Job ID = 11171163 sra ファイルのダウンロード中... Completed: 1338556K bytes transferred in 25 seconds (431983K 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 46218766 spots for /home/okishinya/chipatlas/results/dm3/SRX2564137/SRR5259256.sra Written 46218766 spots for /home/okishinya/chipatlas/results/dm3/SRX2564137/SRR5259256.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: 00:20:33 46218766 reads; of these: 46218766 (100.00%) were unpaired; of these: 3953452 (8.55%) aligned 0 times 34815155 (75.33%) aligned exactly 1 time 7450159 (16.12%) aligned >1 times 91.45% overall alignment rate Time searching: 00:20:34 Overall time: 00:20:34 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] 11351033 / 42265314 = 0.2686 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 12:54:31: # Command line: callpeak -t SRX2564137.bam -f BAM -g dm -n SRX2564137.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2564137.10 # format = BAM # ChIP-seq file = ['SRX2564137.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 12:54:31: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:54:31: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:54:31: # Command line: callpeak -t SRX2564137.bam -f BAM -g dm -n SRX2564137.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2564137.05 # format = BAM # ChIP-seq file = ['SRX2564137.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 12:54:31: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:54:31: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:54:31: # Command line: callpeak -t SRX2564137.bam -f BAM -g dm -n SRX2564137.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2564137.20 # format = BAM # ChIP-seq file = ['SRX2564137.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 12:54:31: #1 read tag files... INFO @ Sat, 08 Sep 2018 12:54:31: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 12:54:38: 1000000 INFO @ Sat, 08 Sep 2018 12:54:39: 1000000 INFO @ Sat, 08 Sep 2018 12:54:39: 1000000 INFO @ Sat, 08 Sep 2018 12:54:46: 2000000 INFO @ Sat, 08 Sep 2018 12:54:47: 2000000 INFO @ Sat, 08 Sep 2018 12:54:47: 2000000 INFO @ Sat, 08 Sep 2018 12:54:53: 3000000 INFO @ Sat, 08 Sep 2018 12:54:56: 3000000 INFO @ Sat, 08 Sep 2018 12:54:56: 3000000 INFO @ Sat, 08 Sep 2018 12:55:01: 4000000 INFO @ Sat, 08 Sep 2018 12:55:04: 4000000 INFO @ Sat, 08 Sep 2018 12:55:04: 4000000 INFO @ Sat, 08 Sep 2018 12:55:09: 5000000 INFO @ Sat, 08 Sep 2018 12:55:12: 5000000 INFO @ Sat, 08 Sep 2018 12:55:12: 5000000 INFO @ Sat, 08 Sep 2018 12:55:16: 6000000 INFO @ Sat, 08 Sep 2018 12:55:20: 6000000 INFO @ Sat, 08 Sep 2018 12:55:20: 6000000 INFO @ Sat, 08 Sep 2018 12:55:24: 7000000 INFO @ Sat, 08 Sep 2018 12:55:28: 7000000 INFO @ Sat, 08 Sep 2018 12:55:28: 7000000 INFO @ Sat, 08 Sep 2018 12:55:31: 8000000 INFO @ Sat, 08 Sep 2018 12:55:36: 8000000 INFO @ Sat, 08 Sep 2018 12:55:36: 8000000 INFO @ Sat, 08 Sep 2018 12:55:38: 9000000 INFO @ Sat, 08 Sep 2018 12:55:44: 9000000 INFO @ Sat, 08 Sep 2018 12:55:44: 9000000 INFO @ Sat, 08 Sep 2018 12:55:46: 10000000 INFO @ Sat, 08 Sep 2018 12:55:52: 10000000 INFO @ Sat, 08 Sep 2018 12:55:52: 10000000 INFO @ Sat, 08 Sep 2018 12:55:53: 11000000 INFO @ Sat, 08 Sep 2018 12:56:00: 12000000 INFO @ Sat, 08 Sep 2018 12:56:01: 11000000 INFO @ Sat, 08 Sep 2018 12:56:01: 11000000 INFO @ Sat, 08 Sep 2018 12:56:08: 13000000 INFO @ Sat, 08 Sep 2018 12:56:09: 12000000 INFO @ Sat, 08 Sep 2018 12:56:09: 12000000 INFO @ Sat, 08 Sep 2018 12:56:15: 14000000 INFO @ Sat, 08 Sep 2018 12:56:17: 13000000 INFO @ Sat, 08 Sep 2018 12:56:17: 13000000 INFO @ Sat, 08 Sep 2018 12:56:22: 15000000 INFO @ Sat, 08 Sep 2018 12:56:25: 14000000 INFO @ Sat, 08 Sep 2018 12:56:26: 14000000 INFO @ Sat, 08 Sep 2018 12:56:30: 16000000 INFO @ Sat, 08 Sep 2018 12:56:34: 15000000 INFO @ Sat, 08 Sep 2018 12:56:34: 15000000 INFO @ Sat, 08 Sep 2018 12:56:37: 17000000 INFO @ Sat, 08 Sep 2018 12:56:42: 16000000 INFO @ Sat, 08 Sep 2018 12:56:42: 16000000 INFO @ Sat, 08 Sep 2018 