Job ID = 11597986 sra ファイルのダウンロード中... Completed: 695571K bytes transferred in 10 seconds (524752K 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 29073741 spots for /home/okishinya/chipatlas/results/dm3/SRX4664651/SRR7813078.sra Written 29073741 spots for /home/okishinya/chipatlas/results/dm3/SRX4664651/SRR7813078.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: 00:13:34 29073741 reads; of these: 29073741 (100.00%) were unpaired; of these: 664660 (2.29%) aligned 0 times 18483007 (63.57%) aligned exactly 1 time 9926074 (34.14%) aligned >1 times 97.71% overall alignment rate Time searching: 00:13:34 Overall time: 00:13:34 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 12 files... [bam_rmdupse_core] 4458589 / 28409081 = 0.1569 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, 30 Jan 2019 17:02:44: # Command line: callpeak -t SRX4664651.bam -f BAM -g dm -n SRX4664651.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664651.10 # format = BAM # ChIP-seq file = ['SRX4664651.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, 30 Jan 2019 17:02:44: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:02:44: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:02:44: # Command line: callpeak -t SRX4664651.bam -f BAM -g dm -n SRX4664651.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664651.05 # format = BAM # ChIP-seq file = ['SRX4664651.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, 30 Jan 2019 17:02:44: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:02:44: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:02:44: # Command line: callpeak -t SRX4664651.bam -f BAM -g dm -n SRX4664651.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664651.20 # format = BAM # ChIP-seq file = ['SRX4664651.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, 30 Jan 2019 17:02:44: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:02:44: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:02:50: 1000000 INFO @ Wed, 30 Jan 2019 17:02:50: 1000000 INFO @ Wed, 30 Jan 2019 17:02:50: 1000000 INFO @ Wed, 30 Jan 2019 17:02:56: 2000000 INFO @ Wed, 30 Jan 2019 17:02:57: 2000000 INFO @ Wed, 30 Jan 2019 17:02:57: 2000000 INFO @ Wed, 30 Jan 2019 17:03:03: 3000000 INFO @ Wed, 30 Jan 2019 17:03:03: 3000000 INFO @ Wed, 30 Jan 2019 17:03:04: 3000000 INFO @ Wed, 30 Jan 2019 17:03:09: 4000000 INFO @ Wed, 30 Jan 2019 17:03:09: 4000000 INFO @ Wed, 30 Jan 2019 17:03:10: 4000000 INFO @ Wed, 30 Jan 2019 17:03:16: 5000000 INFO @ Wed, 30 Jan 2019 17:03:16: 5000000 INFO @ Wed, 30 Jan 2019 17:03:17: 5000000 INFO @ Wed, 30 Jan 2019 17:03:22: 6000000 INFO @ Wed, 30 Jan 2019 17:03:22: 6000000 INFO @ Wed, 30 Jan 2019 17:03:24: 6000000 INFO @ Wed, 30 Jan 2019 17:03:28: 7000000 INFO @ Wed, 30 Jan 2019 17:03:28: 7000000 INFO @ Wed, 30 Jan 2019 17:03:30: 7000000 INFO @ Wed, 30 Jan 2019 17:03:34: 8000000 INFO @ Wed, 30 Jan 2019 17:03:35: 8000000 INFO @ Wed, 30 Jan 2019 17:03:37: 8000000 INFO @ Wed, 30 Jan 2019 17:03:41: 9000000 INFO @ Wed, 30 Jan 2019 17:03:41: 9000000 INFO @ Wed, 30 Jan 2019 17:03:44: 9000000 INFO @ Wed, 30 Jan 2019 17:03:47: 10000000 INFO @ Wed, 30 Jan 2019 17:03:48: 10000000 INFO @ Wed, 30 Jan 2019 17:03:50: 10000000 INFO @ Wed, 30 Jan 2019 17:03:53: 11000000 INFO @ Wed, 30 Jan 2019 17:03:54: 11000000 INFO @ Wed, 30 Jan 2019 17:03:57: 11000000 INFO @ Wed, 30 Jan 2019 17:03:59: 12000000 INFO @ Wed, 30 Jan 2019 17:04:00: 12000000 INFO @ Wed, 30 Jan 2019 17:04:04: 12000000 INFO @ Wed, 30 Jan 2019 17:04:05: 13000000 INFO @ Wed, 30 Jan 2019 17:04:06: 13000000 INFO @ Wed, 30 Jan 2019 17:04:11: 13000000 INFO @ Wed, 30 Jan 2019 17:04:11: 14000000 INFO @ Wed, 30 Jan 2019 17:04:13: 14000000 INFO @ Wed, 