Job ID = 9158487 sra ファイルのダウンロード中... Completed: 2001910K bytes transferred in 18 seconds (879347K bits/sec), in 1 file, 2 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 60988969 spots for /home/okishinya/chipatlas/results/dm3/SRX1361348/SRR2749786.sra Written 60988969 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: 00:37:46 60988969 reads; of these: 60988969 (100.00%) were unpaired; of these: 1668040 (2.73%) aligned 0 times 23261015 (38.14%) aligned exactly 1 time 36059914 (59.13%) aligned >1 times 97.27% overall alignment rate Time searching: 00:37:46 Overall time: 00:37:46 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 28 files... [bam_rmdupse_core] 22357413 / 59320929 = 0.3769 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 17:56:48: # Command line: callpeak -t SRX1361348.bam -f BAM -g dm -n SRX1361348.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1361348.20 # format = BAM # ChIP-seq file = ['SRX1361348.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 17:56:48: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:56:48: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:56:48: # Command line: callpeak -t SRX1361348.bam -f BAM -g dm -n SRX1361348.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1361348.10 # format = BAM # ChIP-seq file = ['SRX1361348.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 17:56:48: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:56:48: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:56:48: # Command line: callpeak -t SRX1361348.bam -f BAM -g dm -n SRX1361348.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1361348.05 # format = BAM # ChIP-seq file = ['SRX1361348.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 17:56:48: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:56:48: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:56:56: 1000000 INFO @ Tue, 27 Jun 2017 17:56:56: 1000000 INFO @ Tue, 27 Jun 2017 17:56:56: 1000000 INFO @ Tue, 27 Jun 2017 17:57:03: 2000000 INFO @ Tue, 27 Jun 2017 17:57:03: 2000000 INFO @ Tue, 27 Jun 2017 17:57:03: 2000000 INFO @ Tue, 27 Jun 2017 17:57:10: 3000000 INFO @ Tue, 27 Jun 2017 17:57:10: 3000000 INFO @ Tue, 27 Jun 2017 17:57:11: 3000000 INFO @ Tue, 27 Jun 2017 17:57:18: 4000000 INFO @ Tue, 27 Jun 2017 17:57:18: 4000000 INFO @ Tue, 27 Jun 2017 17:57:19: 4000000 INFO @ Tue, 27 Jun 2017 17:57:25: 5000000 INFO @ Tue, 27 Jun 2017 17:57:25: 5000000 INFO @ Tue, 27 Jun 2017 17:57:26: 5000000 INFO @ Tue, 27 Jun 2017 17:57:33: 6000000 INFO @ Tue, 27 Jun 2017 17:57:33: 6000000 INFO @ Tue, 27 Jun 2017 17:57:33: 6000000 INFO @ Tue, 27 Jun 2017 17:57:40: 7000000 INFO @ Tue, 27 Jun 2017 17:57:41: 7000000 INFO @ Tue, 27 Jun 2017 17:57:41: 7000000 INFO @ Tue, 27 Jun 2017 17:57:48: 8000000 INFO @ Tue, 27 Jun 2017 17:57:48: 8000000 INFO @ Tue, 27 Jun 2017 17:57:48: 8000000 INFO @ Tue, 27 Jun 2017 17:57:56: 9000000 INFO @ Tue, 27 Jun 2017 17:57:56: 9000000 INFO @ Tue, 27 Jun 2017 17:57:56: 9000000 INFO @ Tue, 27 Jun 2017 17:58:03: 10000000 INFO @ Tue, 27 Jun 2017 17:58:03: 10000000 INFO @ Tue, 27 Jun 2017 17:58:03: 10000000 INFO @ Tue, 27 Jun 2017 17:58:11: 11000000 INFO @ Tue, 27 Jun 2017 17:58:11: 11000000 INFO @ Tue, 27 Jun 2017 17:58:11: 11000000 INFO @ Tue, 27 Jun 2017 17:58:18: 12000000 INFO @ Tue, 27 Jun 2017 17:58:18: 12000000 INFO @ Tue, 27 Jun 2017 17:58:18: 12000000 INFO @ Tue, 27 Jun 2017 17:58:25: 13000000 INFO @ Tue, 27 Jun 2017 17:58:26: 13000000 INFO @ Tue, 27 Jun 2017 17:58:26: 13000000 INFO @ Tue, 27 Jun 2017 17:58:33: 14000000 INFO @ Tue, 27 Jun 2017 17:58:33: 14000000 INFO @ Tue, 27 Jun 2017 17:58:33: 14000000 INFO @ Tue, 27 Jun 2017 17:58:41: 15000000 INFO @ Tue, 27 Jun 2017 17:58:41: 15000000 INFO @ Tue, 27 Jun 2017 17:58:41: 15000000 INFO @ Tue, 27 Jun 2017 17:58:48: 16000000 INFO @ Tue, 27 Jun 2017 17:58:49: 16000000 INFO @ Tue, 27 Jun 2017 17:58:49: 16000000 INFO @ Tue, 27 Jun 2017 17:58:56: 17000000 INFO @ Tue, 27 Jun 2017 17:58:57: 17000000 INFO @ Tue, 27 Jun 2017 17:58:58: 17000000 INFO @ Tue, 27 Jun 2017 17:59:03: 18000000 INFO @ Tue, 27 Jun 2017 17:59:05: 18000000 INFO @ Tue, 27 Jun 2017 17:59:07: 18000000 INFO @ Tue, 27 Jun 2017 17:59:10: 