Job ID = 11598009 sra ファイルのダウンロード中... Completed: 916809K bytes transferred in 15 seconds (500083K 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 38279615 spots for /home/okishinya/chipatlas/results/dm3/SRX4664664/SRR7813091.sra Written 38279615 spots for /home/okishinya/chipatlas/results/dm3/SRX4664664/SRR7813091.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: 00:18:34 38279615 reads; of these: 38279615 (100.00%) were unpaired; of these: 1368556 (3.58%) aligned 0 times 25629533 (66.95%) aligned exactly 1 time 11281526 (29.47%) aligned >1 times 96.42% overall alignment rate Time searching: 00:18:34 Overall time: 00:18:34 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 16 files... [bam_rmdupse_core] 10058962 / 36911059 = 0.2725 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 17:19:26: # Command line: callpeak -t SRX4664664.bam -f BAM -g dm -n SRX4664664.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664664.05 # format = BAM # ChIP-seq file = ['SRX4664664.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 17:19:26: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:19:26: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:19:26: # Command line: callpeak -t SRX4664664.bam -f BAM -g dm -n SRX4664664.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664664.10 # format = BAM # ChIP-seq file = ['SRX4664664.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 17:19:26: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:19:26: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:19:27: # Command line: callpeak -t SRX4664664.bam -f BAM -g dm -n SRX4664664.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664664.20 # format = BAM # ChIP-seq file = ['SRX4664664.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 17:19:27: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:19:27: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:19:34: 1000000 INFO @ Wed, 30 Jan 2019 17:19:36: 1000000 INFO @ Wed, 30 Jan 2019 17:19:36: 1000000 INFO @ Wed, 30 Jan 2019 17:19:41: 2000000 INFO @ Wed, 30 Jan 2019 17:19:44: 2000000 INFO @ Wed, 30 Jan 2019 17:19:46: 2000000 INFO @ Wed, 30 Jan 2019 17:19:50: 3000000 INFO @ Wed, 30 Jan 2019 17:19:51: 3000000 INFO @ Wed, 30 Jan 2019 17:19:55: 3000000 INFO @ Wed, 30 Jan 2019 17:19:58: 4000000 INFO @ Wed, 30 Jan 2019 17:19:59: 4000000 INFO @ Wed, 30 Jan 2019 17:20:03: 4000000 INFO @ Wed, 30 Jan 2019 17:20:05: 5000000 INFO @ Wed, 30 Jan 2019 17:20:06: 5000000 INFO @ Wed, 30 Jan 2019 17:20:12: 5000000 INFO @ Wed, 30 Jan 2019 17:20:14: 6000000 INFO @ Wed, 30 Jan 2019 17:20:14: 6000000 INFO @ Wed, 30 Jan 2019 17:20:20: 6000000 INFO @ Wed, 30 Jan 2019 17:20:22: 7000000 INFO @ Wed, 30 Jan 2019 17:20:23: 7000000 INFO @ Wed, 30 Jan 2019 17:20:29: 7000000 INFO @ Wed, 30 Jan 2019 17:20:29: 8000000 INFO @ Wed, 30 Jan 2019 17:20:31: 8000000 INFO @ Wed, 30 Jan 2019 17:20:37: 8000000 INFO @ Wed, 30 Jan 2019 17:20:38: 9000000 INFO @ Wed, 30 Jan 2019 17:20:40: 9000000 INFO @ Wed, 30 Jan 2019 17:20:46: 9000000 INFO @ Wed, 30 Jan 2019 17:20:47: 10000000 INFO @ Wed, 30 Jan 2019 17:20:47: 10000000 INFO @ Wed, 30 Jan 2019 17:20:54: 11000000 INFO @ Wed, 30 Jan 2019 17:20:55: 11000000 INFO @ Wed, 30 Jan 2019 17:20:55: 10000000 INFO @ Wed, 30 Jan 2019 17:21:01: 12000000 INFO @ Wed, 30 Jan 2019 17:21:02: 12000000 INFO @ Wed, 30 Jan 2019 17:21:03: 11000000 INFO @ Wed, 30 Jan 2019 17:21:08: 13000000 INFO @ Wed, 30 Jan 2019 17:21:10: 13000000 INFO @ Wed, 30 Jan 2019 17:21:11: 12000000 INFO @ Wed, 30 Jan 2019 17:21:16: 14000000 INFO @ Wed, 30 Jan 2019 17:21:18: 14000000 INFO @ Wed, 30 Jan 2019 17:21:20: 13000000 INFO @ Wed, 30 Jan 2019 17:21:24: 15000000 INFO @ Wed, 30 Jan 2019 17:21:25: 15000000 INFO @ Wed, 30 Jan 2019 17:21:28: 14000000 INFO @ Wed, 30 Jan 2019 17:21:33: 16000000 INFO @ Wed, 30 Jan 2019 17:21:33: 16000000 INFO @ Wed, 30 Jan 2019 17:21:37: 15000000 INFO @ Wed, 30 Jan 2019 17:21:41: 17000000 INFO @ Wed, 30 Jan 2019 17:21:42: 17000000 INFO @ Wed, 30 Jan 2019 17:21:44: 16000000 INFO @ Wed, 30 Jan 2019 17:21:50: 18000000 INFO @ Wed, 30 Jan 2019 17:21:50: 18000000 INFO @ Wed, 30 Jan 2019 17:21:52: 17000000 INFO @ Wed, 30 Jan 2019 17:21:59: 19000000 INFO @ Wed, 30 Jan 2019 17:21:59: 19000000 INFO @ Wed, 30 Jan 2019 17:22:01: 18000000 INFO @ Wed, 30 Jan 2019 17:22:07: 20000000 INFO @ Wed, 30 Jan 2019 17:22:07: 20000000 INFO @ Wed, 30 Jan 2019 17:22:09: 19000000 INFO @ Wed, 30 Jan 2019 17:22:15: 21000000 INFO @ Wed, 30 Jan 2019 17:22:17: 20000000 INFO @ Wed, 30 Jan 2019 17:22:18: 21000000 INFO @ Wed, 30 Jan 2019 17:22:24: 22000000 INFO @ Wed, 30 Jan 2019 17:22:26: 21000000 INFO @ Wed, 30 Jan 2019 17:22:26: 22000000 INFO @ Wed, 30 Jan 2019 17:22:31: 23000000 INFO @ Wed, 30 Jan 2019 17:22:34: 22000000 INFO @ Wed, 30 Jan 2019 17:22:34: 23000000 INFO @ Wed, 30 Jan 2019 17:22:38: 24000000 INFO @ Wed, 30 Jan 2019 17:22:42: 23000000 INFO @ Wed, 30 Jan 2019 17:22:45: 24000000 INFO @ Wed, 30 Jan 2019 17:22:46: 25000000 INFO @ Wed, 30 Jan 2019 17:22:49: 24000000 INFO @ Wed, 30 Jan 2019 17:22:53: 25000000 INFO @ Wed, 30 Jan 2019 17:22:54: 26000000 INFO @ Wed, 30 Jan 2019 17:22:58: 25000000 INFO @ Wed, 30 Jan 2019 17:23:00: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:23:00: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:23:00: #1 total tags in treatment: 26852097 INFO @ Wed, 30 Jan 2019 17:23:00: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:23:00: #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 17:23:00: #1 tags after filtering in treatment: 26852097 INFO @ Wed, 30 Jan 2019 17:23:00: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:23:00: #1 finished! INFO @ Wed, 30 Jan 2019 17:23:00: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:23:00: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:23:02: 26000000 INFO @ Wed, 30 Jan 2019 17:23:02: #2 number of paired peaks: 492 WARNING @ Wed, 30 Jan 2019 17:23:02: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Wed, 30 Jan 2019 17:23:02: start model_add_line... INFO @ Wed, 30 Jan 2019 17:23:03: start X-correlation... INFO @ Wed, 30 Jan 2019 17:23:03: end of X-cor INFO @ Wed, 30 Jan 2019 17:23:03: #2 finished! INFO @ Wed, 30 Jan 2019 17:23:03: #2 predicted fragment length is 153 bps INFO @ Wed, 30 Jan 2019 17:23:03: #2 alternative fragment length(s) may be 153,166 bps INFO @ Wed, 30 Jan 2019 17:23:03: #2.2 Generate R script for model : SRX4664664.10_model.r INFO @ Wed, 30 Jan 2019 17:23:03: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:23:03: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:23:08: 26000000 INFO @ Wed, 30 Jan 2019 17:23:10: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:23:10: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:23:10: #1 total tags in treatment: 26852097 INFO @ Wed, 30 Jan 2019 17:23:10: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:23:10: #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 17:23:10: #1 tags after filtering in treatment: 26852097 INFO @ Wed, 30 Jan 2019 17:23:10: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:23:10: #1 finished! INFO @ Wed, 30 Jan 2019 17:23:10: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:23:13: #2 number of paired peaks: 492 WARNING @ Wed, 30 Jan 2019 17:23:13: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Wed, 30 Jan 2019 17:23:13: start model_add_line... INFO @ Wed, 30 Jan 2019 17:23:13: start X-correlation... INFO @ Wed, 30 Jan 2019 17:23:13: end of X-cor INFO @ Wed, 30 Jan 2019 17:23:13: #2 finished! INFO @ Wed, 30 Jan 2019 17:23:13: #2 predicted fragment length is 153 bps INFO @ Wed, 30 Jan 2019 17:23:13: #2 alternative fragment length(s) may be 153,166 bps INFO @ Wed, 30 Jan 2019 17:23:13: #2.2 Generate R script for model : SRX4664664.20_model.r INFO @ Wed, 30 Jan 2019 17:23:13: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:23:13: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:23:15: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:23:15: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:23:15: #1 total tags in treatment: 26852097 INFO @ Wed, 30 Jan 2019 17:23:15: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:23:15: #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 17:23:16: #1 tags after filtering in treatment: 26852097 INFO @ Wed, 30 Jan 2019 17:23:16: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:23:16: #1 finished! INFO @ Wed, 30 Jan 2019 17:23:16: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:23:16: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:23:18: #2 number of paired peaks: 492 WARNING @ Wed, 30 Jan 2019 17:23:18: Fewer paired peaks (492) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 492 pairs to build model! INFO @ Wed, 30 Jan 2019 17:23:18: start model_add_line... INFO @ Wed, 30 Jan 2019 17:23:19: start X-correlation... INFO @ Wed, 30 Jan 2019 17:23:19: end of X-cor INFO @ Wed, 30 Jan 2019 17:23:19: #2 finished! INFO @ Wed, 30 Jan 2019 17:23:19: #2 predicted fragment length is 153 bps INFO @ Wed, 30 Jan 2019 17:23:19: #2 alternative fragment length(s) may be 153,166 bps INFO @ Wed, 30 Jan 2019 17:23:19: #2.2 Generate R script for model : SRX4664664.05_model.r INFO @ Wed, 30 Jan 2019 17:23:19: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:23:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:24:10: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:24:16: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:24:24: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:24:41: #4 Write output xls file... SRX4664664.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:24:41: #4 Write peak in narrowPeak format file... SRX4664664.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:24:41: #4 Write summits bed file... SRX4664664.10_summits.bed INFO @ Wed, 30 Jan 2019 17:24:41: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4437 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:24:49: #4 Write output xls file... SRX4664664.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:24:49: #4 Write peak in narrowPeak format file... SRX4664664.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:24:49: #4 Write summits bed file... SRX4664664.20_summits.bed INFO @ Wed, 30 Jan 2019 17:24:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2628 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:24:58: #4 Write output xls file... SRX4664664.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:24:58: #4 Write peak in narrowPeak format file... SRX4664664.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:24:58: #4 Write summits bed file... SRX4664664.05_summits.bed INFO @ Wed, 30 Jan 2019 17:24:58: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6562 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。