Job ID = 11240715 sra ファイルのダウンロード中... Completed: 895248K bytes transferred in 52 seconds (140719K 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 43396095 spots for /home/okishinya/chipatlas/results/dm3/SRX3630324/SRR6652846.sra Written 43396095 spots for /home/okishinya/chipatlas/results/dm3/SRX3630324/SRR6652846.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: 00:26:29 43396095 reads; of these: 43396095 (100.00%) were unpaired; of these: 1186233 (2.73%) aligned 0 times 11593331 (26.72%) aligned exactly 1 time 30616531 (70.55%) aligned >1 times 97.27% overall alignment rate Time searching: 00:26:29 Overall time: 00:26:29 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] 22758119 / 42209862 = 0.5392 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 21:07:04: # Command line: callpeak -t SRX3630324.bam -f BAM -g dm -n SRX3630324.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3630324.20 # format = BAM # ChIP-seq file = ['SRX3630324.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 21:07:04: #1 read tag files... INFO @ Sun, 07 Oct 2018 21:07:04: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 21:07:04: # Command line: callpeak -t SRX3630324.bam -f BAM -g dm -n SRX3630324.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3630324.10 # format = BAM # ChIP-seq file = ['SRX3630324.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 21:07:04: #1 read tag files... INFO @ Sun, 07 Oct 2018 21:07:04: # Command line: callpeak -t SRX3630324.bam -f BAM -g dm -n SRX3630324.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3630324.05 # format = BAM # ChIP-seq file = ['SRX3630324.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 21:07:04: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 21:07:04: #1 read tag files... INFO @ Sun, 07 Oct 2018 21:07:04: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 21:07:11: 1000000 INFO @ Sun, 07 Oct 2018 21:07:11: 1000000 INFO @ Sun, 07 Oct 2018 21:07:11: 1000000 INFO @ Sun, 07 Oct 2018 21:07:17: 2000000 INFO @ Sun, 07 Oct 2018 21:07:17: 2000000 INFO @ Sun, 07 Oct 2018 21:07:17: 2000000 INFO @ Sun, 07 Oct 2018 21:07:24: 3000000 INFO @ Sun, 07 Oct 2018 21:07:24: 3000000 INFO @ Sun, 07 Oct 2018 21:07:24: 3000000 INFO @ Sun, 07 Oct 2018 21:07:30: 4000000 INFO @ Sun, 07 Oct 2018 21:07:30: 4000000 INFO @ Sun, 07 Oct 2018 21:07:30: 4000000 INFO @ Sun, 07 Oct 2018 21:07:37: 5000000 INFO @ Sun, 07 Oct 2018 21:07:37: 5000000 INFO @ Sun, 07 Oct 2018 21:07:37: 5000000 INFO @ Sun, 07 Oct 2018 21:07:43: 6000000 INFO @ Sun, 07 Oct 2018 21:07:43: 6000000 INFO @ Sun, 07 Oct 2018 21:07:44: 6000000 INFO @ Sun, 07 Oct 2018 21:07:50: 7000000 INFO @ Sun, 07 Oct 2018 21:07:50: 7000000 INFO @ Sun, 07 Oct 2018 21:07:50: 7000000 INFO @ Sun, 07 Oct 2018 21:07:56: 8000000 INFO @ Sun, 07 Oct 2018 21:07:57: 8000000 INFO @ Sun, 07 Oct 2018 21:07:57: 8000000 INFO @ Sun, 07 Oct 2018 21:08:03: 9000000 INFO @ Sun, 07 Oct 2018 21:08:03: 9000000 INFO @ Sun, 07 Oct 2018 21:08:03: 9000000 INFO @ Sun, 07 Oct 2018 21:08:09: 10000000 INFO @ Sun, 07 Oct 2018 21:08:10: 10000000 INFO @ Sun, 07 Oct 2018 21:08:10: 10000000 INFO @ Sun, 07 Oct 2018 21:08:16: 11000000 INFO @ Sun, 07 Oct 2018 21:08:16: 11000000 INFO @ Sun, 07 Oct 2018 21:08:16: 11000000 INFO @ Sun, 07 Oct 2018 21:08:22: 12000000 INFO @ Sun, 07 Oct 2018 21:08:23: 12000000 INFO @ Sun, 07 Oct 2018 21:08:23: 12000000 INFO @ Sun, 07 Oct 2018 21:08:29: 13000000 INFO @ Sun, 07 Oct 2018 21:08:29: 13000000 INFO @ Sun, 07 Oct 2018 21:08:29: 13000000 INFO @ Sun, 07 Oct 2018 21:08:35: 14000000 INFO @ Sun, 07 Oct 2018 21:08:36: 14000000 INFO @ Sun, 07 Oct 2018 21:08:36: 14000000 INFO @ Sun, 07 Oct 2018 21:08:42: 15000000 INFO @ Sun, 07 Oct 2018 21:08:42: 15000000 INFO @ Sun, 07 Oct 2018 21:08:42: 15000000 INFO @ Sun, 07 Oct 2018 21:08:48: 16000000 INFO @ Sun, 07 Oct 2018 21:08:49: 16000000 INFO @ Sun, 07 Oct 2018 21:08:49: 16000000 INFO @ Sun, 07 Oct 2018 21:08:54: 17000000 INFO @ Sun, 07 Oct 2018 21:08:55: 17000000 INFO @ Sun, 07 Oct 2018 21:08:55: 17000000 INFO @ Sun, 07 Oct 2018 21:09:01: 18000000 INFO @ Sun, 07 Oct 2018 21:09:02: 18000000 INFO @ Sun, 07 Oct 2018 21:09:02: 18000000 INFO @ Sun, 07 Oct 2018 21:09:07: 19000000 INFO @ Sun, 07 Oct 2018 21:09:08: 19000000 INFO @ Sun, 07 Oct 2018 21:09:08: 19000000 INFO @ Sun, 07 Oct 2018 21:09:10: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:09:10: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:09:10: #1 total tags in treatment: 19451743 INFO @ Sun, 07 Oct 2018 21:09:10: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:09:10: #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 21:09:11: #1 tags after filtering in treatment: 19451743 INFO @ Sun, 07 Oct 2018 21:09:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:09:11: #1 finished! INFO @ Sun, 07 Oct 2018 21:09:11: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:09:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:09:11: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:09:11: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:09:11: #1 total tags in treatment: 