Job ID = 9159544 sra ファイルのダウンロード中... Completed: 1625311K bytes transferred in 25 seconds (531457K bits/sec), in 13 files, 14 directories. 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 1179845 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175603.sra Written 1179845 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175606.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175604.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175605.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175610.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175607.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175601.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175608.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175602.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175611.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175599.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175609.sra Written 4000000 spots total Written 4000000 spots for /home/okishinya/chipatlas/results/dm3/SRX475421/SRR1175600.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:21:14 49179845 reads; of these: 49179845 (100.00%) were unpaired; of these: 2526355 (5.14%) aligned 0 times 30235882 (61.48%) aligned exactly 1 time 16417608 (33.38%) aligned >1 times 94.86% overall alignment rate Time searching: 00:21:15 Overall time: 00:21:15 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] 13281006 / 46653490 = 0.2847 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, 27 Jun 2017 22:19:01: # Command line: callpeak -t SRX475421.bam -f BAM -g dm -n SRX475421.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX475421.10 # format = BAM # ChIP-seq file = ['SRX475421.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 22:19:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 22:19:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 22:19:01: # Command line: callpeak -t SRX475421.bam -f BAM -g dm -n SRX475421.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX475421.20 # format = BAM # ChIP-seq file = ['SRX475421.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 22:19:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 22:19:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 22:19:01: # Command line: callpeak -t SRX475421.bam -f BAM -g dm -n SRX475421.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX475421.05 # format = BAM # ChIP-seq file = ['SRX475421.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 # Paired-End mode is off INFO @ Tue, 27 Jun 2017 22:19:01: #1 read tag files... INFO @ Tue, 27 Jun 2017 22:19:01: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 22:19:07: 1000000 INFO @ Tue, 27 Jun 2017 22:19:08: 1000000 INFO @ Tue, 27 Jun 2017 22:19:08: 1000000 INFO @ Tue, 27 Jun 2017 22:19:14: 2000000 INFO @ Tue, 27 Jun 2017 22:19:16: 2000000 INFO @ Tue, 27 Jun 2017 22:19:16: 2000000 INFO @ Tue, 27 Jun 2017 22:19:21: 3000000 INFO @ Tue, 27 Jun 2017 22:19:24: 3000000 INFO @ Tue, 27 Jun 2017 22:19:24: 3000000 INFO @ Tue, 27 Jun 2017 22:19:28: 4000000 INFO @ Tue, 27 Jun 2017 22:19:32: 4000000 INFO @ Tue, 27 Jun 2017 22:19:32: 4000000 INFO @ Tue, 27 Jun 2017 22:19:34: 5000000 INFO @ Tue, 27 Jun 2017 22:19:40: 5000000 INFO @ Tue, 27 Jun 2017 22:19:40: 5000000 INFO @ Tue, 27 Jun 2017 22:19:41: 6000000 INFO @ Tue, 27 Jun 2017 22:19:48: 6000000 INFO @ Tue, 27 Jun 2017 22:19:48: 6000000 INFO @ Tue, 27 Jun 2017 22:19:48: 7000000 INFO @ Tue, 27 Jun 2017 22:19:55: 8000000 INFO @ Tue, 27 Jun 2017 22:19:55: 7000000 INFO @ Tue, 27 Jun 2017 22:19:55: 7000000 INFO @ Tue, 27 Jun 2017 22:20:04: 9000000 INFO @ Tue, 27 Jun 2017 22:20:05: 8000000 INFO @ Tue, 27 Jun 2017 22:20:05: 8000000 INFO @ Tue, 27 Jun 2017 22:20:12: 9000000 INFO @ Tue, 27 Jun 2017 22:20:12: 10000000 INFO @ Tue, 27 Jun 2017 22:20:13: 9000000 INFO @ Tue, 27 Jun 2017 22:20:19: 10000000 INFO @ Tue, 27 Jun 2017 22:20:20: 11000000 INFO @ Tue, 27 Jun 2017 22:20:21: 10000000 INFO @ Tue, 27 Jun 2017 22:20:26: 11000000 INFO @ Tue, 27 Jun 2017 22:20:28: 12000000 INFO @ Tue, 27 Jun 2017 22:20:29: 11000000 INFO @ Tue, 27 Jun 2017 22:20:33: 12000000 INFO @ Tue, 27 Jun 2017 22:20:38: 13000000 INFO @ Tue, 27 Jun 2017 22:20:39: 12000000 INFO @ Tue, 27 Jun 2017 22:20:42: 13000000 INFO @ Tue, 27 Jun 2017 22:20:48: 14000000 INFO @ Tue, 27 Jun 