Job ID = 2161256 sra ファイルのダウンロード中... Completed: 176676K bytes transferred in 5 seconds (285596K 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 14916 0 14916 0 0 22075 0 --:--:-- --:--:-- --:--:-- 30754 100 34459 0 34459 0 0 50928 0 --:--:-- --:--:-- --:--:-- 70903 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 7106889 spots for /home/okishinya/chipatlas/results/dm3/SRX013100/SRR030366.sra Written 7106889 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: 00:03:25 7106889 reads; of these: 7106889 (100.00%) were unpaired; of these: 117109 (1.65%) aligned 0 times 3399331 (47.83%) aligned exactly 1 time 3590449 (50.52%) aligned >1 times 98.35% overall alignment rate Time searching: 00:03:25 Overall time: 00:03:25 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] 833353 / 6989780 = 0.1192 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 12:13:20: # Command line: callpeak -t SRX013100.bam -f BAM -g dm -n SRX013100.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX013100.20 # format = BAM # ChIP-seq file = ['SRX013100.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 12:13:20: # Command line: callpeak -t SRX013100.bam -f BAM -g dm -n SRX013100.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX013100.10 # format = BAM # ChIP-seq file = ['SRX013100.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 12:13:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:13:20: # Command line: callpeak -t SRX013100.bam -f BAM -g dm -n SRX013100.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX013100.05 # format = BAM # ChIP-seq file = ['SRX013100.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 12:13:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:13:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:13:20: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:13:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:13:20: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:13:26: 1000000 INFO @ Tue, 21 Apr 2015 12:13:26: 1000000 INFO @ Tue, 21 Apr 2015 12:13:26: 1000000 INFO @ Tue, 21 Apr 2015 12:13:31: 2000000 INFO @ Tue, 21 Apr 2015 12:13:32: 2000000 INFO @ Tue, 21 Apr 2015 12:13:32: 2000000 INFO @ Tue, 21 Apr 2015 12:13:36: 3000000 INFO @ Tue, 21 Apr 2015 12:13:38: 3000000 INFO @ Tue, 21 Apr 2015 12:13:38: 3000000 INFO @ Tue, 21 Apr 2015 12:13:42: 4000000 INFO @ Tue, 21 Apr 2015 12:13:44: 4000000 INFO @ Tue, 21 Apr 2015 12:13:44: 4000000 INFO @ Tue, 21 Apr 2015 12:13:47: 5000000 INFO @ Tue, 21 Apr 2015 12:13:50: 5000000 INFO @ Tue, 21 Apr 2015 12:13:50: 5000000 INFO @ Tue, 21 Apr 2015 12:13:52: 6000000 INFO @ Tue, 21 Apr 2015 12:13:53: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:13:53: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:13:53: #1 total tags in treatment: 6156427 INFO @ Tue, 21 Apr 2015 12:13:53: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:13:53: #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 12:13:54: #1 tags after filtering in treatment: 6156005 INFO @ Tue, 21 Apr 2015 12:13:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:13:54: #1 finished! INFO @ Tue, 21 Apr 2015 12:13:54: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:13:56: #2 number of paired peaks: 876 WARNING @ Tue, 21 Apr 2015 12:13:56: Fewer paired peaks (876) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 876 pairs to build model! INFO @ Tue, 21 Apr 2015 12:13:56: start model_add_line... INFO @ Tue, 21 Apr 2015 12:13:56: 6000000 INFO @ Tue, 21 Apr 2015 12:13:56: 6000000 INFO @ Tue, 21 Apr 2015 12:13:57: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:13:57: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:13:57: #1 total tags in treatment: 6156427 INFO @ Tue, 21 Apr 2015 12:13:57: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:13:57: #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 12:13:57: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 12:13:57: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 12:13:57: #1 total tags in treatment: 6156427 INFO @ Tue, 21 Apr 2015 12:13:57: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:13:57: #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 12:13:58: #1 tags after filtering in treatment: 6156005 INFO @ Tue, 21 Apr 2015 12:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:13:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:13:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:13:58: #1 tags after filtering in treatment: 6156005 INFO @ Tue, 21 Apr 2015 12:13:58: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 12:13:58: #1 finished! INFO @ Tue, 21 Apr 2015 12:13:58: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:13:59: start X-correlation... INFO @ Tue, 21 Apr 2015 12:13:59: end of X-cor INFO @ Tue, 21 Apr 2015 12:13:59: #2 finished! INFO @ Tue, 21 Apr 2015 12:13:59: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 12:13:59: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 12:13:59: #2.2 Generate R script for model : SRX013100.20_model.r WARNING @ Tue, 21 Apr 2015 12:13:59: #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 12:13:59: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 12:13:59: #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 12:13:59: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:13:59: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:13:59: #2 number of paired peaks: 876 WARNING @ Tue, 21 Apr 2015 12:13:59: Fewer paired peaks (876) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 876 pairs to build model! INFO @ Tue, 21 Apr 2015 12:13:59: start model_add_line... INFO @ Tue, 21 Apr 2015 12:14:00: #2 number of paired peaks: 876 WARNING @ Tue, 21 Apr 2015 12:14:00: Fewer paired peaks (876) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 876 pairs to build model! INFO @ Tue, 21 Apr 2015 12:14:00: start model_add_line... INFO @ Tue, 21 Apr 2015 12:14:03: start X-correlation... INFO @ Tue, 21 Apr 2015 12:14:03: end of X-cor INFO @ Tue, 21 Apr 2015 12:14:03: #2 finished! INFO @ Tue, 21 Apr 2015 12:14:03: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 12:14:03: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 12:14:03: #2.2 Generate R script for model : SRX013100.05_model.r WARNING @ Tue, 21 Apr 2015 12:14:03: #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 12:14:03: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 12:14:03: #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 12:14:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:14:03: start X-correlation... INFO @ Tue, 21 Apr 2015 12:14:03: end of X-cor INFO @ Tue, 21 Apr 2015 12:14:03: #2 finished! INFO @ Tue, 21 Apr 2015 12:14:03: #2 predicted fragment length is 42 bps INFO @ Tue, 21 Apr 2015 12:14:03: #2 alternative fragment length(s) may be 42 bps INFO @ Tue, 21 Apr 2015 12:14:03: #2.2 Generate R script for model : SRX013100.10_model.r WARNING @ Tue, 21 Apr 2015 12:14:03: #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 12:14:03: #2 You may need to consider one of the other alternative d(s): 42 WARNING @ Tue, 21 Apr 2015 12:14:03: #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 12:14:03: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:14:03: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:14:35: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:14:36: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:14:37: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:14:58: #4 Write output xls file... SRX013100.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:14:58: #4 Write peak in narrowPeak format file... SRX013100.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:14:58: #4 Write summits bed file... SRX013100.20_summits.bed INFO @ Tue, 21 Apr 2015 12:14:58: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (485 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:15:01: #4 Write output xls file... SRX013100.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:15:01: #4 Write peak in narrowPeak format file... SRX013100.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:15:01: #4 Write summits bed file... SRX013100.05_summits.bed INFO @ Tue, 21 Apr 2015 12:15:01: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2152 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:15:04: #4 Write output xls file... SRX013100.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:15:04: #4 Write peak in narrowPeak format file... SRX013100.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:15:04: #4 Write summits bed file... SRX013100.10_summits.bed INFO @ Tue, 21 Apr 2015 12:15:04: Done! pass1 - making usageList (10 chroms): 4 millis pass2 - checking and writing primary data (787 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。