Job ID = 11597989 sra ファイルのダウンロード中... Completed: 405724K bytes transferred in 11 seconds (300719K 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 16906273 spots for /home/okishinya/chipatlas/results/dm3/SRX4664653/SRR7813080.sra Written 16906273 spots for /home/okishinya/chipatlas/results/dm3/SRX4664653/SRR7813080.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: 00:07:25 16906273 reads; of these: 16906273 (100.00%) were unpaired; of these: 412819 (2.44%) aligned 0 times 11128475 (65.82%) aligned exactly 1 time 5364979 (31.73%) aligned >1 times 97.56% overall alignment rate Time searching: 00:07:25 Overall time: 00:07:25 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 8 files... [bam_rmdupse_core] 1813524 / 16493454 = 0.1100 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 16:54:47: # Command line: callpeak -t SRX4664653.bam -f BAM -g dm -n SRX4664653.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664653.05 # format = BAM # ChIP-seq file = ['SRX4664653.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 16:54:47: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:54:47: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:54:47: # Command line: callpeak -t SRX4664653.bam -f BAM -g dm -n SRX4664653.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664653.20 # format = BAM # ChIP-seq file = ['SRX4664653.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 16:54:47: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:54:47: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:54:47: # Command line: callpeak -t SRX4664653.bam -f BAM -g dm -n SRX4664653.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664653.10 # format = BAM # ChIP-seq file = ['SRX4664653.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 16:54:47: #1 read tag files... INFO @ Wed, 30 Jan 2019 16:54:47: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 16:54:54: 1000000 INFO @ Wed, 30 Jan 2019 16:54:54: 1000000 INFO @ Wed, 30 Jan 2019 16:54:54: 1000000 INFO @ Wed, 30 Jan 2019 16:55:00: 2000000 INFO @ Wed, 30 Jan 2019 16:55:01: 2000000 INFO @ Wed, 30 Jan 2019 16:55:01: 2000000 INFO @ Wed, 30 Jan 2019 16:55:07: 3000000 INFO @ Wed, 30 Jan 2019 16:55:08: 3000000 INFO @ Wed, 30 Jan 2019 16:55:08: 3000000 INFO @ Wed, 30 Jan 2019 16:55:13: 4000000 INFO @ Wed, 30 Jan 2019 16:55:15: 4000000 INFO @ Wed, 30 Jan 2019 16:55:15: 4000000 INFO @ Wed, 30 Jan 2019 16:55:20: 5000000 INFO @ Wed, 30 Jan 2019 16:55:21: 5000000 INFO @ Wed, 30 Jan 2019 16:55:21: 5000000 INFO @ Wed, 30 Jan 2019 16:55:26: 6000000 INFO @ Wed, 30 Jan 2019 16:55:28: 6000000 INFO @ Wed, 30 Jan 2019 16:55:28: 6000000 INFO @ Wed, 30 Jan 2019 16:55:33: 7000000 INFO @ Wed, 30 Jan 2019 16:55:35: 7000000 INFO @ Wed, 30 Jan 2019 16:55:35: 7000000 INFO @ Wed, 30 Jan 2019 16:55:39: 8000000 INFO @ Wed, 30 Jan 2019 16:55:42: 8000000 INFO @ Wed, 30 Jan 2019 16:55:42: 8000000 INFO @ Wed, 30 Jan 2019 16:55:45: 9000000 INFO @ Wed, 30 Jan 2019 16:55:49: 9000000 INFO @ Wed, 30 Jan 2019 16:55:49: 9000000 INFO @ Wed, 30 Jan 2019 16:55:52: 10000000 INFO @ Wed, 30 Jan 2019 16:55:56: 10000000 INFO @ Wed, 30 Jan 2019 16:55:56: 10000000 INFO @ Wed, 30 Jan 2019 16:55:58: 11000000 INFO @ Wed, 30 Jan 2019 16:56:03: 11000000 INFO @ Wed, 30 Jan 2019 16:56:03: 11000000 INFO @ Wed, 30 Jan 2019 16:56:05: 12000000 INFO @ Wed, 30 Jan 2019 16:56:10: 12000000 INFO @ Wed, 30 Jan 2019 16:56:10: 12000000 INFO @ Wed, 30 Jan 2019 16:56:11: 13000000 INFO @ Wed, 30 Jan 2019 16:56:16: 13000000 INFO @ Wed, 30 Jan 2019 16:56:16: 13000000 INFO @ Wed, 30 Jan 2019 16:56:18: 14000000 INFO @ Wed, 30 Jan 2019 16:56:22: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:56:22: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:56:22: #1 total tags in treatment: 14679930 INFO @ Wed, 30 Jan 2019 16:56:22: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:56:22: #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 16:56:23: #1 tags after filtering in treatment: 14679930 INFO @ Wed, 30 Jan 2019 16:56:23: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:56:23: #1 finished! INFO @ Wed, 30 Jan 2019 16:56:23: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:56:23: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:56:23: 14000000 INFO @ Wed, 30 Jan 2019 16:56:23: 14000000 INFO @ Wed, 30 Jan 2019 16:56:24: #2 number of paired peaks: 1023 INFO @ Wed, 30 Jan 2019 16:56:24: start model_add_line... INFO @ Wed, 30 Jan 2019 16:56:24: start X-correlation... INFO @ Wed, 30 Jan 2019 16:56:24: end of X-cor INFO @ Wed, 30 Jan 2019 16:56:24: #2 finished! INFO @ Wed, 30 Jan 2019 16:56:24: #2 predicted fragment length is 47 bps INFO @ Wed, 30 Jan 2019 16:56:24: #2 alternative fragment length(s) may be 47 bps INFO @ Wed, 