2017 22:20:49: 13000000 INFO @ Tue, 27 Jun 2017 22:20:50: 14000000 INFO @ Tue, 27 Jun 2017 22:20:58: 15000000 INFO @ Tue, 27 Jun 2017 22:20:58: 14000000 INFO @ Tue, 27 Jun 2017 22:20:59: 15000000 INFO @ Tue, 27 Jun 2017 22:21:07: 16000000 INFO @ Tue, 27 Jun 2017 22:21:07: 15000000 INFO @ Tue, 27 Jun 2017 22:21:08: 16000000 INFO @ Tue, 27 Jun 2017 22:21:16: 17000000 INFO @ Tue, 27 Jun 2017 22:21:17: 16000000 INFO @ Tue, 27 Jun 2017 22:21:18: 17000000 INFO @ Tue, 27 Jun 2017 22:21:24: 18000000 INFO @ Tue, 27 Jun 2017 22:21:26: 17000000 INFO @ Tue, 27 Jun 2017 22:21:28: 18000000 INFO @ Tue, 27 Jun 2017 22:21:33: 19000000 INFO @ Tue, 27 Jun 2017 22:21:35: 18000000 INFO @ Tue, 27 Jun 2017 22:21:38: 19000000 INFO @ Tue, 27 Jun 2017 22:21:41: 20000000 INFO @ Tue, 27 Jun 2017 22:21:45: 19000000 INFO @ Tue, 27 Jun 2017 22:21:48: 20000000 INFO @ Tue, 27 Jun 2017 22:21:50: 21000000 INFO @ Tue, 27 Jun 2017 22:21:54: 20000000 INFO @ Tue, 27 Jun 2017 22:21:58: 22000000 INFO @ Tue, 27 Jun 2017 22:21:59: 21000000 INFO @ Tue, 27 Jun 2017 22:22:04: 21000000 INFO @ Tue, 27 Jun 2017 22:22:07: 23000000 INFO @ Tue, 27 Jun 2017 22:22:09: 22000000 INFO @ Tue, 27 Jun 2017 22:22:13: 22000000 INFO @ Tue, 27 Jun 2017 22:22:16: 24000000 INFO @ Tue, 27 Jun 2017 22:22:19: 23000000 INFO @ Tue, 27 Jun 2017 22:22:23: 23000000 INFO @ Tue, 27 Jun 2017 22:22:25: 25000000 INFO @ Tue, 27 Jun 2017 22:22:29: 24000000 INFO @ Tue, 27 Jun 2017 22:22:31: 24000000 INFO @ Tue, 27 Jun 2017 22:22:32: 26000000 INFO @ Tue, 27 Jun 2017 22:22:37: 25000000 INFO @ Tue, 27 Jun 2017 22:22:39: 27000000 INFO @ Tue, 27 Jun 2017 22:22:40: 25000000 INFO @ Tue, 27 Jun 2017 22:22:46: 26000000 INFO @ Tue, 27 Jun 2017 22:22:46: 28000000 INFO @ Tue, 27 Jun 2017 22:22:48: 26000000 INFO @ Tue, 27 Jun 2017 22:22:54: 29000000 INFO @ Tue, 27 Jun 2017 22:22:54: 27000000 INFO @ Tue, 27 Jun 2017 22:22:56: 27000000 INFO @ Tue, 27 Jun 2017 22:23:01: 30000000 INFO @ Tue, 27 Jun 2017 22:23:03: 28000000 INFO @ Tue, 27 Jun 2017 22:23:05: 28000000 INFO @ Tue, 27 Jun 2017 22:23:08: 31000000 INFO @ Tue, 27 Jun 2017 22:23:11: 29000000 INFO @ Tue, 27 Jun 2017 22:23:13: 29000000 INFO @ Tue, 27 Jun 2017 22:23:15: 32000000 INFO @ Tue, 27 Jun 2017 22:23:19: 30000000 INFO @ Tue, 27 Jun 2017 22:23:21: 30000000 INFO @ Tue, 27 Jun 2017 22:23:23: 33000000 INFO @ Tue, 27 Jun 2017 22:23:25: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 22:23:25: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 22:23:25: #1 total tags in treatment: 33372484 INFO @ Tue, 27 Jun 2017 22:23:25: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 22:23:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 22:23:26: #1 tags after filtering in treatment: 33372484 INFO @ Tue, 27 Jun 2017 22:23:26: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 22:23:26: #1 finished! INFO @ Tue, 27 Jun 2017 22:23:26: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 22:23:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 22:23:28: 31000000 INFO @ Tue, 27 Jun 2017 22:23:28: #2 number of paired peaks: 427 WARNING @ Tue, 27 Jun 2017 22:23:28: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Tue, 27 Jun 2017 22:23:28: start model_add_line... INFO @ Tue, 27 Jun 2017 22:23:29: start X-correlation... INFO @ Tue, 27 Jun 2017 22:23:29: end of X-cor INFO @ Tue, 27 Jun 2017 22:23:29: #2 finished! INFO @ Tue, 27 Jun 2017 22:23:29: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 22:23:29: #2 alternative fragment length(s) may be 1,10 bps INFO @ Tue, 27 Jun 2017 22:23:29: #2.2 Generate R script for model : SRX475421.10_model.r WARNING @ Tue, 27 Jun 2017 22:23:29: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 22:23:29: #2 You may need to consider one of the other alternative d(s): 1,10 WARNING @ Tue, 27 Jun 2017 22:23:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 22:23:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 22:23:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 22:23:30: 31000000 INFO @ Tue, 27 Jun 2017 22:23:36: 32000000 INFO @ Tue, 27 Jun 2017 22:23:38: 32000000 INFO @ Tue, 27 Jun 2017 22:23:45: 33000000 INFO @ Tue, 27 Jun 2017 22:23:46: 33000000 INFO @ Tue, 27 Jun 2017 22:23:48: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 22:23:48: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 22:23:48: #1 