Job ID = 9158497 sra ファイルのダウンロード中... Completed: 979076K bytes transferred in 10 seconds (756808K 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 43981994 spots for /home/okishinya/chipatlas/results/dm3/SRX1433390/SRR2919806.sra Written 43981994 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: 00:15:54 43981994 reads; of these: 43981994 (100.00%) were unpaired; of these: 1439131 (3.27%) aligned 0 times 31375063 (71.34%) aligned exactly 1 time 11167800 (25.39%) aligned >1 times 96.73% overall alignment rate Time searching: 00:15:54 Overall time: 00:15:54 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] 9556243 / 42542863 = 0.2246 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 17:35:46: # Command line: callpeak -t SRX1433390.bam -f BAM -g dm -n SRX1433390.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1433390.05 # format = BAM # ChIP-seq file = ['SRX1433390.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 17:35:46: # Command line: callpeak -t SRX1433390.bam -f BAM -g dm -n SRX1433390.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1433390.10 # format = BAM # ChIP-seq file = ['SRX1433390.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 17:35:46: # Command line: callpeak -t SRX1433390.bam -f BAM -g dm -n SRX1433390.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1433390.20 # format = BAM # ChIP-seq file = ['SRX1433390.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 17:35:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:35:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:35:46: #1 read tag files... INFO @ Tue, 27 Jun 2017 17:35:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:35:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:35:46: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 17:35:52: 1000000 INFO @ Tue, 27 Jun 2017 17:35:52: 1000000 INFO @ Tue, 27 Jun 2017 17:35:52: 1000000 INFO @ Tue, 27 Jun 2017 17:35:58: 2000000 INFO @ Tue, 27 Jun 2017 17:35:58: 2000000 INFO @ Tue, 27 Jun 2017 17:35:58: 2000000 INFO @ Tue, 27 Jun 2017 17:36:04: 3000000 INFO @ Tue, 27 Jun 2017 17:36:04: 3000000 INFO @ Tue, 27 Jun 2017 17:36:05: 3000000 INFO @ Tue, 27 Jun 2017 17:36:10: 4000000 INFO @ Tue, 27 Jun 2017 17:36:11: 4000000 INFO @ Tue, 27 Jun 2017 17:36:12: 4000000 INFO @ Tue, 27 Jun 2017 17:36:17: 5000000 INFO @ Tue, 27 Jun 2017 17:36:18: 5000000 INFO @ Tue, 27 Jun 2017 17:36:20: 5000000 INFO @ Tue, 27 Jun 2017 17:36:24: 6000000 INFO @ Tue, 27 Jun 2017 17:36:25: 6000000 INFO @ Tue, 27 Jun 2017 17:36:28: 6000000 INFO @ Tue, 27 Jun 2017 17:36:31: 7000000 INFO @ Tue, 27 Jun 2017 17:36:32: 7000000 INFO @ Tue, 27 Jun 2017 17:36:35: 7000000 INFO @ Tue, 27 Jun 2017 17:36:38: 8000000 INFO @ Tue, 27 Jun 2017 17:36:40: 8000000 INFO @ Tue, 27 Jun 2017 17:36:43: 8000000 INFO @ Tue, 27 Jun 2017 17:36:45: 9000000 INFO @ Tue, 27 Jun 2017 17:36:47: 9000000 INFO @ Tue, 27 Jun 2017 17:36:51: 9000000 INFO @ Tue, 27 Jun 2017 17:36:52: 10000000 INFO @ Tue, 27 Jun 2017 17:36:54: 10000000 INFO @ Tue, 27 Jun 2017 17:36:58: 10000000 INFO @ Tue, 27 Jun 2017 17:36:59: 11000000 INFO @ Tue, 27 Jun 2017 17:37:01: 11000000 INFO @ Tue, 27 Jun 2017 17:37:06: 11000000 INFO @ Tue, 27 Jun 2017 17:37:06: 12000000 INFO @ Tue, 27 Jun 2017 17:37:08: 12000000 INFO @ Tue, 27 Jun 2017 17:37:13: 12000000 INFO @ Tue, 27 Jun 2017 17:37:13: 13000000 INFO @ Tue, 27 Jun 2017 17:37:16: 13000000 INFO @ Tue, 27 Jun 2017 17:37:20: 14000000 INFO @ Tue, 27 Jun 2017 17:37:21: 13000000 INFO @ Tue, 27 Jun 2017 17:37:23: 14000000 INFO @ Tue, 27 Jun 2017 17:37:27: 15000000 INFO @ Tue, 27 Jun 2017 17:37:28: 14000000 INFO @ Tue, 27 Jun 2017 17:37:30: 15000000 INFO @ Tue, 27 Jun 2017 17:37:35: 16000000 INFO @ Tue, 27 Jun 2017 17:37:36: 15000000 INFO @ Tue, 27 Jun 2017 17:37:38: 16000000 INFO @ Tue, 27 Jun 2017 17:37:42: 17000000 INFO @ Tue, 27 Jun 2017 17:37:44: 16000000 INFO @ Tue, 27 Jun 2017 17:37:45: 17000000 INFO @ Tue, 27 Jun 2017 17:37:50: 18000000 INFO @ Tue, 27 Jun 2017 17:37:52: 17000000 INFO @ Tue, 27 Jun 