30 Jan 2019 17:04:17: 14000000 INFO @ Wed, 30 Jan 2019 17:04:18: 15000000 INFO @ Wed, 30 Jan 2019 17:04:19: 15000000 INFO @ Wed, 30 Jan 2019 17:04:24: 16000000 INFO @ Wed, 30 Jan 2019 17:04:24: 15000000 INFO @ Wed, 30 Jan 2019 17:04:25: 16000000 INFO @ Wed, 30 Jan 2019 17:04:30: 17000000 INFO @ Wed, 30 Jan 2019 17:04:30: 16000000 INFO @ Wed, 30 Jan 2019 17:04:32: 17000000 INFO @ Wed, 30 Jan 2019 17:04:36: 18000000 INFO @ Wed, 30 Jan 2019 17:04:37: 17000000 INFO @ Wed, 30 Jan 2019 17:04:38: 18000000 INFO @ Wed, 30 Jan 2019 17:04:42: 19000000 INFO @ Wed, 30 Jan 2019 17:04:44: 18000000 INFO @ Wed, 30 Jan 2019 17:04:44: 19000000 INFO @ Wed, 30 Jan 2019 17:04:48: 20000000 INFO @ Wed, 30 Jan 2019 17:04:50: 19000000 INFO @ Wed, 30 Jan 2019 17:04:50: 20000000 INFO @ Wed, 30 Jan 2019 17:04:54: 21000000 INFO @ Wed, 30 Jan 2019 17:04:57: 21000000 INFO @ Wed, 30 Jan 2019 17:04:57: 20000000 INFO @ Wed, 30 Jan 2019 17:05:01: 22000000 INFO @ Wed, 30 Jan 2019 17:05:03: 22000000 INFO @ Wed, 30 Jan 2019 17:05:04: 21000000 INFO @ Wed, 30 Jan 2019 17:05:07: 23000000 INFO @ Wed, 30 Jan 2019 17:05:09: 23000000 INFO @ Wed, 30 Jan 2019 17:05:10: 22000000 INFO @ Wed, 30 Jan 2019 17:05:13: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:05:13: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:05:13: #1 total tags in treatment: 23950492 INFO @ Wed, 30 Jan 2019 17:05:13: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:05:13: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 17:05:13: #1 tags after filtering in treatment: 23950492 INFO @ Wed, 30 Jan 2019 17:05:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:05:13: #1 finished! INFO @ Wed, 30 Jan 2019 17:05:13: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:05:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:05:15: #2 number of paired peaks: 563 WARNING @ Wed, 30 Jan 2019 17:05:15: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Wed, 30 Jan 2019 17:05:15: start model_add_line... INFO @ Wed, 30 Jan 2019 17:05:15: start X-correlation... INFO @ Wed, 30 Jan 2019 17:05:15: end of X-cor INFO @ Wed, 30 Jan 2019 17:05:15: #2 finished! INFO @ Wed, 30 Jan 2019 17:05:15: #2 predicted fragment length is 41 bps INFO @ Wed, 30 Jan 2019 17:05:15: #2 alternative fragment length(s) may be 3,41 bps INFO @ Wed, 30 Jan 2019 17:05:15: #2.2 Generate R script for model : SRX4664651.10_model.r WARNING @ Wed, 30 Jan 2019 17:05:15: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:05:15: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Wed, 30 Jan 2019 17:05:15: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 17:05:15: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:05:15: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:05:16: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:05:16: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:05:16: #1 total tags in treatment: 23950492 INFO @ Wed, 30 Jan 2019 17:05:16: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:05:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 17:05:16: #1 tags after filtering in treatment: 23950492 INFO @ Wed, 30 Jan 2019 17:05:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:05:16: #1 finished! INFO @ Wed, 30 Jan 2019 17:05:16: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:05:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:05:17: 23000000 INFO @ Wed, 30 Jan 2019 17:05:18: #2 number of paired peaks: 563 WARNING @ Wed, 30 Jan 2019 17:05:18: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Wed, 30 Jan 2019 17:05:18: start model_add_line... INFO @ Wed, 30 Jan 2019 17:05:18: start X-correlation... INFO @ Wed, 30 Jan 2019 17:05:18: end of X-cor INFO @ Wed, 