Job ID = 2161433 sra ファイルのダウンロード中... Completed: 483417K bytes transferred in 7 seconds (556275K 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 2540 0 2540 0 0 3442 0 --:--:-- --:--:-- --:--:-- 4643 100 44907 0 44907 0 0 40217 0 --:--:-- 0:00:01 --:--:-- 48548 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 23105084 spots for /home/okishinya/chipatlas/results/dm3/SRX026863/SRR065763.sra Written 23105084 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: 00:09:18 23105084 reads; of these: 23105084 (100.00%) were unpaired; of these: 812845 (3.52%) aligned 0 times 15401474 (66.66%) aligned exactly 1 time 6890765 (29.82%) aligned >1 times 96.48% overall alignment rate Time searching: 00:09:18 Overall time: 00:09:18 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] 3635664 / 22292239 = 0.1631 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 12:55:42: # Command line: callpeak -t SRX026863.bam -f BAM -g dm -n SRX026863.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX026863.05 # format = BAM # ChIP-seq file = ['SRX026863.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 12:55:42: # Command line: callpeak -t SRX026863.bam -f BAM -g dm -n SRX026863.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX026863.10 # format = BAM # ChIP-seq file = ['SRX026863.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 12:55:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:55:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:55:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:55:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:55:42: # Command line: callpeak -t SRX026863.bam -f BAM -g dm -n SRX026863.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX026863.20 # format = BAM # ChIP-seq file = ['SRX026863.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 12:55:42: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:55:42: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:55:47: 1000000 INFO @ Tue, 21 Apr 2015 12:55:47: 1000000 INFO @ Tue, 21 Apr 2015 12:55:48: 1000000 INFO @ Tue, 21 Apr 2015 12:55:52: 2000000 INFO @ Tue, 21 Apr 2015 12:55:52: 2000000 INFO @ Tue, 21 Apr 2015 12:55:53: 2000000 INFO @ Tue, 21 Apr 2015 12:55:57: 3000000 INFO @ Tue, 21 Apr 2015 12:55:58: 3000000 INFO @ Tue, 21 Apr 2015 12:55:58: 3000000 INFO @ Tue, 21 Apr 2015 12:56:02: 4000000 INFO @ Tue, 21 Apr 2015 12:56:03: 4000000 INFO @ Tue, 21 Apr 2015 12:56:03: 4000000 INFO @ Tue, 21 Apr 2015 12:56:07: 5000000 INFO @ Tue, 21 Apr 2015 12:56:08: 5000000 INFO @ Tue, 21 Apr 2015 12:56:08: 5000000 INFO @ Tue, 21 Apr 2015 12:56:12: 6000000 INFO @ Tue, 21 Apr 2015 12:56:13: 6000000 INFO @ Tue, 21 Apr 2015 12:56:13: 6000000 INFO @ Tue, 21 Apr 2015 12:56:17: 7000000 INFO @ Tue, 21 Apr 2015 12:56:18: 7000000 INFO @ Tue, 21 Apr 2015 12:56:19: 7000000 INFO @ Tue, 21 Apr 2015 12:56:22: 8000000 INFO @ Tue, 21 Apr 2015 12:56:23: 8000000 INFO @ Tue, 21 Apr 2015 12:56:24: 8000000 INFO @ Tue, 21 Apr 2015 12:56:26: 9000000 INFO @ Tue, 21 Apr 2015 12:56:28: 9000000 INFO @ Tue, 21 Apr 2015 12:56:29: 9000000 INFO @ Tue, 21 Apr 2015 12:56:31: 10000000 INFO @ Tue, 21 Apr 2015 12:56:34: 10000000 INFO @ Tue, 21 Apr 2015 12:56:34: 10000000 INFO @ Tue, 21 Apr 2015 12:56:36: 11000000 INFO @ Tue, 21 Apr 2015 12:56:39: 11000000 INFO @ Tue, 21 Apr 2015 12:56:39: 11000000 INFO @ Tue, 21 Apr 2015 12:56:41: 12000000 INFO @ Tue, 21 Apr 2015 12:56:44: 12000000 INFO @ Tue, 21 Apr 2015 12:56:45: 12000000 INFO @ Tue, 21 Apr 2015 12:56:45: 13000000 INFO @ Tue, 21 Apr 2015 12:56:49: 13000000 INFO @ Tue, 21 Apr 2015 12:56:50: 13000000 INFO @ Tue, 21 Apr 2015 12:56:50: 14000000 INFO @ Tue, 21 Apr 2015 12:56:55: 14000000 INFO @ Tue, 21 Apr 2015 12:56:55: 15000000 INFO @ Tue, 21 Apr 2015 12:56:55: 14000000 INFO @ Tue, 21 Apr 2015 12:57:00: 16000000 INFO @ Tue, 21 Apr 2015 12:57:00: 15000000 INFO @ Tue, 21 Apr 2015 12:57:00: 15000000 INFO @ Tue, 21 Apr 2015 12:57:05: 17000000 INFO @ Tue, 21 Apr 2015 12:57:05: 16000000 INFO @ Tue, 21 Apr 2015 12:57:06: 16000000 INFO @ Tue, 21 Apr 2015 12:57:09: 18000000 INFO @ Tue, 21 Apr 2015 12:57:11: 17000000 INFO @ Tue, 21 Apr 2015 12:57:11: 17000000 INFO @ Tue, 21 Apr 2015 12:57:13: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:57:13: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:57:13: #1 total tags in treatment: 18656575 INFO @ Tue, 21 Apr 2015 12:57:13: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:57:13: #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 12:57:16: 18000000 INFO @ Tue, 21 Apr 2015 12:57:16: 18000000 INFO @ Tue, 21 Apr 2015 12:57:17: #1 tags after filtering in treatment: 18654684 INFO @ Tue, 21 Apr 2015 12:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:57:17: #1 finished! INFO @ Tue, 21 Apr 2015 12:57:17: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:57:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:57:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:57:20: #1 total tags in treatment: 18656575 INFO @ Tue, 21 Apr 2015 12:57:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:57:20: #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 12:57:20: #2 number of paired peaks: 123 WARNING @ Tue, 21 Apr 2015 12:57:20: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 21 Apr 2015 12:57:20: start model_add_line... INFO @ Tue, 21 Apr 2015 12:57:20: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:57:20: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:57:20: #1 total tags in treatment: 18656575 INFO @ Tue, 21 Apr 2015 12:57:20: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:57:20: #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 12:57:22: start X-correlation... INFO @ Tue, 21 Apr 2015 12:57:22: end of X-cor INFO @ Tue, 21 Apr 2015 12:57:22: #2 finished! INFO @ Tue, 21 Apr 2015 12:57:22: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 12:57:22: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 12:57:22: #2.2 Generate R script for model : SRX026863.05_model.r WARNING @ Tue, 21 Apr 2015 12:57:22: #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 12:57:22: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 12:57:22: #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 12:57:22: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:57:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:57:24: #1 tags after filtering in treatment: 18654684 INFO @ Tue, 21 Apr 2015 12:57:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:57:24: #1 finished! INFO @ Tue, 21 Apr 2015 12:57:24: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:57:24: #1 tags after filtering in treatment: 18654684 INFO @ Tue, 21 Apr 2015 12:57:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:57:24: #1 finished! INFO @ Tue, 21 Apr 2015 12:57:24: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:57:27: #2 number of paired peaks: 123 WARNING @ Tue, 21 Apr 2015 12:57:27: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 21 Apr 2015 12:57:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:57:27: #2 number of paired peaks: 123 WARNING @ Tue, 21 Apr 2015 12:57:27: Fewer paired peaks (123) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 123 pairs to build model! INFO @ Tue, 21 Apr 2015 12:57:27: start model_add_line... INFO @ Tue, 21 Apr 2015 12:57:28: start X-correlation... INFO @ Tue, 21 Apr 2015 12:57:28: end of X-cor INFO @ Tue, 21 Apr 2015 12:57:28: #2 finished! INFO @ Tue, 21 Apr 2015 12:57:28: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 12:57:28: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 12:57:28: #2.2 Generate R script for model : SRX026863.20_model.r WARNING @ Tue, 21 Apr 2015 12:57:28: #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 12:57:28: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 12:57:28: #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 12:57:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:57:28: start X-correlation... INFO @ Tue, 21 Apr 2015 12:57:28: end of X-cor INFO @ Tue, 21 Apr 2015 12:57:28: #2 finished! INFO @ Tue, 21 Apr 2015 12:57:28: #2 predicted fragment length is 39 bps INFO @ Tue, 21 Apr 2015 12:57:28: #2 alternative fragment length(s) may be 39 bps INFO @ Tue, 21 Apr 2015 12:57:28: #2.2 Generate R script for model : SRX026863.10_model.r WARNING @ Tue, 21 Apr 2015 12:57:28: #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 12:57:28: #2 You may need to consider one of the other alternative d(s): 39 WARNING @ Tue, 21 Apr 2015 12:57:28: #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 12:57:28: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:57:28: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:58:46: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:58:56: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:58:59: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:59:52: #4 Write output xls file... SRX026863.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:59:52: #4 Write peak in narrowPeak format file... SRX026863.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:59:52: #4 Write summits bed file... SRX026863.05_summits.bed INFO @ Tue, 21 Apr 2015 12:59:52: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2558 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:00:02: #4 Write output xls file... SRX026863.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:00:02: #4 Write peak in narrowPeak format file... SRX026863.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:00:02: #4 Write summits bed file... SRX026863.10_summits.bed INFO @ Tue, 21 Apr 2015 13:00:02: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1350 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:00:07: #4 Write output xls file... SRX026863.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:00:07: #4 Write peak in narrowPeak format file... SRX026863.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:00:07: #4 Write summits bed file... SRX026863.20_summits.bed INFO @ Tue, 21 Apr 2015 13:00:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (840 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。