Job ID = 2161922 sra ファイルのダウンロード中... Completed: 331615K bytes transferred in 6 seconds (428513K 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 4875 0 --:--:-- --:--:-- --:--:-- 7696 100 45206 0 45206 0 0 50213 0 --:--:-- --:--:-- --:--:-- 63670 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 18243271 spots for /home/okishinya/chipatlas/results/dm3/SRX041385/SRR099114.sra Written 18243271 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: 00:00:01 Multiseed full-index search: 00:03:43 18243271 reads; of these: 18243271 (100.00%) were unpaired; of these: 532532 (2.92%) aligned 0 times 11635979 (63.78%) aligned exactly 1 time 6074760 (33.30%) aligned >1 times 97.08% overall alignment rate Time searching: 00:03:44 Overall time: 00:03:44 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] 3298397 / 17710739 = 0.1862 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 13:23:12: # Command line: callpeak -t SRX041385.bam -f BAM -g dm -n SRX041385.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX041385.05 # format = BAM # ChIP-seq file = ['SRX041385.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 13:23:12: # Command line: callpeak -t SRX041385.bam -f BAM -g dm -n SRX041385.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX041385.10 # format = BAM # ChIP-seq file = ['SRX041385.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 13:23:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:23:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:23:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:23:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:23:12: # Command line: callpeak -t SRX041385.bam -f BAM -g dm -n SRX041385.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX041385.20 # format = BAM # ChIP-seq file = ['SRX041385.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 13:23:12: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:23:12: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:23:17: 1000000 INFO @ Tue, 21 Apr 2015 13:23:17: 1000000 INFO @ Tue, 21 Apr 2015 13:23:17: 1000000 INFO @ Tue, 21 Apr 2015 13:23:23: 2000000 INFO @ Tue, 21 Apr 2015 13:23:23: 2000000 INFO @ Tue, 21 Apr 2015 13:23:23: 2000000 INFO @ Tue, 21 Apr 2015 13:23:28: 3000000 INFO @ Tue, 21 Apr 2015 13:23:29: 3000000 INFO @ Tue, 21 Apr 2015 13:23:29: 3000000 INFO @ Tue, 21 Apr 2015 13:23:33: 4000000 INFO @ Tue, 21 Apr 2015 13:23:34: 4000000 INFO @ Tue, 21 Apr 2015 13:23:34: 4000000 INFO @ Tue, 21 Apr 2015 13:23:38: 5000000 INFO @ Tue, 21 Apr 2015 13:23:40: 5000000 INFO @ Tue, 21 Apr 2015 13:23:40: 5000000 INFO @ Tue, 21 Apr 2015 13:23:42: 6000000 INFO @ Tue, 21 Apr 2015 13:23:45: 6000000 INFO @ Tue, 21 Apr 2015 13:23:45: 6000000 INFO @ Tue, 21 Apr 2015 13:23:47: 7000000 INFO @ Tue, 21 Apr 2015 13:23:51: 7000000 INFO @ Tue, 21 Apr 2015 13:23:51: 7000000 INFO @ Tue, 21 Apr 2015 13:23:52: 8000000 INFO @ Tue, 21 Apr 2015 13:23:56: 8000000 INFO @ Tue, 21 Apr 2015 13:23:56: 8000000 INFO @ Tue, 21 Apr 2015 13:23:57: 9000000 INFO @ Tue, 21 Apr 2015 13:24:02: 10000000 INFO @ Tue, 21 Apr 2015 13:24:02: 9000000 INFO @ Tue, 21 Apr 2015 13:24:02: 9000000 INFO @ Tue, 21 Apr 2015 13:24:06: 11000000 INFO @ Tue, 21 Apr 2015 13:24:07: 10000000 INFO @ Tue, 21 Apr 2015 13:24:07: 10000000 INFO @ Tue, 21 Apr 2015 13:24:11: 12000000 INFO @ Tue, 21 Apr 2015 13:24:13: 11000000 INFO @ Tue, 21 Apr 2015 13:24:13: 11000000 INFO @ Tue, 21 Apr 2015 13:24:16: 13000000 INFO @ Tue, 21 Apr 2015 13:24:19: 12000000 INFO @ Tue, 21 Apr 2015 13:24:19: 12000000 INFO @ Tue, 21 Apr 2015 13:24:21: 14000000 INFO @ Tue, 21 Apr 2015 13:24:23: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:24:23: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:24:23: #1 total tags in treatment: 14412342 INFO @ Tue, 21 Apr 2015 13:24:23: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:24:23: #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 13:24:24: 13000000 INFO @ Tue, 21 Apr 2015 13:24:24: 13000000 INFO @ Tue, 21 Apr 2015 13:24:26: #1 tags after filtering in treatment: 14411820 INFO @ Tue, 21 Apr 2015 13:24:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:24:26: #1 finished! INFO @ Tue, 21 Apr 2015 13:24:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:24:28: #2 number of paired peaks: 106 WARNING @ Tue, 21 Apr 2015 13:24:28: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 21 Apr 2015 13:24:28: start model_add_line... INFO @ Tue, 21 Apr 2015 13:24:30: 14000000 INFO @ Tue, 21 Apr 2015 13:24:30: 14000000 INFO @ Tue, 21 Apr 2015 13:24:30: start X-correlation... INFO @ Tue, 21 Apr 2015 13:24:30: end of X-cor INFO @ Tue, 21 Apr 2015 13:24:30: #2 finished! INFO @ Tue, 21 Apr 2015 13:24:30: #2 predicted fragment length is 35 bps INFO @ Tue, 21 Apr 2015 13:24:30: #2 alternative fragment length(s) may be 4,35 bps INFO @ Tue, 21 Apr 2015 