30 Jan 2019 17:05:18: #2 finished! INFO @ Wed, 30 Jan 2019 17:05:18: #2 predicted fragment length is 41 bps INFO @ Wed, 30 Jan 2019 17:05:18: #2 alternative fragment length(s) may be 3,41 bps INFO @ Wed, 30 Jan 2019 17:05:18: #2.2 Generate R script for model : SRX4664651.20_model.r WARNING @ Wed, 30 Jan 2019 17:05:18: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:05:18: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Wed, 30 Jan 2019 17:05:18: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 17:05:18: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:05:18: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:05:23: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:05:23: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:05:23: #1 total tags in treatment: 23950492 INFO @ Wed, 30 Jan 2019 17:05:23: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:05:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 30 Jan 2019 17:05:23: #1 tags after filtering in treatment: 23950492 INFO @ Wed, 30 Jan 2019 17:05:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:05:23: #1 finished! INFO @ Wed, 30 Jan 2019 17:05:23: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:05:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:05:25: #2 number of paired peaks: 563 WARNING @ Wed, 30 Jan 2019 17:05:25: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Wed, 30 Jan 2019 17:05:25: start model_add_line... INFO @ Wed, 30 Jan 2019 17:05:25: start X-correlation... INFO @ Wed, 30 Jan 2019 17:05:25: end of X-cor INFO @ Wed, 30 Jan 2019 17:05:25: #2 finished! INFO @ Wed, 30 Jan 2019 17:05:25: #2 predicted fragment length is 41 bps INFO @ Wed, 30 Jan 2019 17:05:25: #2 alternative fragment length(s) may be 3,41 bps INFO @ Wed, 30 Jan 2019 17:05:25: #2.2 Generate R script for model : SRX4664651.05_model.r WARNING @ Wed, 30 Jan 2019 17:05:25: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 17:05:25: #2 You may need to consider one of the other alternative d(s): 3,41 WARNING @ Wed, 30 Jan 2019 17:05:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 30 Jan 2019 17:05:25: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:05:25: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:06:00: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:06:04: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:06:12: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:06:24: #4 Write output xls file... SRX4664651.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:06:25: #4 Write peak in narrowPeak format file... SRX4664651.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:06:25: #4 Write summits bed file... SRX4664651.10_summits.bed INFO @ Wed, 30 Jan 2019 17:06:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2941 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:06:27: #4 Write output xls file... SRX4664651.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:06:27: #4 Write peak in narrowPeak format file... SRX4664651.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:06:27: #4 Write summits bed file... SRX4664651.20_summits.bed INFO @ Wed, 30 Jan 2019 17:06:27: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1692 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:06:36: #4 Write output xls file... SRX4664651.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:06:36: #4 Write peak in narrowPeak format file... SRX4664651.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:06:36: #4 Write summits bed file... SRX4664651.05_summits.bed INFO @ Wed, 30 Jan 2019 17:06:36: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4367 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。