Job ID = 9031599 sra ファイルのダウンロード中... Completed: 1551700K bytes transferred in 25 seconds (491110K bits/sec), in 12 files, 13 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- 0:00:06 --:--:-- 0 100 7663 0 7663 0 0 1077 0 --:--:-- 0:00:07 --:--:-- 11403 100 38246 0 38246 0 0 4622 0 --:--:-- 0:00:08 --:--:-- 20842 100 54410 0 54410 0 0 6445 0 --:--:-- 0:00:08 --:--:-- 27205 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 2923573 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175655.sra Written 2923573 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175659.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175658.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175660.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175662.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175663.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175653.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175656.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175657.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175652.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175654.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475425/SRR1175661.sra Written 4000000 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: 00:20:25 46923573 reads; of these: 46923573 (100.00%) were unpaired; of these: 2483638 (5.29%) aligned 0 times 28633579 (61.02%) aligned exactly 1 time 15806356 (33.69%) aligned >1 times 94.71% overall alignment rate Time searching: 00:20:25 Overall time: 00:20:25 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_sort_core] merging from 20 files... [bam_rmdupse_core] 15731645 / 44439935 = 0.3540 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 @ Sat, 03 Jun 2017 20:53:17: # Command line: callpeak -t SRX475425.bam -f BAM -g dm -n SRX475425.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX475425.05 # format = BAM # ChIP-seq file = ['SRX475425.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 @ Sat, 03 Jun 2017 20:53:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:53:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:53:17: # Command line: callpeak -t SRX475425.bam -f BAM -g dm -n SRX475425.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX475425.10 # format = BAM # ChIP-seq file = ['SRX475425.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 @ Sat, 03 Jun 2017 20:53:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:53:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:53:17: # Command line: callpeak -t SRX475425.bam -f BAM -g dm -n SRX475425.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX475425.20 # format = BAM # ChIP-seq file = ['SRX475425.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 @ Sat, 03 Jun 2017 20:53:17: #1 read tag files... INFO @ Sat, 03 Jun 2017 20:53:17: #1 read treatment tags... INFO @ Sat, 03 Jun 2017 20:53:23: 1000000 INFO @ Sat, 03 Jun 2017 20:53:23: 1000000 INFO @ Sat, 03 Jun 2017 20:53:23: 1000000 INFO @ Sat, 03 Jun 2017 20:53:30: 2000000 INFO @ Sat, 03 Jun 2017 20:53:30: 2000000 INFO @ Sat, 03 Jun 2017 20:53:30: 2000000 INFO @ Sat, 03 Jun 2017 20:53:36: 3000000 INFO @ Sat, 03 Jun 2017 20:53:37: 3000000 INFO @ Sat, 03 Jun 2017 20:53:37: 3000000 INFO @ Sat, 03 Jun 2017 20:53:42: 4000000 INFO @ Sat, 03 Jun 2017 20:53:43: 4000000 INFO @ Sat, 03 Jun 2017 20:53:43: 4000000 INFO @ Sat, 03 Jun 2017 20:53:49: 5000000 INFO @ Sat, 03 Jun 2017 20:53:50: 5000000 INFO @ Sat, 03 Jun 2017 20:53:50: 5000000 INFO @ Sat, 03 Jun 2017 20:53:55: 6000000 INFO @ Sat, 03 Jun 2017 20:53:57: 6000000 INFO @ Sat, 03 Jun 2017 20:53:57: 6000000 INFO @ Sat, 03 Jun 2017 20:54:01: 7000000 INFO @ Sat, 03 Jun 2017 20:54:03: 7000000 INFO @ Sat, 03 Jun 2017 20:54:03: 7000000 INFO @ Sat, 03 Jun 2017 20:54:08: 8000000 INFO @ Sat, 03 Jun 2017 20:54:10: 8000000 INFO @ Sat, 03 Jun 2017 20:54:10: 8000000 INFO @ Sat, 03 Jun 2017 20:54:14: 9000000 INFO @ Sat, 03 Jun 2017 20:54:17: 9000000 INFO @ Sat, 03 Jun 2017 20:54:17: 9000000 INFO @ Sat, 03 Jun 2017 20:54:20: 10000000 INFO @ Sat, 03 Jun 2017 20:54:23: 10000000 INFO @ Sat, 03 Jun 2017 20:54:23: 10000000 INFO @ Sat, 03 Jun 2017 20:54:26: 11000000 INFO @ Sat, 03 Jun 2017 20:54:30: 