Job ID = 11171161 sra ファイルのダウンロード中... Completed: 2039522K bytes transferred in 99 seconds (168524K 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... Read 54567797 spots for /home/okishinya/chipatlas/results/dm3/SRX2564135/SRR5259254.sra Written 54567797 spots for /home/okishinya/chipatlas/results/dm3/SRX2564135/SRR5259254.sra 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: 00:20:59 54567797 reads; of these: 54567797 (100.00%) were unpaired; of these: 6609430 (12.11%) aligned 0 times 41796174 (76.59%) aligned exactly 1 time 6162193 (11.29%) aligned >1 times 87.89% overall alignment rate Time searching: 00:21:00 Overall time: 00:21:00 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] 12138407 / 47958367 = 0.2531 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, 08 Sep 2018 13:03:43: # Command line: callpeak -t SRX2564135.bam -f BAM -g dm -n SRX2564135.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2564135.05 # format = BAM # ChIP-seq file = ['SRX2564135.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 @ Sat, 08 Sep 2018 13:03:43: # Command line: callpeak -t SRX2564135.bam -f BAM -g dm -n SRX2564135.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2564135.20 # format = BAM # ChIP-seq file = ['SRX2564135.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 @ Sat, 08 Sep 2018 13:03:43: # Command line: callpeak -t SRX2564135.bam -f BAM -g dm -n SRX2564135.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2564135.10 # format = BAM # ChIP-seq file = ['SRX2564135.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 @ Sat, 08 Sep 2018 13:03:43: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:03:43: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:03:43: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:03:43: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:03:43: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:03:43: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:03:52: 1000000 INFO @ Sat, 08 Sep 2018 13:03:52: 1000000 INFO @ Sat, 08 Sep 2018 13:03:52: 1000000 INFO @ Sat, 08 Sep 2018 13:04:00: 2000000 INFO @ Sat, 08 Sep 2018 13:04:01: 2000000 INFO @ Sat, 08 Sep 2018 13:04:01: 2000000 INFO @ Sat, 08 Sep 2018 13:04:08: 3000000 INFO @ Sat, 08 Sep 2018 13:04:09: 3000000 INFO @ Sat, 08 Sep 2018 13:04:10: 3000000 INFO @ Sat, 08 Sep 2018 13:04:17: 4000000 INFO @ Sat, 08 Sep 2018 13:04:18: 4000000 INFO @ Sat, 08 Sep 2018 13:04:20: 4000000 INFO @ Sat, 08 Sep 2018 13:04:25: 5000000 INFO @ Sat, 08 Sep 2018 13:04:27: 5000000 INFO @ Sat, 08 Sep 2018 13:04:29: 5000000 INFO @ Sat, 08 Sep 2018 13:04:33: 6000000 INFO @ Sat, 08 Sep 2018 13:04:37: 6000000 INFO @ Sat, 08 Sep 2018 13:04:38: 6000000 INFO @ Sat, 08 Sep 2018 13:04:41: 7000000 INFO @ Sat, 08 Sep 2018 13:04:46: 7000000 INFO @ Sat, 08 Sep 2018 13:04:48: 7000000 INFO @ Sat, 08 Sep 2018 13:04:49: 8000000 INFO @ Sat, 08 Sep 2018 13:04:55: 8000000 INFO @ Sat, 08 Sep 2018 13:04:57: 9000000 INFO @ Sat, 08 Sep 2018 13:04:58: 8000000 INFO @ Sat, 08 Sep 2018 13:05:04: 9000000 INFO @ Sat, 08 Sep 2018 13:05:05: 10000000 INFO @ Sat, 08 Sep 2018 13:05:07: 9000000 INFO @ Sat, 08 Sep 2018 13:05:13: 11000000 INFO @ Sat, 08 Sep 2018 13:05:14: 10000000 INFO @ Sat, 08 Sep 2018 13:05:17: 10000000 INFO @ Sat, 08 Sep 2018 13:05:21: 12000000 INFO @ Sat, 08 Sep 2018 13:05:23: 11000000 INFO @ Sat, 08 Sep 2018 13:05:26: 11000000 INFO @ Sat, 08 Sep 2018 13:05:30: 13000000 INFO @ Sat, 08 Sep 2018 13:05:32: 12000000 INFO @ Sat, 08 Sep 2018 13:05:36: 12000000 INFO @ Sat, 08 Sep 2018 13:05:38: 14000000 INFO @ Sat, 08 Sep 2018 13:05:41: 13000000 INFO @ Sat, 08 Sep 2018 13:05:46: 15000000 INFO @ Sat, 08 Sep 2018 13:05:46: 13000000 INFO @ Sat, 08 Sep 2018 13:05:51: 14000000 INFO @ Sat, 08 Sep 2018 13:05:54: 16000000 INFO @ Sat, 08 Sep 2018 13:05:55: 14000000 INFO @ Sat, 08 Sep 2018 13:06:00: 15000000 INFO @ Sat, 08 Sep 2018 13:06:02: 17000000 INFO @ Sat, 08 Sep 2018 13:06:05: 15000000 INFO @ Sat, 08 Sep 2018 13:06:09: 16000000 INFO @ Sat, 08 Sep 2018 13:06:10: 18000000 INFO @ Sat, 08 Sep 2018 13:06:15: 16000000 INFO @ Sat, 08 Sep 2018 13:06:18: 19000000 INFO @ Sat, 08 Sep 2018 13:06:18: 17000000 INFO @ Sat, 08 Sep 2018 13:06:24: 17000000 INFO @ Sat, 08 Sep 2018 13:06:26: 20000000 INFO @ Sat, 08 Sep 2018 13:06:27: 18000000 INFO @ Sat, 08 Sep 2018 13:06:34: 21000000 INFO @ Sat, 08 Sep 2018 13:06:34: 18000000 INFO @ Sat, 08 Sep 2018 13:06:36: 19000000 INFO @ Sat, 08 Sep 2018 13:06:42: 22000000 INFO @ Sat, 08 Sep 2018 13:06:43: 19000000 INFO @ Sat, 08 Sep 2018 13:06:45: 20000000 INFO @ Sat, 08 Sep 2018 13:06:50: 23000000 INFO @ Sat, 08 Sep 2018 13:06:53: 20000000 INFO @ Sat, 08 Sep 2018 13:06:54: 21000000 INFO @ Sat, 08 Sep 2018 13:06:58: 24000000 INFO @ Sat, 08 Sep 2018 13:07:03: 21000000 INFO @ Sat, 08 Sep 2018 13:07:03: 22000000 INFO @ Sat, 08 Sep 2018 13:07:06: 25000000 INFO @ Sat, 08 Sep 2018 13:07:12: 22000000 INFO @ Sat, 08 Sep 2018 13:07:13: 23000000 INFO @ Sat, 08 Sep 2018 13:07:14: 26000000 INFO @ Sat, 08 Sep 2018 13:07:22: 24000000 INFO @ Sat, 08 Sep 2018 13:07:22: 23000000 INFO @ Sat, 08 Sep 2018 13:07:22: 27000000 INFO @ Sat, 08 Sep 2018 13:07:30: 28000000 INFO @ Sat, 08 Sep 2018 13:07:31: 25000000 INFO @ Sat, 08 Sep 2018 13:07:31: 24000000 INFO @ Sat, 08 Sep 2018 13:07:38: 29000000 INFO @ Sat, 08 Sep 2018 13:07:40: 26000000 INFO @ Sat, 08 Sep 2018 13:07:41: 25000000 INFO @ Sat, 08 Sep 2018 13:07:46: 30000000 INFO @ Sat, 08 Sep 2018 13:07:49: 27000000 INFO @ Sat, 08 Sep 2018 13:07:51: 26000000 INFO @ Sat, 08 Sep 2018 13:07:54: 31000000 INFO @ Sat, 08 Sep 2018 13:07:58: 28000000 INFO @ Sat, 08 Sep 2018 13:08:00: 27000000 INFO @ Sat, 08 Sep 2018 13:08:02: 32000000 INFO @ Sat, 08 Sep 2018 13:08:08: 29000000 INFO @ Sat, 08 Sep 2018 13:08:10: 28000000 INFO @ Sat, 08 Sep 2018 13:08:10: 33000000 INFO @ Sat, 08 Sep 2018 13:08:17: 30000000 INFO @ Sat, 08 Sep 2018 13:08:18: 34000000 INFO @ Sat, 08 Sep 2018 13:08:20: 29000000 INFO @ Sat, 08 Sep 2018 13:08:26: 31000000 INFO @ Sat, 08 Sep 2018 13:08:26: 35000000 INFO @ Sat, 08 Sep 2018 13:08:30: 30000000 INFO @ Sat, 08 Sep 2018 13:08:33: #1 tag size is determined as 74 bps INFO @ Sat, 08 Sep 2018 13:08:33: #1 tag size = 74 INFO @ Sat, 08 Sep 2018 13:08:33: #1 total tags in treatment: 35819960 INFO @ Sat, 08 Sep 2018 13:08:33: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:08:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:08:34: #1 tags after filtering in treatment: 35819960 INFO @ Sat, 08 Sep 2018 13:08:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:08:34: #1 finished! INFO @ Sat, 08 Sep 2018 13:08:34: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:08:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:08:35: 32000000 INFO @ Sat, 08 Sep 2018 13:08:37: #2 number of paired peaks: 129 WARNING @ Sat, 08 Sep 2018 13:08:37: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 08 Sep 2018 13:08:37: start model_add_line... INFO @ Sat, 08 Sep 2018 13:08:37: start X-correlation... INFO @ Sat, 08 Sep 2018 13:08:37: end of X-cor INFO @ Sat, 08 Sep 2018 13:08:37: #2 finished! INFO @ Sat, 08 Sep 2018 13:08:37: #2 predicted fragment length is 120 bps INFO @ Sat, 08 Sep 2018 13:08:37: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sat, 08 Sep 2018 13:08:37: #2.2 Generate R script for model : SRX2564135.10_model.r WARNING @ Sat, 08 Sep 2018 13:08:37: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:08:37: #2 You may need to consider one of the other alternative d(s): 4,120 WARNING @ Sat, 08 Sep 2018 13:08:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:08:37: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:08:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:08:39: 31000000 INFO @ Sat, 08 Sep 2018 13:08:45: 33000000 INFO @ Sat, 08 Sep 2018 13:08:49: 32000000 INFO @ Sat, 08 Sep 2018 13:08:54: 34000000 INFO @ Sat, 08 Sep 2018 13:08:58: 33000000 INFO @ Sat, 08 Sep 2018 13:09:04: 35000000 INFO @ Sat, 08 Sep 2018 13:09:08: 34000000 INFO @ Sat, 08 Sep 2018 13:09:11: #1 tag size is determined as 74 bps INFO @ Sat, 08 Sep 2018 13:09:11: #1 tag size = 74 INFO @ Sat, 08 Sep 2018 13:09:11: #1 total tags in treatment: 35819960 INFO @ Sat, 08 Sep 2018 13:09:11: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:09:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:09:12: #1 tags after filtering in treatment: 35819960 INFO @ Sat, 08 Sep 2018 13:09:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:09:12: #1 finished! INFO @ Sat, 08 Sep 2018 13:09:12: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:09:14: #2 number of paired peaks: 129 WARNING @ Sat, 08 Sep 2018 13:09:14: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 08 Sep 2018 13:09:14: start model_add_line... INFO @ Sat, 08 Sep 2018 13:09:15: start X-correlation... INFO @ Sat, 08 Sep 2018 13:09:15: end of X-cor INFO @ Sat, 08 Sep 2018 13:09:15: #2 finished! INFO @ Sat, 08 Sep 2018 13:09:15: #2 predicted fragment length is 120 bps INFO @ Sat, 08 Sep 2018 13:09:15: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sat, 08 Sep 2018 13:09:15: #2.2 Generate R script for model : SRX2564135.20_model.r WARNING @ Sat, 08 Sep 2018 13:09:15: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:09:15: #2 You may need to consider one of the other alternative d(s): 4,120 WARNING @ Sat, 08 Sep 2018 13:09:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:09:15: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:09:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:09:17: 35000000 INFO @ Sat, 08 Sep 2018 13:09:25: #1 tag size is determined as 74 bps INFO @ Sat, 08 Sep 2018 13:09:25: #1 tag size = 74 INFO @ Sat, 08 Sep 2018 13:09:25: #1 total tags in treatment: 35819960 INFO @ Sat, 08 Sep 2018 13:09:25: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:09:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:09:25: #1 tags after filtering in treatment: 35819960 INFO @ Sat, 08 Sep 2018 13:09:25: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:09:25: #1 finished! INFO @ Sat, 08 Sep 2018 13:09:25: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:09:25: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:09:28: #2 number of paired peaks: 129 WARNING @ Sat, 08 Sep 2018 13:09:28: Fewer paired peaks (129) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 129 pairs to build model! INFO @ Sat, 08 Sep 2018 13:09:28: start model_add_line... INFO @ Sat, 08 Sep 2018 13:09:28: start X-correlation... INFO @ Sat, 08 Sep 2018 13:09:28: end of X-cor INFO @ Sat, 08 Sep 2018 13:09:28: #2 finished! INFO @ Sat, 08 Sep 2018 13:09:28: #2 predicted fragment length is 120 bps INFO @ Sat, 08 Sep 2018 13:09:28: #2 alternative fragment length(s) may be 4,120 bps INFO @ Sat, 08 Sep 2018 13:09:28: #2.2 Generate R script for model : SRX2564135.05_model.r WARNING @ Sat, 08 Sep 2018 13:09:28: #2 Since the d (120) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:09:28: #2 You may need to consider one of the other alternative d(s): 4,120 WARNING @ Sat, 08 Sep 2018 13:09:28: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:09:28: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:09:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:09:52: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:26: #4 Write output xls file... SRX2564135.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:10:26: #4 Write peak in narrowPeak format file... SRX2564135.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:10:26: #4 Write summits bed file... SRX2564135.10_summits.bed INFO @ Sat, 08 Sep 2018 13:10:26: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8243 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:10:28: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:10:41: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:11:03: #4 Write output xls file... SRX2564135.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:03: #4 Write peak in narrowPeak format file... SRX2564135.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:03: #4 Write summits bed file... SRX2564135.20_summits.bed INFO @ Sat, 08 Sep 2018 13:11:03: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5200 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:11:19: #4 Write output xls file... SRX2564135.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:11:19: #4 Write peak in narrowPeak format file... SRX2564135.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:11:19: #4 Write summits bed file... SRX2564135.05_summits.bed INFO @ Sat, 08 Sep 2018 13:11:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11257 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。