Job ID = 11240711 sra ファイルのダウンロード中... Completed: 573595K bytes transferred in 9 seconds (517355K 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 27609372 spots for /home/okishinya/chipatlas/results/dm3/SRX3630320/SRR6652842.sra Written 27609372 spots for /home/okishinya/chipatlas/results/dm3/SRX3630320/SRR6652842.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:19:04 27609372 reads; of these: 27609372 (100.00%) were unpaired; of these: 551273 (2.00%) aligned 0 times 7420861 (26.88%) aligned exactly 1 time 19637238 (71.13%) aligned >1 times 98.00% overall alignment rate Time searching: 00:19:04 Overall time: 00:19:04 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 12 files... [bam_rmdupse_core] 11054173 / 27058099 = 0.4085 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 @ Sun, 07 Oct 2018 20:55:07: # Command line: callpeak -t SRX3630320.bam -f BAM -g dm -n SRX3630320.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3630320.20 # format = BAM # ChIP-seq file = ['SRX3630320.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 @ Sun, 07 Oct 2018 20:55:07: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:55:07: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:55:07: # Command line: callpeak -t SRX3630320.bam -f BAM -g dm -n SRX3630320.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3630320.05 # format = BAM # ChIP-seq file = ['SRX3630320.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 @ Sun, 07 Oct 2018 20:55:07: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:55:07: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:55:07: # Command line: callpeak -t SRX3630320.bam -f BAM -g dm -n SRX3630320.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3630320.10 # format = BAM # ChIP-seq file = ['SRX3630320.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 @ Sun, 07 Oct 2018 20:55:07: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:55:07: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:55:14: 1000000 INFO @ Sun, 07 Oct 2018 20:55:14: 1000000 INFO @ Sun, 07 Oct 2018 20:55:14: 1000000 INFO @ Sun, 07 Oct 2018 20:55:21: 2000000 INFO @ Sun, 07 Oct 2018 20:55:21: 2000000 INFO @ Sun, 07 Oct 2018 20:55:21: 2000000 INFO @ Sun, 07 Oct 2018 20:55:27: 3000000 INFO @ Sun, 07 Oct 2018 20:55:28: 3000000 INFO @ Sun, 07 Oct 2018 20:55:28: 3000000 INFO @ Sun, 07 Oct 2018 20:55:34: 4000000 INFO @ Sun, 07 Oct 2018 20:55:34: 4000000 INFO @ Sun, 07 Oct 2018 20:55:34: 4000000 INFO @ Sun, 07 Oct 2018 20:55:40: 5000000 INFO @ Sun, 07 Oct 2018 20:55:41: 5000000 INFO @ Sun, 07 Oct 2018 20:55:41: 5000000 INFO @ Sun, 07 Oct 2018 20:55:47: 6000000 INFO @ Sun, 07 Oct 2018 20:55:48: 6000000 INFO @ Sun, 07 Oct 2018 20:55:48: 6000000 INFO @ Sun, 07 Oct 2018 20:55:53: 7000000 INFO @ Sun, 07 Oct 2018 20:55:55: 7000000 INFO @ Sun, 07 Oct 2018 20:55:55: 7000000 INFO @ Sun, 07 Oct 2018 20:56:00: 8000000 INFO @ Sun, 07 Oct 2018 20:56:01: 8000000 INFO @ Sun, 07 Oct 2018 20:56:02: 8000000 INFO @ Sun, 07 Oct 2018 20:56:07: 9000000 INFO @ Sun, 07 Oct 2018 20:56:08: 9000000 INFO @ Sun, 07 Oct 2018 20:56:09: 9000000 INFO @ Sun, 07 Oct 2018 20:56:13: 10000000 INFO @ Sun, 07 Oct 2018 20:56:15: 10000000 INFO @ Sun, 07 Oct 2018 20:56:15: 10000000 INFO @ Sun, 07 Oct 2018 20:56:20: 11000000 INFO @ Sun, 07 Oct 2018 20:56:22: 11000000 INFO @ Sun, 07 Oct 2018 20:56:22: 11000000 INFO @ Sun, 07 Oct 2018 20:56:27: 12000000 INFO @ Sun, 07 Oct 2018 20:56:29: 12000000 INFO @ Sun, 07 Oct 2018 20:56:29: 12000000 INFO @ Sun, 07 Oct 2018 20:56:33: 13000000 INFO @ Sun, 07 Oct 2018 20:56:36: 13000000 INFO @ Sun, 07 Oct 2018 20:56:37: 13000000 INFO @ Sun, 07 Oct 2018 20:56:40: 14000000 INFO @ Sun, 07 Oct 2018 20:56:43: 14000000 INFO @ Sun, 07 Oct 2018 20:56:44: 14000000 INFO @ Sun, 07 Oct 2018 20:56:47: 15000000 INFO @ Sun, 07 Oct 2018 20:56:50: 15000000 INFO @ Sun, 07 Oct 2018 20:56:51: 15000000 INFO @ Sun, 07 Oct 2018 20:56:54: 16000000 INFO @ Sun, 07 Oct 2018 20:56:54: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:56:54: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:56:54: #1 total tags in treatment: 16003926 INFO @ Sun, 07 Oct 2018 20:56:54: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:56:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:56:54: #1 tags after filtering in treatment: 16003926 INFO @ Sun, 07 Oct 2018 20:56:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:56:54: #1 finished! INFO @ Sun, 07 Oct 2018 20:56:54: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:56:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:56:56: #2 number of paired peaks: 3842 INFO @ Sun, 07 Oct 2018 20:56:56: start model_add_line... INFO @ Sun, 07 Oct 2018 20:56:56: start X-correlation... INFO @ Sun, 07 Oct 2018 20:56:56: end of X-cor INFO @ Sun, 07 Oct 2018 20:56:56: #2 finished! INFO @ Sun, 07 Oct 2018 20:56:56: #2 predicted fragment length is 51 bps INFO @ Sun, 07 Oct 2018 