30 Jan 2019 16:56:24: #2.2 Generate R script for model : SRX4664653.10_model.r WARNING @ Wed, 30 Jan 2019 16:56:24: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:56:24: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Wed, 30 Jan 2019 16:56:24: #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 16:56:24: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:56:24: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:56:28: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:56:28: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:56:28: #1 total tags in treatment: 14679930 INFO @ Wed, 30 Jan 2019 16:56:28: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:56:28: #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 16:56:28: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 16:56:28: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 16:56:28: #1 total tags in treatment: 14679930 INFO @ Wed, 30 Jan 2019 16:56:28: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 16:56:28: #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 16:56:28: #1 tags after filtering in treatment: 14679930 INFO @ Wed, 30 Jan 2019 16:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:56:28: #1 finished! INFO @ Wed, 30 Jan 2019 16:56:28: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:56:28: #1 tags after filtering in treatment: 14679930 INFO @ Wed, 30 Jan 2019 16:56:28: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 16:56:28: #1 finished! INFO @ Wed, 30 Jan 2019 16:56:28: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 16:56:28: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 16:56:29: #2 number of paired peaks: 1023 INFO @ Wed, 30 Jan 2019 16:56:29: start model_add_line... INFO @ Wed, 30 Jan 2019 16:56:30: start X-correlation... INFO @ Wed, 30 Jan 2019 16:56:30: end of X-cor INFO @ Wed, 30 Jan 2019 16:56:30: #2 finished! INFO @ Wed, 30 Jan 2019 16:56:30: #2 predicted fragment length is 47 bps INFO @ Wed, 30 Jan 2019 16:56:30: #2 alternative fragment length(s) may be 47 bps INFO @ Wed, 30 Jan 2019 16:56:30: #2.2 Generate R script for model : SRX4664653.20_model.r WARNING @ Wed, 30 Jan 2019 16:56:30: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:56:30: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Wed, 30 Jan 2019 16:56:30: #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 16:56:30: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:56:30: #2 number of paired peaks: 1023 INFO @ Wed, 30 Jan 2019 16:56:30: start model_add_line... INFO @ Wed, 30 Jan 2019 16:56:30: start X-correlation... INFO @ Wed, 30 Jan 2019 16:56:30: end of X-cor INFO @ Wed, 30 Jan 2019 16:56:30: #2 finished! INFO @ Wed, 30 Jan 2019 16:56:30: #2 predicted fragment length is 47 bps INFO @ Wed, 30 Jan 2019 16:56:30: #2 alternative fragment length(s) may be 47 bps INFO @ Wed, 30 Jan 2019 16:56:30: #2.2 Generate R script for model : SRX4664653.05_model.r WARNING @ Wed, 30 Jan 2019 16:56:30: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 30 Jan 2019 16:56:30: #2 You may need to consider one of the other alternative d(s): 47 WARNING @ Wed, 30 Jan 2019 16:56:30: #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 16:56:30: #3 Call peaks... INFO @ Wed, 30 Jan 2019 16:56:30: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 16:56:55: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:57:00: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:57:03: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 16:57:12: #4 Write output xls file... SRX4664653.10_peaks.xls INFO @ Wed, 30 Jan 2019 16:57:12: #4 Write peak in narrowPeak format file... SRX4664653.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:57:12: #4 Write summits bed file... SRX4664653.10_summits.bed INFO @ Wed, 30 Jan 2019 16:57:12: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2596 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:57:17: #4 Write output xls file... SRX4664653.20_peaks.xls INFO @ Wed, 30 Jan 2019 16:57:17: #4 Write peak in narrowPeak format file... SRX4664653.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:57:17: #4 Write summits bed file... SRX4664653.20_summits.bed INFO @ Wed, 30 Jan 2019 16:57:17: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1423 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 16:57:19: #4 Write output xls file... SRX4664653.05_peaks.xls INFO @ Wed, 30 Jan 2019 16:57:19: #4 Write peak in narrowPeak format file... SRX4664653.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 16:57:19: #4 Write summits bed file... SRX4664653.05_summits.bed INFO @ Wed, 30 Jan 2019 16:57:19: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3744 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。