11000000 INFO @ Sat, 03 Jun 2017 20:54:30: 11000000 INFO @ Sat, 03 Jun 2017 20:54:33: 12000000 INFO @ Sat, 03 Jun 2017 20:54:37: 12000000 INFO @ Sat, 03 Jun 2017 20:54:37: 12000000 INFO @ Sat, 03 Jun 2017 20:54:39: 13000000 INFO @ Sat, 03 Jun 2017 20:54:43: 13000000 INFO @ Sat, 03 Jun 2017 20:54:44: 13000000 INFO @ Sat, 03 Jun 2017 20:54:45: 14000000 INFO @ Sat, 03 Jun 2017 20:54:50: 14000000 INFO @ Sat, 03 Jun 2017 20:54:50: 14000000 INFO @ Sat, 03 Jun 2017 20:54:52: 15000000 INFO @ Sat, 03 Jun 2017 20:54:57: 15000000 INFO @ Sat, 03 Jun 2017 20:54:57: 15000000 INFO @ Sat, 03 Jun 2017 20:54:58: 16000000 INFO @ Sat, 03 Jun 2017 20:55:04: 16000000 INFO @ Sat, 03 Jun 2017 20:55:04: 16000000 INFO @ Sat, 03 Jun 2017 20:55:04: 17000000 INFO @ Sat, 03 Jun 2017 20:55:11: 18000000 INFO @ Sat, 03 Jun 2017 20:55:11: 17000000 INFO @ Sat, 03 Jun 2017 20:55:11: 17000000 INFO @ Sat, 03 Jun 2017 20:55:17: 19000000 INFO @ Sat, 03 Jun 2017 20:55:18: 18000000 INFO @ Sat, 03 Jun 2017 20:55:19: 18000000 INFO @ Sat, 03 Jun 2017 20:55:23: 20000000 INFO @ Sat, 03 Jun 2017 20:55:25: 19000000 INFO @ Sat, 03 Jun 2017 20:55:26: 19000000 INFO @ Sat, 03 Jun 2017 20:55:30: 21000000 INFO @ Sat, 03 Jun 2017 20:55:33: 20000000 INFO @ Sat, 03 Jun 2017 20:55:33: 20000000 INFO @ Sat, 03 Jun 2017 20:55:36: 22000000 INFO @ Sat, 03 Jun 2017 20:55:40: 21000000 INFO @ Sat, 03 Jun 2017 20:55:40: 21000000 INFO @ Sat, 03 Jun 2017 20:55:43: 23000000 INFO @ Sat, 03 Jun 2017 20:55:47: 22000000 INFO @ Sat, 03 Jun 2017 20:55:48: 22000000 INFO @ Sat, 03 Jun 2017 20:55:49: 24000000 INFO @ Sat, 03 Jun 2017 20:55:55: 23000000 INFO @ Sat, 03 Jun 2017 20:55:55: 23000000 INFO @ Sat, 03 Jun 2017 20:55:56: 25000000 INFO @ Sat, 03 Jun 2017 20:56:02: 26000000 INFO @ Sat, 03 Jun 2017 20:56:03: 24000000 INFO @ Sat, 03 Jun 2017 20:56:03: 24000000 INFO @ Sat, 03 Jun 2017 20:56:09: 27000000 INFO @ Sat, 03 Jun 2017 20:56:10: 25000000 INFO @ Sat, 03 Jun 2017 20:56:11: 25000000 INFO @ Sat, 03 Jun 2017 20:56:15: 28000000 INFO @ Sat, 03 Jun 2017 20:56:18: 26000000 INFO @ Sat, 03 Jun 2017 20:56:18: 26000000 INFO @ Sat, 03 Jun 2017 20:56:20: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:56:20: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:56:20: #1 total tags in treatment: 28708290 INFO @ Sat, 03 Jun 2017 20:56:20: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:56:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 20:56:26: #1 tags after filtering in treatment: 28700657 INFO @ Sat, 03 Jun 2017 20:56:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:56:26: #1 finished! INFO @ Sat, 03 Jun 2017 20:56:26: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:56:26: 27000000 INFO @ Sat, 03 Jun 2017 20:56:26: 27000000 INFO @ Sat, 03 Jun 2017 20:56:30: #2 number of paired peaks: 961 WARNING @ Sat, 03 Jun 2017 20:56:30: Fewer paired peaks (961) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 961 pairs to build model! INFO @ Sat, 03 Jun 2017 20:56:30: start model_add_line... INFO @ Sat, 03 Jun 2017 20:56:34: 28000000 INFO @ Sat, 03 Jun 2017 20:56:34: 28000000 INFO @ Sat, 03 Jun 2017 20:56:40: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:56:40: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:56:40: #1 total tags in treatment: 28708290 INFO @ Sat, 03 Jun 2017 20:56:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:56:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 20:56:40: #1 tag size is determined as 50 bps INFO @ Sat, 03 Jun 2017 20:56:40: #1 tag size = 50 INFO @ Sat, 03 Jun 2017 20:56:40: #1 total tags in treatment: 28708290 INFO @ Sat, 03 Jun 2017 20:56:40: #1 user defined the maximum tags... INFO @ Sat, 03 Jun 2017 20:56:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 03 Jun 2017 20:56:45: #1 tags after filtering in treatment: 28700657 INFO @ Sat, 03 Jun 2017 20:56:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:56:45: #1 finished! INFO @ Sat, 03 Jun 2017 20:56:45: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:56:47: #1 tags after filtering in treatment: 28700657 INFO @ Sat, 03 Jun 2017 20:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 03 Jun 2017 20:56:47: #1 finished! INFO @ Sat, 03 Jun 2017 20:56:47: #2 Build Peak Model... INFO @ Sat, 03 Jun 2017 20:56:49: start X-correlation... INFO @ Sat, 03 Jun 2017 20:56:49: end of X-cor INFO @ Sat, 03 Jun 2017 20:56:49: #2 finished! INFO @ Sat, 03 Jun 2017 20:56:49: #2 predicted fragment length is 74 bps INFO @ Sat, 03 Jun 2017 20:56:49: #2 alternative fragment length(s) may be 2,74 bps INFO @ Sat, 03 Jun 2017 20:56:49: #2.2 Generate R script for model : SRX475425.05_model.r WARNING @ Sat, 03 Jun 2017 20:56:49: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:56:49: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Sat, 03 Jun 2017 20:56:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 20:56:49: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:56:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:56:50: #2 number of paired peaks: 961 WARNING @ Sat, 03 Jun 2017 20:56:50: Fewer paired peaks (961) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 961 pairs to build model! INFO @ Sat, 03 Jun 2017 20:56:50: start model_add_line... INFO @ Sat, 03 Jun 2017 20:56:51: #2 number of paired peaks: 961 WARNING @ Sat, 03 Jun 2017 20:56:51: Fewer paired peaks (961) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 961 pairs to build model! INFO @ Sat, 03 Jun 2017 20:56:51: start model_add_line... INFO @ Sat, 03 Jun 2017 20:57:09: start X-correlation... INFO @ Sat, 03 Jun 2017 20:57:09: end of X-cor INFO @ Sat, 03 Jun 2017 20:57:09: #2 finished! INFO @ Sat, 03 Jun 2017 20:57:09: #2 predicted fragment length is 74 bps INFO @ Sat, 03 Jun 2017 20:57:09: #2 alternative fragment length(s) may be 2,74 bps INFO @ Sat, 03 Jun 2017 20:57:09: #2.2 Generate R script for model : SRX475425.20_model.r WARNING @ Sat, 03 Jun 2017 20:57:09: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:57:09: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Sat, 03 Jun 2017 20:57:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 20:57:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:57:09: start X-correlation... INFO @ Sat, 03 Jun 2017 20:57:09: end of X-cor INFO @ Sat, 03 Jun 2017 20:57:09: #2 finished! INFO @ Sat, 03 Jun 2017 20:57:09: #2 predicted fragment length is 74 bps INFO @ Sat, 03 Jun 2017 20:57:09: #2 alternative fragment length(s) may be 2,74 bps INFO @ Sat, 03 Jun 2017 20:57:09: #2.2 Generate R script for model : SRX475425.10_model.r WARNING @ Sat, 03 Jun 2017 20:57:09: #2 Since the d (74) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 03 Jun 2017 20:57:09: #2 You may need to consider one of the other alternative d(s): 2,74 WARNING @ Sat, 03 Jun 2017 20:57:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 03 Jun 2017 20:57:09: #3 Call peaks... INFO @ Sat, 03 Jun 2017 20:57:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 03 Jun 2017 20:59:07: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:59:22: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 20:59:38: #3 Call peaks for each chromosome... INFO @ Sat, 03 Jun 2017 21:00:51: #4 Write output xls file... SRX475425.05_peaks.xls INFO @ Sat, 03 Jun 2017 21:00:51: #4 Write peak in narrowPeak format file... SRX475425.05_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 21:00:51: #4 Write summits bed file... SRX475425.05_summits.bed INFO @ Sat, 03 Jun 2017 21:00:51: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (5800 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 21:00:57: #4 Write output xls file... SRX475425.20_peaks.xls INFO @ Sat, 03 Jun 2017 21:00:57: #4 Write peak in narrowPeak format file... SRX475425.20_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 21:00:57: #4 Write summits bed file... SRX475425.20_summits.bed INFO @ Sat, 03 Jun 2017 21:00:57: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2374 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 03 Jun 2017 21:01:24: #4 Write output xls file... SRX475425.10_peaks.xls INFO @ Sat, 03 Jun 2017 21:01:24: #4 Write peak in narrowPeak format file... SRX475425.10_peaks.narrowPeak INFO @ Sat, 03 Jun 2017 21:01:24: #4 Write summits bed file... SRX475425.10_summits.bed INFO @ Sat, 03 Jun 2017 21:01:24: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3623 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。