2017 17:37:53: 18000000 INFO @ Tue, 27 Jun 2017 17:37:58: 19000000 INFO @ Tue, 27 Jun 2017 17:38:00: 18000000 INFO @ Tue, 27 Jun 2017 17:38:01: 19000000 INFO @ Tue, 27 Jun 2017 17:38:06: 20000000 INFO @ Tue, 27 Jun 2017 17:38:08: 20000000 INFO @ Tue, 27 Jun 2017 17:38:08: 19000000 INFO @ Tue, 27 Jun 2017 17:38:13: 21000000 INFO @ Tue, 27 Jun 2017 17:38:17: 21000000 INFO @ Tue, 27 Jun 2017 17:38:18: 20000000 INFO @ Tue, 27 Jun 2017 17:38:22: 22000000 INFO @ Tue, 27 Jun 2017 17:38:26: 21000000 INFO @ Tue, 27 Jun 2017 17:38:26: 22000000 INFO @ Tue, 27 Jun 2017 17:38:30: 23000000 INFO @ Tue, 27 Jun 2017 17:38:35: 22000000 INFO @ Tue, 27 Jun 2017 17:38:36: 23000000 INFO @ Tue, 27 Jun 2017 17:38:38: 24000000 INFO @ Tue, 27 Jun 2017 17:38:44: 23000000 INFO @ Tue, 27 Jun 2017 17:38:45: 24000000 INFO @ Tue, 27 Jun 2017 17:38:46: 25000000 INFO @ Tue, 27 Jun 2017 17:38:54: 26000000 INFO @ Tue, 27 Jun 2017 17:38:54: 24000000 INFO @ Tue, 27 Jun 2017 17:38:54: 25000000 INFO @ Tue, 27 Jun 2017 17:39:02: 27000000 INFO @ Tue, 27 Jun 2017 17:39:02: 25000000 INFO @ Tue, 27 Jun 2017 17:39:03: 26000000 INFO @ Tue, 27 Jun 2017 17:39:10: 28000000 INFO @ Tue, 27 Jun 2017 17:39:11: 27000000 INFO @ Tue, 27 Jun 2017 17:39:12: 26000000 INFO @ Tue, 27 Jun 2017 17:39:18: 29000000 INFO @ Tue, 27 Jun 2017 17:39:20: 28000000 INFO @ Tue, 27 Jun 2017 17:39:21: 27000000 INFO @ Tue, 27 Jun 2017 17:39:26: 30000000 INFO @ Tue, 27 Jun 2017 17:39:28: 29000000 INFO @ Tue, 27 Jun 2017 17:39:30: 28000000 INFO @ Tue, 27 Jun 2017 17:39:33: 31000000 INFO @ Tue, 27 Jun 2017 17:39:37: 30000000 INFO @ Tue, 27 Jun 2017 17:39:38: 29000000 INFO @ Tue, 27 Jun 2017 17:39:41: 32000000 INFO @ Tue, 27 Jun 2017 17:39:45: 31000000 INFO @ Tue, 27 Jun 2017 17:39:49: 30000000 INFO @ Tue, 27 Jun 2017 17:39:49: #1 tag size is determined as 49 bps INFO @ Tue, 27 Jun 2017 17:39:49: #1 tag size = 49 INFO @ Tue, 27 Jun 2017 17:39:49: #1 total tags in treatment: 32986620 INFO @ Tue, 27 Jun 2017 17:39:49: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:39:49: #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 17:39:50: #1 tags after filtering in treatment: 32986620 INFO @ Tue, 27 Jun 2017 17:39:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:39:50: #1 finished! INFO @ Tue, 27 Jun 2017 17:39:50: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:39:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:39:52: #2 number of paired peaks: 108 WARNING @ Tue, 27 Jun 2017 17:39:52: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Tue, 27 Jun 2017 17:39:52: start model_add_line... INFO @ Tue, 27 Jun 2017 17:39:52: start X-correlation... INFO @ Tue, 27 Jun 2017 17:39:52: end of X-cor INFO @ Tue, 27 Jun 2017 17:39:52: #2 finished! INFO @ Tue, 27 Jun 2017 17:39:52: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 17:39:52: #2 alternative fragment length(s) may be 2,12,24 bps INFO @ Tue, 27 Jun 2017 17:39:52: #2.2 Generate R script for model : SRX1433390.10_model.r WARNING @ Tue, 27 Jun 2017 17:39:52: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 17:39:52: #2 You may need to consider one of the other alternative d(s): 2,12,24 WARNING @ Tue, 27 Jun 2017 17:39:52: #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 17:39:52: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:39:52: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:39:53: 32000000 INFO @ Tue, 27 Jun 2017 17:39:58: 31000000 INFO @ Tue, 27 Jun 2017 17:40:03: #1 tag size is determined as 49 bps INFO @ Tue, 27 Jun 2017 17:40:03: #1 tag size = 49 INFO @ Tue, 27 Jun 2017 17:40:03: #1 total tags in treatment: 32986620 INFO @ Tue, 27 Jun 2017 17:40:03: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:40:03: #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 17:40:04: #1 tags after filtering in treatment: 32986620 INFO @ Tue, 27 Jun 2017 17:40:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:40:04: #1 finished! INFO @ Tue, 27 Jun 2017 