13:24:30: #2.2 Generate R script for model : SRX041385.05_model.r WARNING @ Tue, 21 Apr 2015 13:24:30: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:24:30: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Tue, 21 Apr 2015 13:24:30: #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 13:24:30: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:24:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:24:32: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:24:32: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:24:32: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:24:32: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:24:32: #1 total tags in treatment: 14412342 INFO @ Tue, 21 Apr 2015 13:24:32: #1 total tags in treatment: 14412342 INFO @ Tue, 21 Apr 2015 13:24:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:24:32: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:24:32: #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 13:24:32: #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 13:24:35: #1 tags after filtering in treatment: 14411820 INFO @ Tue, 21 Apr 2015 13:24:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:24:35: #1 finished! INFO @ Tue, 21 Apr 2015 13:24:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:24:35: #1 tags after filtering in treatment: 14411820 INFO @ Tue, 21 Apr 2015 13:24:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:24:35: #1 finished! INFO @ Tue, 21 Apr 2015 13:24:35: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:24:37: #2 number of paired peaks: 106 WARNING @ Tue, 21 Apr 2015 13:24:37: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 21 Apr 2015 13:24:37: start model_add_line... INFO @ Tue, 21 Apr 2015 13:24:38: #2 number of paired peaks: 106 WARNING @ Tue, 21 Apr 2015 13:24:38: Fewer paired peaks (106) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 106 pairs to build model! INFO @ Tue, 21 Apr 2015 13:24:38: start model_add_line... INFO @ Tue, 21 Apr 2015 13:24:39: start X-correlation... INFO @ Tue, 21 Apr 2015 13:24:39: end of X-cor INFO @ Tue, 21 Apr 2015 13:24:39: #2 finished! INFO @ Tue, 21 Apr 2015 13:24:39: #2 predicted fragment length is 35 bps INFO @ Tue, 21 Apr 2015 13:24:39: #2 alternative fragment length(s) may be 4,35 bps INFO @ Tue, 21 Apr 2015 13:24:39: #2.2 Generate R script for model : SRX041385.20_model.r WARNING @ Tue, 21 Apr 2015 13:24:39: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:24:39: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Tue, 21 Apr 2015 13:24:39: #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 13:24:39: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:24:39: start X-correlation... INFO @ Tue, 21 Apr 2015 13:24:39: end of X-cor INFO @ Tue, 21 Apr 2015 13:24:39: #2 finished! INFO @ Tue, 21 Apr 2015 13:24:39: #2 predicted fragment length is 35 bps INFO @ Tue, 21 Apr 2015 13:24:39: #2 alternative fragment length(s) may be 4,35 bps INFO @ Tue, 21 Apr 2015 13:24:39: #2.2 Generate R script for model : SRX041385.10_model.r WARNING @ Tue, 21 Apr 2015 13:24:39: #2 Since the d (35) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:24:39: #2 You may need to consider one of the other alternative d(s): 4,35 WARNING @ Tue, 21 Apr 2015 13:24:39: #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 13:24:39: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:25:43: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:25:48: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:25:53: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:26:37: #4 Write output xls file... SRX041385.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:26:37: #4 Write peak in narrowPeak format file... SRX041385.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:26:37: #4 Write summits bed file... SRX041385.05_summits.bed INFO @ Tue, 21 Apr 2015 13:26:37: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1588 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:26:42: #4 Write output xls file... SRX041385.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:26:42: #4 Write peak in narrowPeak format file... SRX041385.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:26:42: #4 Write summits bed file... SRX041385.10_summits.bed INFO @ Tue, 21 Apr 2015 13:26:42: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (959 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:26:47: #4 Write output xls file... SRX041385.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:26:47: #4 Write peak in narrowPeak format file... SRX041385.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:26:47: #4 Write summits bed file... SRX041385.20_summits.bed INFO @ Tue, 21 Apr 2015 13:26:47: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (547 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。