Job ID = 2161257 sra ファイルのダウンロード中... Completed: 223261K bytes transferred in 5 seconds (359258K 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 --:--:-- --:--:-- --:--:-- 0 101 5460 0 5460 0 0 10709 0 --:--:-- --:--:-- --:--:-- 17115 100 34477 0 34477 0 0 49303 0 --:--:-- --:--:-- --:--:-- 67734 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 8403975 spots for /home/okishinya/chipatlas/results/dm3/SRX013101/SRR030367.sra Written 8403975 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: 00:03:51 8403975 reads; of these: 8403975 (100.00%) were unpaired; of these: 202811 (2.41%) aligned 0 times 4087511 (48.64%) aligned exactly 1 time 4113653 (48.95%) aligned >1 times 97.59% overall alignment rate Time searching: 00:03:51 Overall time: 00:03:51 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] 1037018 / 8201164 = 0.1264 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 12:14:47: # Command line: callpeak -t SRX013101.bam -f BAM -g dm -n SRX013101.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013101.05 # format = BAM # ChIP-seq file = ['SRX013101.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 12:14:47: # Command line: callpeak -t SRX013101.bam -f BAM -g dm -n SRX013101.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013101.20 # format = BAM # ChIP-seq file = ['SRX013101.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 12:14:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:14:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:14:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:14:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:14:47: # Command line: callpeak -t SRX013101.bam -f BAM -g dm -n SRX013101.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013101.10 # format = BAM # ChIP-seq file = ['SRX013101.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 12:14:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:14:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:14:52: 1000000 INFO @ Tue, 21 Apr 2015 12:14:52: 1000000 INFO @ Tue, 21 Apr 2015 12:14:52: 1000000 INFO @ Tue, 21 Apr 2015 12:14:58: 2000000 INFO @ Tue, 21 Apr 2015 12:14:58: 2000000 INFO @ Tue, 21 Apr 2015 12:14:58: 2000000 INFO @ Tue, 21 Apr 2015 12:15:03: 3000000 INFO @ Tue, 21 Apr 2015 12:15:03: 3000000 INFO @ Tue, 21 Apr 2015 12:15:03: 3000000 INFO @ Tue, 21 Apr 2015 12:15:08: 4000000 INFO @ Tue, 21 Apr 2015 12:15:08: 4000000 INFO @ Tue, 21 Apr 2015 12:15:08: 4000000 INFO @ Tue, 21 Apr 2015 12:15:13: 5000000 INFO @ Tue, 21 Apr 2015 12:15:13: 5000000 INFO @ Tue, 21 Apr 2015 12:15:13: 5000000 INFO @ Tue, 21 Apr 2015 12:15:19: 6000000 INFO @ Tue, 21 Apr 2015 12:15:19: 6000000 INFO @ Tue, 21 Apr 2015 12:15:19: 6000000 INFO @ Tue, 21 Apr 2015 12:15:24: 7000000 INFO @ Tue, 21 Apr 2015 12:15:24: 7000000 INFO @ Tue, 21 Apr 2015 12:15:24: 7000000 INFO @ Tue, 21 Apr 2015 12:15:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:15:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:15:25: #1 total tags in treatment: 7164146 INFO @ Tue, 21 Apr 2015 12:15:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:15:25: #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 12:15:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:15:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:15:25: #1 total tags in treatment: 7164146 INFO @ Tue, 21 Apr 2015 12:15:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:15:25: #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 12:15:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:15:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:15:25: #1 total tags in treatment: 7164146 INFO @ Tue, 21 Apr 2015 12:15:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:15:25: #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 12:15:26: #1 tags after filtering in treatment: 7163668 INFO @ Tue, 21 Apr 2015 12:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:15:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:15:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:15:26: #1 tags after filtering in treatment: 7163668 INFO @ Tue, 21 Apr 2015 12:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:15:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:15:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:15:26: #1 tags after filtering in treatment: 7163668 INFO @ Tue, 21 Apr 2015 12:15:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:15:26: #1 finished! INFO @ Tue, 21 Apr 2015 12:15:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:15:28: #2 number of paired peaks: 636 WARNING @ Tue, 21 Apr 2015 12:15:28: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Tue, 21 Apr 2015 12:15:28: start model_add_line... INFO @ Tue, 21 Apr 2015 12:15:28: #2 number of paired peaks: 636 WARNING @ Tue, 21 Apr 2015 12:15:28: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Tue, 21 Apr 2015 12:15:28: start model_add_line... INFO @ Tue, 21 Apr 2015 12:15:28: #2 number of paired peaks: 636 WARNING @ Tue, 21 Apr 2015 12:15:28: Fewer paired peaks (636) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 636 pairs to build model! INFO @ Tue, 21 Apr 2015 12:15:28: start model_add_line... INFO @ Tue, 21 Apr 2015 12:15:31: start X-correlation... INFO @ Tue, 21 Apr 2015 12:15:31: end of X-cor INFO @ Tue, 21 Apr 2015 12:15:31: #2 finished! INFO @ Tue, 21 Apr 2015 12:15:31: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 12:15:31: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 12:15:31: #2.2 Generate R script for model : SRX013101.20_model.r WARNING @ Tue, 21 Apr 2015 12:15:31: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:15:31: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 12:15:31: #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 12:15:31: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:15:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:15:31: start X-correlation... INFO @ Tue, 21 Apr 2015 12:15:31: end of X-cor INFO @ Tue, 21 Apr 2015 12:15:31: #2 finished! INFO @ Tue, 21 Apr 2015 12:15:31: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 12:15:31: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 12:15:31: #2.2 Generate R script for model : SRX013101.05_model.r WARNING @ Tue, 21 Apr 2015 12:15:31: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:15:31: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 12:15:31: #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 12:15:31: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:15:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:15:31: start X-correlation... INFO @ Tue, 21 Apr 2015 12:15:31: end of X-cor INFO @ Tue, 21 Apr 2015 12:15:31: #2 finished! INFO @ Tue, 21 Apr 2015 12:15:31: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 12:15:31: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 12:15:31: #2.2 Generate R script for model : SRX013101.10_model.r WARNING @ Tue, 21 Apr 2015 12:15:31: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:15:31: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 12:15:31: #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 12:15:31: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:15:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:16:10: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:16:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:16:11: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:16:37: #4 Write output xls file... SRX013101.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:16:37: #4 Write peak in narrowPeak format file... SRX013101.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:16:37: #4 Write summits bed file... SRX013101.20_summits.bed INFO @ Tue, 21 Apr 2015 12:16:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (508 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:16:41: #4 Write output xls file... SRX013101.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:16:41: #4 Write peak in narrowPeak format file... SRX013101.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:16:41: #4 Write summits bed file... SRX013101.05_summits.bed INFO @ Tue, 21 Apr 2015 12:16:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1963 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:16:43: #4 Write output xls file... SRX013101.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:16:43: #4 Write peak in narrowPeak format file... SRX013101.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:16:43: #4 Write summits bed file... SRX013101.10_summits.bed INFO @ Tue, 21 Apr 2015 12:16:43: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (806 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。