17:40:04: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:40:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:40:06: #2 number of paired peaks: 108 WARNING @ Tue, 27 Jun 2017 17:40:06: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Tue, 27 Jun 2017 17:40:06: start model_add_line... INFO @ Tue, 27 Jun 2017 17:40:06: start X-correlation... INFO @ Tue, 27 Jun 2017 17:40:06: end of X-cor INFO @ Tue, 27 Jun 2017 17:40:06: #2 finished! INFO @ Tue, 27 Jun 2017 17:40:06: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 17:40:06: #2 alternative fragment length(s) may be 2,12,24 bps INFO @ Tue, 27 Jun 2017 17:40:06: #2.2 Generate R script for model : SRX1433390.20_model.r WARNING @ Tue, 27 Jun 2017 17:40:06: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 17:40:06: #2 You may need to consider one of the other alternative d(s): 2,12,24 WARNING @ Tue, 27 Jun 2017 17:40:06: #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 17:40:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:40:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:40:07: 32000000 INFO @ Tue, 27 Jun 2017 17:40:17: #1 tag size is determined as 49 bps INFO @ Tue, 27 Jun 2017 17:40:17: #1 tag size = 49 INFO @ Tue, 27 Jun 2017 17:40:17: #1 total tags in treatment: 32986620 INFO @ Tue, 27 Jun 2017 17:40:17: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 17:40:17: #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 17:40:18: #1 tags after filtering in treatment: 32986620 INFO @ Tue, 27 Jun 2017 17:40:18: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 17:40:18: #1 finished! INFO @ Tue, 27 Jun 2017 17:40:18: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 17:40:18: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 17:40:20: #2 number of paired peaks: 108 WARNING @ Tue, 27 Jun 2017 17:40:20: Fewer paired peaks (108) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 108 pairs to build model! INFO @ Tue, 27 Jun 2017 17:40:20: start model_add_line... INFO @ Tue, 27 Jun 2017 17:40:21: start X-correlation... INFO @ Tue, 27 Jun 2017 17:40:21: end of X-cor INFO @ Tue, 27 Jun 2017 17:40:21: #2 finished! INFO @ Tue, 27 Jun 2017 17:40:21: #2 predicted fragment length is 2 bps INFO @ Tue, 27 Jun 2017 17:40:21: #2 alternative fragment length(s) may be 2,12,24 bps INFO @ Tue, 27 Jun 2017 17:40:21: #2.2 Generate R script for model : SRX1433390.05_model.r WARNING @ Tue, 27 Jun 2017 17:40:21: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 17:40:21: #2 You may need to consider one of the other alternative d(s): 2,12,24 WARNING @ Tue, 27 Jun 2017 17:40:21: #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 17:40:21: #3 Call peaks... INFO @ Tue, 27 Jun 2017 17:40:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 17:40:46: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:41:09: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:41:16: #4 Write output xls file... SRX1433390.10_peaks.xls INFO @ Tue, 27 Jun 2017 17:41:16: #4 Write peak in narrowPeak format file... SRX1433390.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:41:16: #4 Write summits bed file... SRX1433390.10_summits.bed INFO @ Tue, 27 Jun 2017 17:41:16: Done! pass1 - making usageList (0 chroms): 4 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 17:41:20: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 17:41:40: #4 Write output xls file... SRX1433390.20_peaks.xls INFO @ Tue, 27 Jun 2017 17:41:40: #4 Write peak in narrowPeak format file... SRX1433390.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:41:40: #4 Write summits bed file... SRX1433390.20_summits.bed INFO @ Tue, 27 Jun 2017 17:41:40: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 17:41:50: #4 Write output xls file... SRX1433390.05_peaks.xls INFO @ Tue, 27 Jun 2017 17:41:50: #4 Write peak in narrowPeak format file... SRX1433390.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 17:41:50: #4 Write summits bed file... SRX1433390.05_summits.bed INFO @ Tue, 27 Jun 2017 17:41:50: 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。