20:56:56: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 07 Oct 2018 20:56:56: #2.2 Generate R script for model : SRX3630320.20_model.r WARNING @ Sun, 07 Oct 2018 20:56:56: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:56:56: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 07 Oct 2018 20:56:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:56:56: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:56:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:56:58: 16000000 INFO @ Sun, 07 Oct 2018 20:56:58: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:56:58: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:56:58: #1 total tags in treatment: 16003926 INFO @ Sun, 07 Oct 2018 20:56:58: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:56:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:56:58: #1 tags after filtering in treatment: 16003926 INFO @ Sun, 07 Oct 2018 20:56:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:56:58: #1 finished! INFO @ Sun, 07 Oct 2018 20:56:58: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:56:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:56:58: 16000000 INFO @ Sun, 07 Oct 2018 20:56:59: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:56:59: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:56:59: #1 total tags in treatment: 16003926 INFO @ Sun, 07 Oct 2018 20:56:59: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:56:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:56:59: #1 tags after filtering in treatment: 16003926 INFO @ Sun, 07 Oct 2018 20:56:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:56:59: #1 finished! INFO @ Sun, 07 Oct 2018 20:56:59: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:56:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:57:00: #2 number of paired peaks: 3842 INFO @ Sun, 07 Oct 2018 20:57:00: start model_add_line... INFO @ Sun, 07 Oct 2018 20:57:00: start X-correlation... INFO @ Sun, 07 Oct 2018 20:57:00: end of X-cor INFO @ Sun, 07 Oct 2018 20:57:00: #2 finished! INFO @ Sun, 07 Oct 2018 20:57:00: #2 predicted fragment length is 51 bps INFO @ Sun, 07 Oct 2018 20:57:00: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 07 Oct 2018 20:57:00: #2.2 Generate R script for model : SRX3630320.05_model.r WARNING @ Sun, 07 Oct 2018 20:57:00: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:57:00: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 07 Oct 2018 20:57:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:57:00: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:57:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:57:01: #2 number of paired peaks: 3842 INFO @ Sun, 07 Oct 2018 20:57:01: start model_add_line... INFO @ Sun, 07 Oct 2018 20:57:01: start X-correlation... INFO @ Sun, 07 Oct 2018 20:57:01: end of X-cor INFO @ Sun, 07 Oct 2018 20:57:01: #2 finished! INFO @ Sun, 07 Oct 2018 20:57:01: #2 predicted fragment length is 51 bps INFO @ Sun, 07 Oct 2018 20:57:01: #2 alternative fragment length(s) may be 4,51 bps INFO @ Sun, 07 Oct 2018 20:57:01: #2.2 Generate R script for model : SRX3630320.10_model.r WARNING @ Sun, 07 Oct 2018 20:57:01: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 20:57:01: #2 You may need to consider one of the other alternative d(s): 4,51 WARNING @ Sun, 07 Oct 2018 20:57:01: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 20:57:01: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:57:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:57:30: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:57:34: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:57:35: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:57:49: #4 Write output xls file... SRX3630320.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:57:49: #4 Write peak in narrowPeak format file... SRX3630320.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:57:49: #4 Write summits bed file... SRX3630320.20_summits.bed INFO @ Sun, 07 Oct 2018 20:57:49: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2507 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:57:54: #4 Write output xls file... SRX3630320.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:57:54: #4 Write peak in narrowPeak format file... SRX3630320.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:57:54: #4 Write summits bed file... SRX3630320.05_summits.bed INFO @ Sun, 07 Oct 2018 20:57:54: Done! INFO @ Sun, 07 Oct 2018 20:57:54: #4 Write output xls file... SRX3630320.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:57:55: #4 Write peak in narrowPeak format file... SRX3630320.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:57:55: #4 Write summits bed file... SRX3630320.10_summits.bed pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (19628 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:57:55: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9565 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。