Job ID = 2161572 sra ファイルのダウンロード中... Completed: 755356K bytes transferred in 8 seconds (689923K bits/sec), in 2 files, 3 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 44920 0 44920 0 0 47261 0 --:--:-- --:--:-- --:--:-- 59183 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 15209955 spots for /home/okishinya/chipatlas/results/dm3/SRX032109/SRR073926.sra Written 15209955 spots total Written 19382151 spots for /home/okishinya/chipatlas/results/dm3/SRX032109/SRR073925.sra Written 19382151 spots total 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: 00:26:03 34592106 reads; of these: 34592106 (100.00%) were unpaired; of these: 1684051 (4.87%) aligned 0 times 14037070 (40.58%) aligned exactly 1 time 18870985 (54.55%) aligned >1 times 95.13% overall alignment rate Time searching: 00:26:03 Overall time: 00:26:03 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_sort_core] merging from 12 files... [bam_rmdupse_core] 24698232 / 32908055 = 0.7505 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 13:25:43: # Command line: callpeak -t SRX032109.bam -f BAM -g dm -n SRX032109.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX032109.05 # format = BAM # ChIP-seq file = ['SRX032109.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 13:25:43: # Command line: callpeak -t SRX032109.bam -f BAM -g dm -n SRX032109.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX032109.10 # format = BAM # ChIP-seq file = ['SRX032109.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 13:25:43: # Command line: callpeak -t SRX032109.bam -f BAM -g dm -n SRX032109.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX032109.20 # format = BAM # ChIP-seq file = ['SRX032109.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 13:25:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:25:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:25:43: #1 read tag files... INFO @ Tue, 21 Apr 2015 13:25:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:25:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:25:43: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 13:25:49: 1000000 INFO @ Tue, 21 Apr 2015 13:25:49: 1000000 INFO @ Tue, 21 Apr 2015 13:25:49: 1000000 INFO @ Tue, 21 Apr 2015 13:25:54: 2000000 INFO @ Tue, 21 Apr 2015 13:25:54: 2000000 INFO @ Tue, 21 Apr 2015 13:25:54: 2000000 INFO @ Tue, 21 Apr 2015 13:25:59: 3000000 INFO @ Tue, 21 Apr 2015 13:25:59: 3000000 INFO @ Tue, 21 Apr 2015 13:26:00: 3000000 INFO @ Tue, 21 Apr 2015 13:26:04: 4000000 INFO @ Tue, 21 Apr 2015 13:26:04: 4000000 INFO @ Tue, 21 Apr 2015 13:26:05: 4000000 INFO @ Tue, 21 Apr 2015 13:26:09: 5000000 INFO @ Tue, 21 Apr 2015 13:26:09: 5000000 INFO @ Tue, 21 Apr 2015 13:26:11: 5000000 INFO @ Tue, 21 Apr 2015 13:26:14: 6000000 INFO @ Tue, 21 Apr 2015 13:26:15: 6000000 INFO @ Tue, 21 Apr 2015 13:26:16: 6000000 INFO @ Tue, 21 Apr 2015 13:26:19: 7000000 INFO @ Tue, 21 Apr 2015 13:26:20: 7000000 INFO @ Tue, 21 Apr 2015 13:26:21: 7000000 INFO @ Tue, 21 Apr 2015 13:26:24: 8000000 INFO @ Tue, 21 Apr 2015 13:26:25: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:26:25: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:26:25: #1 total tags in treatment: 8209823 INFO @ Tue, 21 Apr 2015 13:26:25: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:26:25: #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 13:26:25: 8000000 INFO @ Tue, 21 Apr 2015 13:26:26: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:26:26: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:26:26: #1 total tags in treatment: 8209823 INFO @ Tue, 21 Apr 2015 13:26:26: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:26:26: #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 13:26:26: #1 tags after filtering in treatment: 8208230 INFO @ Tue, 21 Apr 2015 13:26:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:26:26: #1 finished! INFO @ Tue, 21 Apr 2015 13:26:26: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:26:27: 8000000 INFO @ Tue, 21 Apr 2015 13:26:28: #1 tags after filtering in treatment: 8208230 INFO @ Tue, 21 Apr 2015 13:26:28: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:26:28: #1 finished! INFO @ Tue, 21 Apr 2015 13:26:28: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:26:28: #1 tag size is determined as 36 bps INFO @ Tue, 21 Apr 2015 13:26:28: #1 tag size = 36 INFO @ Tue, 21 Apr 2015 13:26:28: #1 total tags in treatment: 