12:09:44: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:44: #1 tags after filtering in treatment: 7309302 INFO @ Tue, 21 Apr 2015 12:09:44: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:44: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:44: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:44: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:44: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:44: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:44: #2 predicted fragment length is 49 bps INFO @ Tue, 21 Apr 2015 12:09:44: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 21 Apr 2015 12:09:44: #2.2 Generate R script for model : SRX013079.10_model.r WARNING @ Tue, 21 Apr 2015 12:09:44: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:09:44: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 21 Apr 2015 12:09:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:09:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:45: #2 number of paired peaks: 114 WARNING @ Tue, 21 Apr 2015 12:09:45: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 21 Apr 2015 12:09:45: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:45: 7000000 INFO @ Tue, 21 Apr 2015 12:09:46: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:46: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:46: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:46: #2 predicted fragment length is 49 bps INFO @ Tue, 21 Apr 2015 12:09:46: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 21 Apr 2015 12:09:46: #2.2 Generate R script for model : SRX013079.05_model.r WARNING @ Tue, 21 Apr 2015 12:09:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:09:46: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 21 Apr 2015 12:09:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:09:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:09:47: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:09:47: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:09:47: #1 total tags in treatment: 7309992 INFO @ Tue, 21 Apr 2015 12:09:47: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:09:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:09:49: #1 tags after filtering in treatment: 7309302 INFO @ Tue, 21 Apr 2015 12:09:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:09:49: #1 finished! INFO @ Tue, 21 Apr 2015 12:09:49: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:09:50: #2 number of paired peaks: 114 WARNING @ Tue, 21 Apr 2015 12:09:50: Fewer paired peaks (114) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 114 pairs to build model! INFO @ Tue, 21 Apr 2015 12:09:50: start model_add_line... INFO @ Tue, 21 Apr 2015 12:09:51: start X-correlation... INFO @ Tue, 21 Apr 2015 12:09:51: end of X-cor INFO @ Tue, 21 Apr 2015 12:09:51: #2 finished! INFO @ Tue, 21 Apr 2015 12:09:51: #2 predicted fragment length is 49 bps INFO @ Tue, 21 Apr 2015 12:09:51: #2 alternative fragment length(s) may be 49 bps INFO @ Tue, 21 Apr 2015 12:09:51: #2.2 Generate R script for model : SRX013079.20_model.r WARNING @ Tue, 21 Apr 2015 12:09:51: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:09:51: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Tue, 21 Apr 2015 12:09:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 21 Apr 2015 12:09:51: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:09:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:10:23: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:29: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:30: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:10:52: #4 Write output xls file... SRX013079.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:52: #4 Write peak in narrowPeak format file... SRX013079.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:52: #4 Write summits bed file... SRX013079.10_summits.bed INFO @ Tue, 21 Apr 2015 12:10:52: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (681 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:10:58: #4 Write output xls file... SRX013079.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:10:58: #4 Write peak in narrowPeak format file... SRX013079.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:10:58: #4 Write summits bed file... SRX013079.20_summits.bed INFO @ Tue, 21 Apr 2015 12:10:59: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (315 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:11:00: #4 Write output xls file... SRX013079.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:11:00: #4 Write peak in narrowPeak format file... SRX013079.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:11:00: #4 Write summits bed file... SRX013079.05_summits.bed INFO @ Tue, 21 Apr 2015 12:11:00: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1091 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。