12:56:44: 18000000 INFO @ Sat, 08 Sep 2018 12:56:50: 17000000 INFO @ Sat, 08 Sep 2018 12:56:50: 17000000 INFO @ Sat, 08 Sep 2018 12:56:52: 19000000 INFO @ Sat, 08 Sep 2018 12:56:59: 18000000 INFO @ Sat, 08 Sep 2018 12:56:59: 18000000 INFO @ Sat, 08 Sep 2018 12:56:59: 20000000 INFO @ Sat, 08 Sep 2018 12:57:06: 21000000 INFO @ Sat, 08 Sep 2018 12:57:07: 19000000 INFO @ Sat, 08 Sep 2018 12:57:07: 19000000 INFO @ Sat, 08 Sep 2018 12:57:14: 22000000 INFO @ Sat, 08 Sep 2018 12:57:15: 20000000 INFO @ Sat, 08 Sep 2018 12:57:15: 20000000 INFO @ Sat, 08 Sep 2018 12:57:21: 23000000 INFO @ Sat, 08 Sep 2018 12:57:23: 21000000 INFO @ Sat, 08 Sep 2018 12:57:24: 21000000 INFO @ Sat, 08 Sep 2018 12:57:28: 24000000 INFO @ Sat, 08 Sep 2018 12:57:32: 22000000 INFO @ Sat, 08 Sep 2018 12:57:32: 22000000 INFO @ Sat, 08 Sep 2018 12:57:36: 25000000 INFO @ Sat, 08 Sep 2018 12:57:40: 23000000 INFO @ Sat, 08 Sep 2018 12:57:40: 23000000 INFO @ Sat, 08 Sep 2018 12:57:43: 26000000 INFO @ Sat, 08 Sep 2018 12:57:48: 24000000 INFO @ Sat, 08 Sep 2018 12:57:49: 24000000 INFO @ Sat, 08 Sep 2018 12:57:51: 27000000 INFO @ Sat, 08 Sep 2018 12:57:57: 25000000 INFO @ Sat, 08 Sep 2018 12:57:57: 25000000 INFO @ Sat, 08 Sep 2018 12:57:58: 28000000 INFO @ Sat, 08 Sep 2018 12:58:05: 26000000 INFO @ Sat, 08 Sep 2018 12:58:05: 26000000 INFO @ Sat, 08 Sep 2018 12:58:05: 29000000 INFO @ Sat, 08 Sep 2018 12:58:13: 30000000 INFO @ Sat, 08 Sep 2018 12:58:14: 27000000 INFO @ Sat, 08 Sep 2018 12:58:14: 27000000 INFO @ Sat, 08 Sep 2018 12:58:20: #1 tag size is determined as 72 bps INFO @ Sat, 08 Sep 2018 12:58:20: #1 tag size = 72 INFO @ Sat, 08 Sep 2018 12:58:20: #1 total tags in treatment: 30914281 INFO @ Sat, 08 Sep 2018 12:58:20: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:58:20: #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 12:58:20: #1 tags after filtering in treatment: 30914281 INFO @ Sat, 08 Sep 2018 12:58:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:58:20: #1 finished! INFO @ Sat, 08 Sep 2018 12:58:20: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:58:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:58:22: 28000000 INFO @ Sat, 08 Sep 2018 12:58:22: 28000000 INFO @ Sat, 08 Sep 2018 12:58:23: #2 number of paired peaks: 725 WARNING @ Sat, 08 Sep 2018 12:58:23: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Sat, 08 Sep 2018 12:58:23: start model_add_line... INFO @ Sat, 08 Sep 2018 12:58:23: start X-correlation... INFO @ Sat, 08 Sep 2018 12:58:23: end of X-cor INFO @ Sat, 08 Sep 2018 12:58:23: #2 finished! INFO @ Sat, 08 Sep 2018 12:58:23: #2 predicted fragment length is 139 bps INFO @ Sat, 08 Sep 2018 12:58:23: #2 alternative fragment length(s) may be 2,139 bps INFO @ Sat, 08 Sep 2018 12:58:23: #2.2 Generate R script for model : SRX2564137.10_model.r WARNING @ Sat, 08 Sep 2018 12:58:23: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:58:23: #2 You may need to consider one of the other alternative d(s): 2,139 WARNING @ Sat, 08 Sep 2018 12:58:23: #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 12:58:23: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:58:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:58:30: 29000000 INFO @ Sat, 08 Sep 2018 12:58:30: 29000000 INFO @ Sat, 08 Sep 2018 12:58:39: 30000000 INFO @ Sat, 08 Sep 2018 12:58:39: 30000000 INFO @ Sat, 08 Sep 2018 12:58:46: #1 tag size is determined as 72 bps INFO @ Sat, 08 Sep 2018 12:58:46: #1 tag size = 72 INFO @ Sat, 08 Sep 2018 12:58:46: #1 total tags in treatment: 30914281 INFO @ Sat, 08 Sep 2018 12:58:46: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:58:46: #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 12:58:47: #1 tag size is determined as 72 bps INFO @ Sat, 08 Sep 2018 12:58:47: #1 tag size = 72 INFO @ Sat, 08 Sep 2018 12:58:47: #1 total tags in treatment: 30914281 INFO @ Sat, 08 Sep 2018 12:58:47: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 12:58:47: #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 