8209823 INFO @ Tue, 21 Apr 2015 13:26:28: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 13:26:28: #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 13:26:28: #2 number of paired peaks: 3067 INFO @ Tue, 21 Apr 2015 13:26:28: start model_add_line... INFO @ Tue, 21 Apr 2015 13:26:30: #1 tags after filtering in treatment: 8208230 INFO @ Tue, 21 Apr 2015 13:26:30: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 21 Apr 2015 13:26:30: #1 finished! INFO @ Tue, 21 Apr 2015 13:26:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 13:26:30: #2 number of paired peaks: 3067 INFO @ Tue, 21 Apr 2015 13:26:30: start model_add_line... INFO @ Tue, 21 Apr 2015 13:26:31: #2 number of paired peaks: 3067 INFO @ Tue, 21 Apr 2015 13:26:31: start model_add_line... INFO @ Tue, 21 Apr 2015 13:26:44: start X-correlation... INFO @ Tue, 21 Apr 2015 13:26:44: end of X-cor INFO @ Tue, 21 Apr 2015 13:26:44: #2 finished! INFO @ Tue, 21 Apr 2015 13:26:44: #2 predicted fragment length is 43 bps INFO @ Tue, 21 Apr 2015 13:26:44: #2 alternative fragment length(s) may be 43 bps INFO @ Tue, 21 Apr 2015 13:26:44: #2.2 Generate R script for model : SRX032109.05_model.r WARNING @ Tue, 21 Apr 2015 13:26:44: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:26:44: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Tue, 21 Apr 2015 13:26:44: #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 13:26:44: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:26:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:26:45: start X-correlation... INFO @ Tue, 21 Apr 2015 13:26:45: end of X-cor INFO @ Tue, 21 Apr 2015 13:26:45: #2 finished! INFO @ Tue, 21 Apr 2015 13:26:45: #2 predicted fragment length is 43 bps INFO @ Tue, 21 Apr 2015 13:26:45: #2 alternative fragment length(s) may be 43 bps INFO @ Tue, 21 Apr 2015 13:26:45: #2.2 Generate R script for model : SRX032109.10_model.r WARNING @ Tue, 21 Apr 2015 13:26:45: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:26:45: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Tue, 21 Apr 2015 13:26:45: #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 13:26:45: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:26:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:26:46: start X-correlation... INFO @ Tue, 21 Apr 2015 13:26:46: end of X-cor INFO @ Tue, 21 Apr 2015 13:26:46: #2 finished! INFO @ Tue, 21 Apr 2015 13:26:46: #2 predicted fragment length is 43 bps INFO @ Tue, 21 Apr 2015 13:26:46: #2 alternative fragment length(s) may be 43 bps INFO @ Tue, 21 Apr 2015 13:26:46: #2.2 Generate R script for model : SRX032109.20_model.r WARNING @ Tue, 21 Apr 2015 13:26:46: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 21 Apr 2015 13:26:46: #2 You may need to consider one of the other alternative d(s): 43 WARNING @ Tue, 21 Apr 2015 13:26:46: #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 13:26:46: #3 Call peaks... INFO @ Tue, 21 Apr 2015 13:26:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 13:27:28: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:27:28: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:27:30: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 13:27:59: #4 Write output xls file... SRX032109.20_peaks.xls INFO @ Tue, 21 Apr 2015 13:27:59: #4 Write peak in narrowPeak format file... SRX032109.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:27:59: #4 Write summits bed file... SRX032109.20_summits.bed INFO @ Tue, 21 Apr 2015 13:27:59: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (1251 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:28:03: #4 Write output xls file... SRX032109.10_peaks.xls INFO @ Tue, 21 Apr 2015 13:28:03: #4 Write peak in narrowPeak format file... SRX032109.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:28:03: #4 Write summits bed file... SRX032109.10_summits.bed INFO @ Tue, 21 Apr 2015 13:28:03: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2301 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 13:28:04: #4 Write output xls file... SRX032109.05_peaks.xls INFO @ Tue, 21 Apr 2015 13:28:04: #4 Write peak in narrowPeak format file... SRX032109.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 13:28:04: #4 Write summits bed file... SRX032109.05_summits.bed INFO @ Tue, 21 Apr 2015 13:28:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9241 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。