19000000 INFO @ Tue, 27 Jun 2017 17:59:13: 19000000 INFO @ Tue, 27 Jun 2017 17:59:16: 19000000 INFO @ Tue, 27 Jun 2017 17:59:18: 20000000 INFO @ Tue, 27 Jun 2017 17:59:22: 20000000 INFO @ Tue, 27 Jun 2017 17:59:24: 20000000 INFO @ Tue, 27 Jun 2017 17:59:26: 21000000 INFO @ Tue, 27 Jun 2017 17:59:32: 21000000 INFO @ Tue, 27 Jun 2017 17:59:32: 21000000 INFO @ Tue, 27 Jun 2017 17:59:35: 22000000 INFO @ Tue, 27 Jun 2017 17:59:40: 22000000 INFO @ Tue, 27 Jun 2017 17:59:41: 22000000 INFO @ Tue, 27 Jun 2017 17:59:43: 23000000 INFO @ Tue, 27 Jun 2017 17:59:48: 23000000 INFO @ Tue, 27 Jun 2017 17:59:50: 23000000 INFO @ Tue, 27 Jun 2017 17:59:52: 24000000 INFO @ Tue, 27 Jun 2017 17:59:57: 24000000 INFO @ Tue, 27 Jun 2017 17:59:59: 24000000 INFO @ Tue, 27 Jun 2017 18:00:00: 25000000 INFO @ Tue, 27 Jun 2017 18:00:05: 25000000 INFO @ Tue, 27 Jun 2017 18:00:08: 26000000 INFO @ Tue, 27 Jun 2017 18:00:08: 25000000 INFO @ Tue, 27 Jun 2017 18:00:15: 26000000 INFO @ Tue, 27 Jun 2017 18:00:16: 27000000 INFO @ Tue, 27 Jun 2017 18:00:17: 26000000 INFO @ Tue, 27 Jun 2017 18:00:22: 27000000 INFO @ Tue, 27 Jun 2017 18:00:24: 28000000 INFO @ Tue, 27 Jun 2017 18:00:26: 27000000 INFO @ Tue, 27 Jun 2017 18:00:30: 28000000 INFO @ Tue, 27 Jun 2017 18:00:33: 29000000 INFO @ Tue, 27 Jun 2017 18:00:36: 28000000 INFO @ Tue, 27 Jun 2017 18:00:38: 29000000 INFO @ Tue, 27 Jun 2017 18:00:40: 30000000 INFO @ Tue, 27 Jun 2017 18:00:45: 29000000 INFO @ Tue, 27 Jun 2017 18:00:46: 30000000 INFO @ Tue, 27 Jun 2017 18:00:48: 31000000 INFO @ Tue, 27 Jun 2017 18:00:53: 30000000 INFO @ Tue, 27 Jun 2017 18:00:55: 31000000 INFO @ Tue, 27 Jun 2017 18:00:56: 32000000 INFO @ Tue, 27 Jun 2017 18:01:01: 31000000 INFO @ Tue, 27 Jun 2017 18:01:03: 32000000 INFO @ Tue, 27 Jun 2017 18:01:03: 33000000 INFO @ Tue, 27 Jun 2017 18:01:09: 32000000 INFO @ Tue, 27 Jun 2017 18:01:11: 33000000 INFO @ Tue, 27 Jun 2017 18:01:11: 34000000 INFO @ Tue, 27 Jun 2017 18:01:19: 33000000 INFO @ Tue, 27 Jun 2017 18:01:19: 34000000 INFO @ Tue, 27 Jun 2017 18:01:19: 35000000 INFO @ Tue, 27 Jun 2017 18:01:26: 35000000 INFO @ Tue, 27 Jun 2017 18:01:27: 36000000 INFO @ Tue, 27 Jun 2017 18:01:28: 34000000 INFO @ Tue, 27 Jun 2017 18:01:34: 36000000 INFO @ Tue, 27 Jun 2017 18:01:35: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 18:01:35: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 18:01:35: #1 total tags in treatment: 36963516 INFO @ Tue, 27 Jun 2017 18:01:35: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:01:35: #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 18:01:36: #1 tags after filtering in treatment: 36963516 INFO @ Tue, 27 Jun 2017 18:01:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 18:01:36: #1 finished! INFO @ Tue, 27 Jun 2017 18:01:36: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:01:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:01:37: 35000000 INFO @ Tue, 27 Jun 2017 18:01:39: #2 number of paired peaks: 186 WARNING @ Tue, 27 Jun 2017 18:01:39: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 27 Jun 2017 18:01:39: start model_add_line... INFO @ Tue, 27 Jun 2017 18:01:39: start X-correlation... INFO @ Tue, 27 Jun 2017 18:01:39: end of X-cor INFO @ Tue, 27 Jun 2017 18:01:39: #2 finished! INFO @ Tue, 27 Jun 2017 18:01:39: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 18:01:39: #2 alternative fragment length(s) may be 1,19,567,573 bps INFO @ Tue, 27 Jun 2017 18:01:39: #2.2 Generate R script for model : SRX1361348.05_model.r WARNING @ Tue, 27 Jun 2017 18:01:39: #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 18:01:39: #2 You may need to consider one of the other alternative d(s): 1,19,567,573 WARNING @ Tue, 27 Jun 2017 18:01:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 18:01:39: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:01:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:01:41: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 18:01:41: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 18:01:41: #1 total tags in treatment: 36963516 INFO @ Tue, 27 Jun 2017 18:01:41: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:01:41: #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 