12:58:47: #1 tags after filtering in treatment: 30914281 INFO @ Sat, 08 Sep 2018 12:58:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:58:47: #1 finished! INFO @ Sat, 08 Sep 2018 12:58:47: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:58:47: #1 tags after filtering in treatment: 30914281 INFO @ Sat, 08 Sep 2018 12:58:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 12:58:47: #1 finished! INFO @ Sat, 08 Sep 2018 12:58:47: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 12:58:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 12:58:49: #2 number of paired peaks: 725 WARNING @ Sat, 08 Sep 2018 12:58:49: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Sat, 08 Sep 2018 12:58:49: start model_add_line... INFO @ Sat, 08 Sep 2018 12:58:49: #2 number of paired peaks: 725 WARNING @ Sat, 08 Sep 2018 12:58:49: Fewer paired peaks (725) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 725 pairs to build model! INFO @ Sat, 08 Sep 2018 12:58:49: start model_add_line... INFO @ Sat, 08 Sep 2018 12:58:50: start X-correlation... INFO @ Sat, 08 Sep 2018 12:58:50: end of X-cor INFO @ Sat, 08 Sep 2018 12:58:50: #2 finished! INFO @ Sat, 08 Sep 2018 12:58:50: #2 predicted fragment length is 139 bps INFO @ Sat, 08 Sep 2018 12:58:50: #2 alternative fragment length(s) may be 2,139 bps INFO @ Sat, 08 Sep 2018 12:58:50: #2.2 Generate R script for model : SRX2564137.20_model.r WARNING @ Sat, 08 Sep 2018 12:58:50: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:58:50: #2 You may need to consider one of the other alternative d(s): 2,139 WARNING @ Sat, 08 Sep 2018 12:58:50: #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 12:58:50: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:58:50: start X-correlation... INFO @ Sat, 08 Sep 2018 12:58:50: end of X-cor INFO @ Sat, 08 Sep 2018 12:58:50: #2 finished! INFO @ Sat, 08 Sep 2018 12:58:50: #2 predicted fragment length is 139 bps INFO @ Sat, 08 Sep 2018 12:58:50: #2 alternative fragment length(s) may be 2,139 bps INFO @ Sat, 08 Sep 2018 12:58:50: #2.2 Generate R script for model : SRX2564137.05_model.r WARNING @ Sat, 08 Sep 2018 12:58:50: #2 Since the d (139) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 12:58:50: #2 You may need to consider one of the other alternative d(s): 2,139 WARNING @ Sat, 08 Sep 2018 12:58:50: #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 12:58:50: #3 Call peaks... INFO @ Sat, 08 Sep 2018 12:58:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 12:59:29: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:59:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 12:59:59: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:00:04: #4 Write output xls file... SRX2564137.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:00:04: #4 Write peak in narrowPeak format file... SRX2564137.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:00:04: #4 Write summits bed file... SRX2564137.10_summits.bed INFO @ Sat, 08 Sep 2018 13:00:04: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (531 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:00:28: #4 Write output xls file... SRX2564137.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:00:28: #4 Write peak in narrowPeak format file... SRX2564137.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:00:28: #4 Write summits bed file... SRX2564137.20_summits.bed INFO @ Sat, 08 Sep 2018 13:00:28: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (144 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:00:31: #4 Write output xls file... SRX2564137.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:00:31: #4 Write peak in narrowPeak format file... SRX2564137.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:00:31: #4 Write summits bed file... SRX2564137.05_summits.bed INFO @ Sat, 08 Sep 2018 13:00:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1595 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。