Job ID = 10451021 sra ファイルのダウンロード中... Completed: 570276K bytes transferred in 30 seconds (153816K bits/sec), in 1 file. 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 31833990 spots for /home/okishinya/chipatlas/results/dm3/SRX3404053/SRR6303530.sra Written 31833990 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:26:41 31833990 reads; of these: 31833990 (100.00%) were unpaired; of these: 785638 (2.47%) aligned 0 times 21692798 (68.14%) aligned exactly 1 time 9355554 (29.39%) aligned >1 times 97.53% overall alignment rate Time searching: 00:26:42 Overall time: 00:26:42 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 16 files... [bam_rmdupse_core] 3323018 / 31048352 = 0.1070 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 @ Wed, 07 Feb 2018 15:51:40: # Command line: callpeak -t SRX3404053.bam -f BAM -g dm -n SRX3404053.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3404053.10 # format = BAM # ChIP-seq file = ['SRX3404053.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 @ Wed, 07 Feb 2018 15:51:40: # Command line: callpeak -t SRX3404053.bam -f BAM -g dm -n SRX3404053.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3404053.05 # format = BAM # ChIP-seq file = ['SRX3404053.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 @ Wed, 07 Feb 2018 15:51:40: # Command line: callpeak -t SRX3404053.bam -f BAM -g dm -n SRX3404053.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3404053.20 # format = BAM # ChIP-seq file = ['SRX3404053.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 @ Wed, 07 Feb 2018 15:51:40: #1 read tag files... INFO @ Wed, 07 Feb 2018 15:51:40: #1 read tag files... INFO @ Wed, 07 Feb 2018 15:51:40: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 15:51:40: #1 read tag files... INFO @ Wed, 07 Feb 2018 15:51:40: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 15:51:40: #1 read treatment tags... INFO @ Wed, 07 Feb 2018 15:51:50: 1000000 INFO @ Wed, 07 Feb 2018 15:51:57: 1000000 INFO @ Wed, 07 Feb 2018 15:51:58: 1000000 INFO @ Wed, 07 Feb 2018 15:51:59: 2000000 INFO @ Wed, 07 Feb 2018 15:52:07: 3000000 INFO @ Wed, 07 Feb 2018 15:52:13: 2000000 INFO @ Wed, 07 Feb 2018 15:52:15: 2000000 INFO @ Wed, 07 Feb 2018 15:52:16: 4000000 INFO @ Wed, 07 Feb 2018 15:52:25: 5000000 INFO @ Wed, 07 Feb 2018 15:52:33: 3000000 INFO @ Wed, 07 Feb 2018 15:52:33: 3000000 INFO @ Wed, 07 Feb 2018 15:52:34: 6000000 INFO @ Wed, 07 Feb 2018 15:52:42: 7000000 INFO @ Wed, 07 Feb 2018 15:52:50: 4000000 INFO @ Wed, 07 Feb 2018 15:52:51: 8000000 INFO @ Wed, 07 Feb 2018 15:52:52: 4000000 INFO @ Wed, 07 Feb 2018 15:52:59: 9000000 INFO @ Wed, 07 Feb 2018 15:53:05: 5000000 INFO @ Wed, 07 Feb 2018 15:53:08: 10000000 INFO @ Wed, 07 Feb 2018 15:53:12: 5000000 INFO @ Wed, 07 Feb 2018 15:53:17: 11000000 INFO @ Wed, 07 Feb 2018 15:53:18: 6000000 INFO @ Wed, 07 Feb 2018 15:53:25: 12000000 INFO @ Wed, 07 Feb 2018 15:53:31: 6000000 INFO @ Wed, 07 Feb 2018 15:53:32: 7000000 INFO @ Wed, 07 Feb 2018 15:53:34: 13000000 INFO @ Wed, 07 Feb 2018 15:53:44: 14000000 INFO @ Wed, 07 Feb 2018 15:53:46: 8000000 INFO @ Wed, 07 Feb 2018 15:53:46: 7000000 INFO @ Wed, 07 Feb 2018 15:53:53: 15000000 INFO @ Wed, 07 Feb 2018 15:54:00: 9000000 INFO @ Wed, 07 Feb 2018 15:54:02: 8000000 INFO @ Wed, 07 Feb 2018 15:54:02: 16000000 INFO @ Wed, 07 Feb 2018 15:54:12: 17000000 INFO @ Wed, 07 Feb 2018 15:54:13: 10000000 INFO @ Wed, 07 Feb 2018 15:54:17: 9000000 INFO @ Wed, 07 Feb 2018 15:54:21: 18000000 INFO @ Wed, 07 Feb 2018 15:54:28: 11000000 INFO @ Wed, 07 Feb 2018 15:54:31: 19000000 INFO @ Wed, 07 Feb 2018 15:54:34: 10000000 INFO @ Wed, 07 Feb 2018 15:54:41: 20000000 INFO @ Wed, 07 Feb 2018 15:54:43: 12000000 INFO @ Wed, 07 Feb 2018 15:54:49: 11000000 INFO @ Wed, 07 Feb 2018 15:54:51: 21000000 INFO @ Wed, 07 Feb 2018 15:54:57: 13000000 INFO @ Wed, 07 Feb 2018 15:55:00: 22000000 INFO @ Wed, 07 Feb 