18:01:42: #1 tags after filtering in treatment: 36963516 INFO @ Tue, 27 Jun 2017 18:01:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 18:01:42: #1 finished! INFO @ Tue, 27 Jun 2017 18:01:42: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:01:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:01:44: #2 number of paired peaks: 186 WARNING @ Tue, 27 Jun 2017 18:01:44: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 27 Jun 2017 18:01:44: start model_add_line... INFO @ Tue, 27 Jun 2017 18:01:44: 36000000 INFO @ Tue, 27 Jun 2017 18:01:45: start X-correlation... INFO @ Tue, 27 Jun 2017 18:01:45: end of X-cor INFO @ Tue, 27 Jun 2017 18:01:45: #2 finished! INFO @ Tue, 27 Jun 2017 18:01:45: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 18:01:45: #2 alternative fragment length(s) may be 1,19,567,573 bps INFO @ Tue, 27 Jun 2017 18:01:45: #2.2 Generate R script for model : SRX1361348.20_model.r WARNING @ Tue, 27 Jun 2017 18:01:45: #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 18:01:45: #2 You may need to consider one of the other alternative d(s): 1,19,567,573 WARNING @ Tue, 27 Jun 2017 18:01:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 18:01:45: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:01:52: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 18:01:52: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 18:01:52: #1 total tags in treatment: 36963516 INFO @ Tue, 27 Jun 2017 18:01:52: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:01:52: #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 18:01:53: #1 tags after filtering in treatment: 36963516 INFO @ Tue, 27 Jun 2017 18:01:53: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 18:01:53: #1 finished! INFO @ Tue, 27 Jun 2017 18:01:53: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:01:53: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:01:55: #2 number of paired peaks: 186 WARNING @ Tue, 27 Jun 2017 18:01:55: Fewer paired peaks (186) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 186 pairs to build model! INFO @ Tue, 27 Jun 2017 18:01:55: start model_add_line... INFO @ Tue, 27 Jun 2017 18:01:56: start X-correlation... INFO @ Tue, 27 Jun 2017 18:01:56: end of X-cor INFO @ Tue, 27 Jun 2017 18:01:56: #2 finished! INFO @ Tue, 27 Jun 2017 18:01:56: #2 predicted fragment length is 1 bps INFO @ Tue, 27 Jun 2017 18:01:56: #2 alternative fragment length(s) may be 1,19,567,573 bps INFO @ Tue, 27 Jun 2017 18:01:56: #2.2 Generate R script for model : SRX1361348.10_model.r WARNING @ Tue, 27 Jun 2017 18:01:56: #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 18:01:56: #2 You may need to consider one of the other alternative d(s): 1,19,567,573 WARNING @ Tue, 27 Jun 2017 18:01:56: #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 18:01:56: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:01:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:02:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:02:40: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:02:50: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:03:00: #4 Write output xls file... SRX1361348.05_peaks.xls INFO @ Tue, 27 Jun 2017 18:03:00: #4 Write peak in narrowPeak format file... SRX1361348.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:03:00: #4 Write summits bed file... SRX1361348.05_summits.bed INFO @ Tue, 27 Jun 2017 18:03:00: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:03:08: #4 Write output xls file... SRX1361348.20_peaks.xls INFO @ Tue, 27 Jun 2017 18:03:08: #4 Write peak in narrowPeak format file... SRX1361348.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:03:08: #4 Write summits bed file... SRX1361348.20_summits.bed INFO @ Tue, 27 Jun 2017 18:03:08: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:03:20: #4 Write output xls file... SRX1361348.10_peaks.xls INFO @ Tue, 27 Jun 2017 18:03:20: #4 Write peak in narrowPeak format file... SRX1361348.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:03:20: #4 Write summits bed file... SRX1361348.10_summits.bed INFO @ Tue, 27 Jun 2017 18:03:20: 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。