total tags in treatment: 33372484 INFO @ Tue, 27 Jun 2017 22:23:48: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 22:23:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 22:23:49: #1 tags after filtering in treatment: 33372484 INFO @ Tue, 27 Jun 2017 22:23:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 22:23:49: #1 finished! INFO @ Tue, 27 Jun 2017 22:23:49: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 22:23:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 22:23:49: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 22:23:49: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 22:23:49: #1 total tags in treatment: 33372484 INFO @ Tue, 27 Jun 2017 22:23:49: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 22:23:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 22:23:50: #1 tags after filtering in treatment: 33372484 INFO @ Tue, 27 Jun 2017 22:23:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 22:23:50: #1 finished! INFO @ Tue, 27 Jun 2017 22:23:50: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 22:23:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 22:23:51: #2 number of paired peaks: 427 WARNING @ Tue, 27 Jun 2017 22:23:51: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Tue, 27 Jun 2017 22:23:51: start model_add_line... INFO @ Tue, 27 Jun 2017 22:23:51: start X-correlation... INFO @ Tue, 27 Jun 2017 22:23:51: end of X-cor INFO @ Tue, 27 Jun 2017 22:23:51: #2 finished! INFO @ Tue, 27 Jun 2017 22:23:51: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 22:23:51: #2 alternative fragment length(s) may be 1,10 bps INFO @ Tue, 27 Jun 2017 22:23:51: #2.2 Generate R script for model : SRX475421.20_model.r WARNING @ Tue, 27 Jun 2017 22:23:51: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 22:23:51: #2 You may need to consider one of the other alternative d(s): 1,10 WARNING @ Tue, 27 Jun 2017 22:23:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 22:23:51: #3 Call peaks... INFO @ Tue, 27 Jun 2017 22:23:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 22:23:52: #2 number of paired peaks: 427 WARNING @ Tue, 27 Jun 2017 22:23:52: Fewer paired peaks (427) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 427 pairs to build model! INFO @ Tue, 27 Jun 2017 22:23:52: start model_add_line... INFO @ Tue, 27 Jun 2017 22:23:53: start X-correlation... INFO @ Tue, 27 Jun 2017 22:23:53: end of X-cor INFO @ Tue, 27 Jun 2017 22:23:53: #2 finished! INFO @ Tue, 27 Jun 2017 22:23:53: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 22:23:53: #2 alternative fragment length(s) may be 1,10 bps INFO @ Tue, 27 Jun 2017 22:23:53: #2.2 Generate R script for model : SRX475421.05_model.r WARNING @ Tue, 27 Jun 2017 22:23:53: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 22:23:53: #2 You may need to consider one of the other alternative d(s): 1,10 WARNING @ Tue, 27 Jun 2017 22:23:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 22:23:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 22:23:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 22:24:24: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 22:24:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 22:24:49: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 22:24:54: #4 Write output xls file... SRX475421.10_peaks.xls INFO @ Tue, 27 Jun 2017 22:24:54: #4 Write peak in narrowPeak format file... SRX475421.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 22:24:54: #4 Write summits bed file... SRX475421.10_summits.bed INFO @ Tue, 27 Jun 2017 22:24:54: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 22:25:10: #4 Write output xls file... SRX475421.05_peaks.xls INFO @ Tue, 27 Jun 2017 22:25:10: #4 Write peak in narrowPeak format file... SRX475421.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 22:25:10: #4 Write summits bed file... SRX475421.05_summits.bed INFO @ Tue, 27 Jun 2017 22:25:10: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 22:25:15: #4 Write output xls file... SRX475421.20_peaks.xls INFO @ Tue, 27 Jun 2017 22:25:15: #4 Write peak in narrowPeak format file... SRX475421.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 22:25:15: #4 Write summits bed file... SRX475421.20_summits.bed INFO @ Tue, 27 Jun 2017 22:25:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。