2018 15:55:01: 12000000 INFO @ Wed, 07 Feb 2018 15:55:05: 14000000 INFO @ Wed, 07 Feb 2018 15:55:09: 23000000 INFO @ Wed, 07 Feb 2018 15:55:09: 13000000 INFO @ Wed, 07 Feb 2018 15:55:13: 15000000 INFO @ Wed, 07 Feb 2018 15:55:18: 14000000 INFO @ Wed, 07 Feb 2018 15:55:18: 24000000 INFO @ Wed, 07 Feb 2018 15:55:21: 16000000 INFO @ Wed, 07 Feb 2018 15:55:26: 15000000 INFO @ Wed, 07 Feb 2018 15:55:27: 25000000 INFO @ Wed, 07 Feb 2018 15:55:30: 17000000 INFO @ Wed, 07 Feb 2018 15:55:34: 16000000 INFO @ Wed, 07 Feb 2018 15:55:36: 26000000 INFO @ Wed, 07 Feb 2018 15:55:38: 18000000 INFO @ Wed, 07 Feb 2018 15:55:43: 17000000 INFO @ Wed, 07 Feb 2018 15:55:46: 19000000 INFO @ Wed, 07 Feb 2018 15:55:46: 27000000 INFO @ Wed, 07 Feb 2018 15:55:52: 18000000 INFO @ Wed, 07 Feb 2018 15:55:54: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:55:54: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:55:54: #1 total tags in treatment: 27725334 INFO @ Wed, 07 Feb 2018 15:55:54: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:55:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:55:55: 20000000 INFO @ Wed, 07 Feb 2018 15:55:55: #1 tags after filtering in treatment: 27725334 INFO @ Wed, 07 Feb 2018 15:55:55: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:55:55: #1 finished! INFO @ Wed, 07 Feb 2018 15:55:55: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:55:55: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:55:57: #2 number of paired peaks: 141 WARNING @ Wed, 07 Feb 2018 15:55:57: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Wed, 07 Feb 2018 15:55:57: start model_add_line... INFO @ Wed, 07 Feb 2018 15:55:58: start X-correlation... INFO @ Wed, 07 Feb 2018 15:55:58: end of X-cor INFO @ Wed, 07 Feb 2018 15:55:58: #2 finished! INFO @ Wed, 07 Feb 2018 15:55:58: #2 predicted fragment length is 1 bps INFO @ Wed, 07 Feb 2018 15:55:58: #2 alternative fragment length(s) may be 1,10,37,554 bps INFO @ Wed, 07 Feb 2018 15:55:58: #2.2 Generate R script for model : SRX3404053.05_model.r WARNING @ Wed, 07 Feb 2018 15:55:58: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 15:55:58: #2 You may need to consider one of the other alternative d(s): 1,10,37,554 WARNING @ Wed, 07 Feb 2018 15:55:58: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 15:55:58: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:55:58: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:56:01: 19000000 INFO @ Wed, 07 Feb 2018 15:56:03: 21000000 INFO @ Wed, 07 Feb 2018 15:56:09: 20000000 INFO @ Wed, 07 Feb 2018 15:56:11: 22000000 INFO @ Wed, 07 Feb 2018 15:56:18: 21000000 INFO @ Wed, 07 Feb 2018 15:56:19: 23000000 INFO @ Wed, 07 Feb 2018 15:56:32: 24000000 INFO @ Wed, 07 Feb 2018 15:56:34: 22000000 INFO @ Wed, 07 Feb 2018 15:56:41: 25000000 INFO @ Wed, 07 Feb 2018 15:56:48: 23000000 INFO @ Wed, 07 Feb 2018 15:56:49: 26000000 INFO @ Wed, 07 Feb 2018 15:56:57: 27000000 INFO @ Wed, 07 Feb 2018 15:56:57: 24000000 INFO @ Wed, 07 Feb 2018 15:56:58: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:57:03: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:57:03: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:57:03: #1 total tags in treatment: 27725334 INFO @ Wed, 07 Feb 2018 15:57:03: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:57:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:57:04: #1 tags after filtering in treatment: 27725334 INFO @ Wed, 07 Feb 2018 15:57:04: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:57:04: #1 finished! INFO @ Wed, 07 Feb 2018 15:57:04: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:57:04: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:57:05: 25000000 INFO @ Wed, 07 Feb 2018 15:57:06: #2 number of paired peaks: 141 WARNING @ Wed, 07 Feb 2018 15:57:06: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Wed, 07 Feb 2018 15:57:06: start