Job ID = 2161561 sra ファイルのダウンロード中... Completed: 341858K bytes transferred in 6 seconds (445873K 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 44520 0 44520 0 0 50241 0 --:--:-- --:--:-- --:--:-- 64057 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 17781478 spots for /home/okishinya/chipatlas/results/dm3/SRX030150/SRR071265.sra Written 17781478 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: 00:05:40 17781478 reads; of these: 17781478 (100.00%) were unpaired; of these: 5507362 (30.97%) aligned 0 times 6025098 (33.88%) aligned exactly 1 time 6249018 (35.14%) aligned >1 times 69.03% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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] 4526093 / 12274116 = 0.3688 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 12:57:47: # Command line: callpeak -t SRX030150.bam -f BAM -g dm -n SRX030150.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX030150.20 # format = BAM # ChIP-seq file = ['SRX030150.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 12:57:47: # Command line: callpeak -t SRX030150.bam -f BAM -g dm -n SRX030150.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX030150.10 # format = BAM # ChIP-seq file = ['SRX030150.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 12:57:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:57:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:57:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:57:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:57:47: # Command line: callpeak -t SRX030150.bam -f BAM -g dm -n SRX030150.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX030150.05 # format = BAM # ChIP-seq file = ['SRX030150.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 12:57:47: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:57:47: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:57:52: 1000000 INFO @ Tue, 21 Apr 2015 12:57:52: 1000000 INFO @ Tue, 21 Apr 2015 12:57:52: 1000000 INFO @ Tue, 21 Apr 2015 12:57:57: 2000000 INFO @ Tue, 21 Apr 2015 12:57:58: 2000000 INFO @ Tue, 21 Apr 2015 12:57:58: 2000000 INFO @ Tue, 21 Apr 2015 12:58:03: 3000000 INFO @ Tue, 21 Apr 2015 12:58:03: 3000000 INFO @ Tue, 21 Apr 2015 12:58:03: 3000000 INFO @ Tue, 21 Apr 2015 12:58:08: 4000000 INFO @ Tue, 21 Apr 2015 12:58:08: 4000000 INFO @ Tue, 21 Apr 2015 12:58:09: 4000000 INFO @ Tue, 21 Apr 2015 12:58:13: 5000000 INFO @ Tue, 21 Apr 2015 12:58:14: 5000000 INFO @ Tue, 21 Apr 2015 12:58:15: 5000000 INFO @ Tue, 21 Apr 2015 12:58:18: 6000000 INFO @ Tue, 21 Apr 2015 12:58:20: 6000000 INFO @ Tue, 21 Apr 2015 12:58:21: 6000000 INFO @ Tue, 21 Apr 2015 12:58:23: 7000000 INFO @ Tue, 21 Apr 2015 12:58:25: 7000000 INFO @ Tue, 21 Apr 2015 12:58:26: 7000000 INFO @ Tue, 21 Apr 2015 12:58:27: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:58:27: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:58:27: #1 total tags in treatment: 7748023 INFO @ Tue, 21 Apr 2015 12:58:27: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:58:27: #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 12:58:29: #1 tags after filtering in treatment: 7747345 INFO @ Tue, 21 Apr 2015 12:58:29: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:58:29: #1 finished! INFO @ Tue, 21 Apr 2015 12:58:29: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:58:29: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:58:29: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:58:29: #1 total tags in treatment: 7748023 INFO @ Tue, 21 Apr 2015 12:58:29: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:58:29: #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 12:58:30: #2 number of paired peaks: 520 WARNING @ Tue, 21 Apr 2015 12:58:30: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Tue, 21 Apr 2015 12:58:30: start model_add_line... INFO @ Tue, 21 Apr 2015 12:58:31: #1 tags after filtering in treatment: 7747345 INFO @ Tue, 21 Apr 2015 12:58:31: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:58:31: #1 finished! INFO @ Tue, 21 Apr 2015 12:58:31: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:58:31: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:58:31: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:58:31: #1 total tags in treatment: 7748023 INFO @ Tue, 21 Apr 2015 12:58:31: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:58:31: #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 12:58:32: #1 tags after filtering in treatment: 7747345 INFO @ Tue, 21 Apr 2015 12:58:32: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:58:32: #1 finished! INFO @ Tue, 21 Apr 2015 12:58:32: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:58:32: #2 number of paired peaks: 520 WARNING @ Tue, 21 Apr 2015 12:58:32: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Tue, 21 Apr 2015 12:58:32: start model_add_line... INFO @ Tue, 21 Apr 2015 12:58:33: #2 number of paired peaks: 520 WARNING @ Tue, 21 Apr 2015 12:58:33: Fewer paired peaks (520) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 520 pairs to build model! INFO @ Tue, 21 Apr 2015 12:58:33: start model_add_line... INFO @ Tue, 21 Apr 2015 12:58:34: start X-correlation... INFO @ Tue, 21 Apr 2015 12:58:34: end of X-cor INFO @ Tue, 21 Apr 2015 12:58:34: #2 finished! INFO @ Tue, 21 Apr 2015 12:58:34: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 12:58:34: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 12:58:34: #2.2 Generate R script for model : SRX030150.05_model.r WARNING @ Tue, 21 Apr 2015 12:58:34: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:58:34: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 12:58:34: #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 12:58:34: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:58:34: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:58:36: start X-correlation... INFO @ Tue, 21 Apr 2015 12:58:36: end of X-cor INFO @ Tue, 21 Apr 2015 12:58:36: #2 finished! INFO @ Tue, 21 Apr 2015 12:58:36: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 12:58:36: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 12:58:36: #2.2 Generate R script for model : SRX030150.20_model.r WARNING @ Tue, 21 Apr 2015 12:58:36: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:58:36: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 12:58:36: #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 12:58:36: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:58:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:58:37: start X-correlation... INFO @ Tue, 21 Apr 2015 12:58:37: end of X-cor INFO @ Tue, 21 Apr 2015 12:58:37: #2 finished! INFO @ Tue, 21 Apr 2015 12:58:37: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 12:58:37: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 12:58:37: #2.2 Generate R script for model : SRX030150.10_model.r WARNING @ Tue, 21 Apr 2015 12:58:37: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 12:58:37: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 12:58:37: #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 12:58:37: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:59:18: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:59:19: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:59:20: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:59:51: #4 Write output xls file... SRX030150.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:51: #4 Write peak in narrowPeak format file... SRX030150.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:51: #4 Write summits bed file... SRX030150.05_summits.bed INFO @ Tue, 21 Apr 2015 12:59:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2038 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:59:51: #4 Write output xls file... SRX030150.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:51: #4 Write peak in narrowPeak format file... SRX030150.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:51: #4 Write summits bed file... SRX030150.20_summits.bed INFO @ Tue, 21 Apr 2015 12:59:51: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (1174 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:59:54: #4 Write output xls file... SRX030150.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:54: #4 Write peak in narrowPeak format file... SRX030150.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:54: #4 Write summits bed file... SRX030150.10_summits.bed INFO @ Tue, 21 Apr 2015 12:59:54: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1615 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。