Job ID = 2162377 sra ファイルのダウンロード中... Completed: 1093061K bytes transferred in 12 seconds (736909K 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 36798 0 36798 0 0 49271 0 --:--:-- --:--:-- --:--:-- 66302 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 47603779 spots for /home/okishinya/chipatlas/results/dm3/SRX054533/SRR167348.sra Written 47603779 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: 00:07:03 47603779 reads; of these: 47603779 (100.00%) were unpaired; of these: 33476962 (70.32%) aligned 0 times 10682089 (22.44%) aligned exactly 1 time 3444728 (7.24%) aligned >1 times 29.68% overall alignment rate Time searching: 00:07:03 Overall time: 00:07:03 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] 7087792 / 14126817 = 0.5017 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 13:49:30: # Command line: callpeak -t SRX054533.bam -f BAM -g dm -n SRX054533.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX054533.10 # format = BAM # ChIP-seq file = ['SRX054533.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 13:49:30: # Command line: callpeak -t SRX054533.bam -f BAM -g dm -n SRX054533.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX054533.05 # format = BAM # ChIP-seq file = ['SRX054533.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 13:49:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:49:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:49:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:49:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:49:30: # Command line: callpeak -t SRX054533.bam -f BAM -g dm -n SRX054533.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX054533.20 # format = BAM # ChIP-seq file = ['SRX054533.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 13:49:30: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:49:30: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:49:35: 1000000 INFO @ Tue, 21 Apr 2015 13:49:35: 1000000 INFO @ Tue, 21 Apr 2015 13:49:35: 1000000 INFO @ Tue, 21 Apr 2015 13:49:40: 2000000 INFO @ Tue, 21 Apr 2015 13:49:41: 2000000 INFO @ Tue, 21 Apr 2015 13:49:41: 2000000 INFO @ Tue, 21 Apr 2015 13:49:45: 3000000 INFO @ Tue, 21 Apr 2015 13:49:46: 3000000 INFO @ Tue, 21 Apr 2015 13:49:47: 3000000 INFO @ Tue, 21 Apr 2015 13:49:50: 4000000 INFO @ Tue, 21 Apr 2015 13:49:52: 4000000 INFO @ Tue, 21 Apr 2015 13:49:53: 4000000 INFO @ Tue, 21 Apr 2015 13:49:56: 5000000 INFO @ Tue, 21 Apr 2015 13:49:57: 5000000 INFO @ Tue, 21 Apr 2015 13:49:59: 5000000 INFO @ Tue, 21 Apr 2015 13:50:01: 6000000 INFO @ Tue, 21 Apr 2015 13:50:03: 6000000 INFO @ Tue, 21 Apr 2015 13:50:05: 6000000 INFO @ Tue, 21 Apr 2015 13:50:06: 7000000 INFO @ Tue, 21 Apr 2015 13:50:06: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:50:06: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:50:06: #1 total tags in treatment: 7039025 INFO @ Tue, 21 Apr 2015 13:50:06: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:50:06: #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 13:50:07: #1 tags after filtering in treatment: 7038333 INFO @ Tue, 21 Apr 2015 13:50:07: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:50:07: #1 finished! INFO @ Tue, 21 Apr 2015 13:50:07: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:50:09: #2 number of paired peaks: 1291 INFO @ Tue, 21 Apr 2015 13:50:09: start model_add_line... INFO @ Tue, 21 Apr 2015 13:50:09: 7000000 INFO @ Tue, 21 Apr 2015 13:50:09: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:50:09: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:50:09: #1 total tags in treatment: 7039025 INFO @ Tue, 21 Apr 2015 13:50:09: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:50:09: #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 13:50:10: #1 tags after filtering in treatment: 7038333 INFO @ Tue, 21 Apr 2015 13:50:10: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:50:10: #1 finished! INFO @ Tue, 21 Apr 2015 13:50:10: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:50:11: 7000000 INFO @ Tue, 21 Apr 2015 13:50:11: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:50:11: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:50:11: #1 total tags in treatment: 7039025 INFO @ Tue, 21 Apr 2015 13:50:11: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:50:11: #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 13:50:12: #2 number of paired peaks: 1291 INFO @ Tue, 21 Apr 2015 13:50:12: start model_add_line... INFO @ Tue, 21 Apr 2015 13:50:13: #1 tags after filtering in treatment: 7038333 INFO @ Tue, 21 Apr 2015 13:50:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:50:13: #1 finished! INFO @ Tue, 21 Apr 2015 13:50:13: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:50:14: #2 number of paired peaks: 1291 INFO @ Tue, 21 Apr 2015 13:50:14: start model_add_line... INFO @ Tue, 21 Apr 2015 13:50:16: start X-correlation... INFO @ Tue, 21 Apr 2015 13:50:16: end of X-cor INFO @ Tue, 21 Apr 2015 13:50:16: #2 finished! INFO @ Tue, 21 Apr 2015 13:50:16: #2 predicted fragment length is 70 bps INFO @ Tue, 21 Apr 2015 13:50:16: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 21 Apr 2015 13:50:16: #2.2 Generate R script for model : SRX054533.20_model.r WARNING @ Tue, 21 Apr 2015 13:50:16: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:50:16: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 21 Apr 2015 13:50:16: #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 13:50:16: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:50:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:50:19: start X-correlation... INFO @ Tue, 21 Apr 2015 13:50:19: end of X-cor INFO @ Tue, 21 Apr 2015 13:50:19: #2 finished! INFO @ Tue, 21 Apr 2015 13:50:19: #2 predicted fragment length is 70 bps INFO @ Tue, 21 Apr 2015 13:50:19: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 21 Apr 2015 13:50:19: #2.2 Generate R script for model : SRX054533.10_model.r WARNING @ Tue, 21 Apr 2015 13:50:19: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:50:19: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 21 Apr 2015 13:50:19: #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 13:50:19: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:50:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:50:21: start X-correlation... INFO @ Tue, 21 Apr 2015 13:50:21: end of X-cor INFO @ Tue, 21 Apr 2015 13:50:21: #2 finished! INFO @ Tue, 21 Apr 2015 13:50:21: #2 predicted fragment length is 70 bps INFO @ Tue, 21 Apr 2015 13:50:21: #2 alternative fragment length(s) may be 70 bps INFO @ Tue, 21 Apr 2015 13:50:21: #2.2 Generate R script for model : SRX054533.05_model.r WARNING @ Tue, 21 Apr 2015 13:50:21: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:50:21: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Tue, 21 Apr 2015 13:50:21: #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 13:50:21: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:50:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:50:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:50:59: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:51:01: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:51:24: #4 Write output xls file... SRX054533.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:51:24: #4 Write peak in narrowPeak format file... SRX054533.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:51:24: #4 Write summits bed file... SRX054533.20_summits.bed INFO @ Tue, 21 Apr 2015 13:51:24: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1999 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:51:31: #4 Write output xls file... SRX054533.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:51:31: #4 Write peak in narrowPeak format file... SRX054533.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:51:31: #4 Write summits bed file... SRX054533.10_summits.bed INFO @ Tue, 21 Apr 2015 13:51:31: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4232 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:51:32: #4 Write output xls file... SRX054533.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:51:33: #4 Write peak in narrowPeak format file... SRX054533.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:51:33: #4 Write summits bed file... SRX054533.05_summits.bed INFO @ Tue, 21 Apr 2015 13:51:33: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7805 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。