model_add_line... INFO @ Wed, 07 Feb 2018 15:57:07: start X-correlation... INFO @ Wed, 07 Feb 2018 15:57:07: end of X-cor INFO @ Wed, 07 Feb 2018 15:57:07: #2 finished! INFO @ Wed, 07 Feb 2018 15:57:07: #2 predicted fragment length is 1 bps INFO @ Wed, 07 Feb 2018 15:57:07: #2 alternative fragment length(s) may be 1,10,37,554 bps INFO @ Wed, 07 Feb 2018 15:57:07: #2.2 Generate R script for model : SRX3404053.20_model.r WARNING @ Wed, 07 Feb 2018 15:57:07: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 15:57:07: #2 You may need to consider one of the other alternative d(s): 1,10,37,554 WARNING @ Wed, 07 Feb 2018 15:57:07: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 15:57:07: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:57:07: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:57:14: 26000000 INFO @ Wed, 07 Feb 2018 15:57:22: 27000000 INFO @ Wed, 07 Feb 2018 15:57:29: #4 Write output xls file... SRX3404053.05_peaks.xls INFO @ Wed, 07 Feb 2018 15:57:29: #4 Write peak in narrowPeak format file... SRX3404053.05_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:57:29: #4 Write summits bed file... SRX3404053.05_summits.bed INFO @ Wed, 07 Feb 2018 15:57:29: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:57:30: #1 tag size is determined as 51 bps INFO @ Wed, 07 Feb 2018 15:57:30: #1 tag size = 51 INFO @ Wed, 07 Feb 2018 15:57:30: #1 total tags in treatment: 27725334 INFO @ Wed, 07 Feb 2018 15:57:30: #1 user defined the maximum tags... INFO @ Wed, 07 Feb 2018 15:57:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 07 Feb 2018 15:57:30: #1 tags after filtering in treatment: 27725334 INFO @ Wed, 07 Feb 2018 15:57:30: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 07 Feb 2018 15:57:30: #1 finished! INFO @ Wed, 07 Feb 2018 15:57:30: #2 Build Peak Model... INFO @ Wed, 07 Feb 2018 15:57:30: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 07 Feb 2018 15:57:33: #2 number of paired peaks: 141 WARNING @ Wed, 07 Feb 2018 15:57:33: Fewer paired peaks (141) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 141 pairs to build model! INFO @ Wed, 07 Feb 2018 15:57:33: start model_add_line... INFO @ Wed, 07 Feb 2018 15:57:33: start X-correlation... INFO @ Wed, 07 Feb 2018 15:57:33: end of X-cor INFO @ Wed, 07 Feb 2018 15:57:33: #2 finished! INFO @ Wed, 07 Feb 2018 15:57:33: #2 predicted fragment length is 1 bps INFO @ Wed, 07 Feb 2018 15:57:33: #2 alternative fragment length(s) may be 1,10,37,554 bps INFO @ Wed, 07 Feb 2018 15:57:33: #2.2 Generate R script for model : SRX3404053.10_model.r WARNING @ Wed, 07 Feb 2018 15:57:33: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 07 Feb 2018 15:57:33: #2 You may need to consider one of the other alternative d(s): 1,10,37,554 WARNING @ Wed, 07 Feb 2018 15:57:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 07 Feb 2018 15:57:33: #3 Call peaks... INFO @ Wed, 07 Feb 2018 15:57:33: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 07 Feb 2018 15:58:07: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:58:33: #3 Call peaks for each chromosome... INFO @ Wed, 07 Feb 2018 15:58:38: #4 Write output xls file... SRX3404053.20_peaks.xls INFO @ Wed, 07 Feb 2018 15:58:38: #4 Write peak in narrowPeak format file... SRX3404053.20_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:58:38: #4 Write summits bed file... SRX3404053.20_summits.bed INFO @ Wed, 07 Feb 2018 15:58:38: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Wed, 07 Feb 2018 15:59:03: #4 Write output xls file... SRX3404053.10_peaks.xls INFO @ Wed, 07 Feb 2018 15:59:03: #4 Write peak in narrowPeak format file... SRX3404053.10_peaks.narrowPeak INFO @ Wed, 07 Feb 2018 15:59:03: #4 Write summits bed file... SRX3404053.10_summits.bed INFO @ Wed, 07 Feb 2018 15:59:03: Done! pass1 - making usageList (0 chroms): 2 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。