19451743 INFO @ Sun, 07 Oct 2018 21:09:11: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:09:11: #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 21:09:11: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 21:09:11: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 21:09:11: #1 total tags in treatment: 19451743 INFO @ Sun, 07 Oct 2018 21:09:11: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:09:11: #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 21:09:12: #1 tags after filtering in treatment: 19451743 INFO @ Sun, 07 Oct 2018 21:09:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:09:12: #1 finished! INFO @ Sun, 07 Oct 2018 21:09:12: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:09:12: #1 tags after filtering in treatment: 19451743 INFO @ Sun, 07 Oct 2018 21:09:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:09:12: #1 finished! INFO @ Sun, 07 Oct 2018 21:09:12: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:09:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:09:13: #2 number of paired peaks: 5867 INFO @ Sun, 07 Oct 2018 21:09:13: start model_add_line... INFO @ Sun, 07 Oct 2018 21:09:13: start X-correlation... INFO @ Sun, 07 Oct 2018 21:09:13: end of X-cor INFO @ Sun, 07 Oct 2018 21:09:13: #2 finished! INFO @ Sun, 07 Oct 2018 21:09:13: #2 predicted fragment length is 40 bps INFO @ Sun, 07 Oct 2018 21:09:13: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 07 Oct 2018 21:09:13: #2.2 Generate R script for model : SRX3630324.20_model.r WARNING @ Sun, 07 Oct 2018 21:09:13: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:09:13: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 07 Oct 2018 21:09:13: #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 21:09:13: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:09:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:09:14: #2 number of paired peaks: 5867 INFO @ Sun, 07 Oct 2018 21:09:14: start model_add_line... INFO @ Sun, 07 Oct 2018 21:09:14: #2 number of paired peaks: 5867 INFO @ Sun, 07 Oct 2018 21:09:14: start model_add_line... INFO @ Sun, 07 Oct 2018 21:09:14: start X-correlation... INFO @ Sun, 07 Oct 2018 21:09:14: end of X-cor INFO @ Sun, 07 Oct 2018 21:09:14: #2 finished! INFO @ Sun, 07 Oct 2018 21:09:14: #2 predicted fragment length is 40 bps INFO @ Sun, 07 Oct 2018 21:09:14: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 07 Oct 2018 21:09:14: #2.2 Generate R script for model : SRX3630324.05_model.r WARNING @ Sun, 07 Oct 2018 21:09:14: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:09:14: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 07 Oct 2018 21:09:14: #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 21:09:14: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:09:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:09:14: start X-correlation... INFO @ Sun, 07 Oct 2018 21:09:14: end of X-cor INFO @ Sun, 07 Oct 2018 21:09:14: #2 finished! INFO @ Sun, 07 Oct 2018 21:09:14: #2 predicted fragment length is 40 bps INFO @ Sun, 07 Oct 2018 21:09:14: #2 alternative fragment length(s) may be 4,40 bps INFO @ Sun, 07 Oct 2018 21:09:14: #2.2 Generate R script for model : SRX3630324.10_model.r WARNING @ Sun, 07 Oct 2018 21:09:15: #2 Since the d (40) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 07 Oct 2018 21:09:15: #2 You may need to consider one of the other alternative d(s): 4,40 WARNING @ Sun, 07 Oct 2018 21:09:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 07 Oct 2018 21:09:15: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:09:15: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:09:50: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:09:51: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:09:52: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:10:12: #4 Write output xls file... SRX3630324.05_peaks.xls INFO @ Sun, 07 Oct 2018 21:10:12: #4 Write peak in narrowPeak format file... SRX3630324.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:10:12: #4 Write summits bed file... SRX3630324.05_summits.bed INFO @ Sun, 07 Oct 2018 21:10:12: #4 Write output xls file... SRX3630324.20_peaks.xls INFO @ Sun, 07 Oct 2018 21:10:12: Done! INFO @ Sun, 07 Oct 2018 21:10:12: #4 Write peak in narrowPeak format file... SRX3630324.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:10:12: #4 Write summits bed file... SRX3630324.20_summits.bed INFO @ Sun, 07 Oct 2018 21:10:12: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3689 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (24056 records, 4 fields): 27 millis INFO @ Sun, 07 Oct 2018 21:10:13: #4 Write output xls file... SRX3630324.10_peaks.xls CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 21:10:13: #4 Write peak in narrowPeak format file... SRX3630324.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:10:13: #4 Write summits bed file... SRX3630324.10_summits.bed INFO @ Sun, 07 Oct 2018 21:10:13: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (14053 records, 4 fields): 17 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。