Job ID = 11598005 sra ファイルのダウンロード中... Completed: 700351K bytes transferred in 11 seconds (514934K 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 29186201 spots for /home/okishinya/chipatlas/results/dm3/SRX4664660/SRR7813087.sra Written 29186201 spots for /home/okishinya/chipatlas/results/dm3/SRX4664660/SRR7813087.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:12:51 29186201 reads; of these: 29186201 (100.00%) were unpaired; of these: 1030207 (3.53%) aligned 0 times 18411501 (63.08%) aligned exactly 1 time 9744493 (33.39%) aligned >1 times 96.47% overall alignment rate Time searching: 00:12:52 Overall time: 00:12:52 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] 7125427 / 28155994 = 0.2531 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 17:07:42: # Command line: callpeak -t SRX4664660.bam -f BAM -g dm -n SRX4664660.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4664660.10 # format = BAM # ChIP-seq file = ['SRX4664660.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 17:07:42: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:07:42: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:07:42: # Command line: callpeak -t SRX4664660.bam -f BAM -g dm -n SRX4664660.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4664660.05 # format = BAM # ChIP-seq file = ['SRX4664660.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 17:07:42: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:07:42: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:07:42: # Command line: callpeak -t SRX4664660.bam -f BAM -g dm -n SRX4664660.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4664660.20 # format = BAM # ChIP-seq file = ['SRX4664660.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 17:07:42: #1 read tag files... INFO @ Wed, 30 Jan 2019 17:07:42: #1 read treatment tags... INFO @ Wed, 30 Jan 2019 17:07:49: 1000000 INFO @ Wed, 30 Jan 2019 17:07:49: 1000000 INFO @ Wed, 30 Jan 2019 17:07:49: 1000000 INFO @ Wed, 30 Jan 2019 17:07:57: 2000000 INFO @ Wed, 30 Jan 2019 17:07:57: 2000000 INFO @ Wed, 30 Jan 2019 17:07:57: 2000000 INFO @ Wed, 30 Jan 2019 17:08:04: 3000000 INFO @ Wed, 30 Jan 2019 17:08:04: 3000000 INFO @ Wed, 30 Jan 2019 17:08:04: 3000000 INFO @ Wed, 30 Jan 2019 17:08:11: 4000000 INFO @ Wed, 30 Jan 2019 17:08:11: 4000000 INFO @ Wed, 30 Jan 2019 17:08:11: 4000000 INFO @ Wed, 30 Jan 2019 17:08:17: 5000000 INFO @ Wed, 30 Jan 2019 17:08:18: 5000000 INFO @ Wed, 30 Jan 2019 17:08:18: 5000000 INFO @ Wed, 30 Jan 2019 17:08:24: 6000000 INFO @ Wed, 30 Jan 2019 17:08:25: 6000000 INFO @ Wed, 30 Jan 2019 17:08:25: 6000000 INFO @ Wed, 30 Jan 2019 17:08:31: 7000000 INFO @ Wed, 30 Jan 2019 17:08:32: 7000000 INFO @ Wed, 30 Jan 2019 17:08:32: 7000000 INFO @ Wed, 30 Jan 2019 17:08:39: 8000000 INFO @ Wed, 30 Jan 2019 17:08:39: 8000000 INFO @ Wed, 30 Jan 2019 17:08:40: 8000000 INFO @ Wed, 30 Jan 2019 17:08:46: 9000000 INFO @ Wed, 30 Jan 2019 17:08:47: 9000000 INFO @ Wed, 30 Jan 2019 17:08:47: 9000000 INFO @ Wed, 30 Jan 2019 17:08:54: 10000000 INFO @ Wed, 30 Jan 2019 17:08:54: 10000000 INFO @ Wed, 30 Jan 2019 17:08:55: 10000000 INFO @ Wed, 30 Jan 2019 17:09:01: 11000000 INFO @ Wed, 30 Jan 2019 17:09:02: 11000000 INFO @ Wed, 30 Jan 2019 17:09:03: 11000000 INFO @ Wed, 30 Jan 2019 17:09:09: 12000000 INFO @ Wed, 30 Jan 2019 17:09:09: 12000000 INFO @ Wed, 30 Jan 2019 17:09:10: 12000000 INFO @ Wed, 30 Jan 2019 17:09:16: 13000000 INFO @ Wed, 30 Jan 2019 17:09:16: 13000000 INFO @ Wed, 30 Jan 2019 17:09:17: 13000000 INFO @ Wed, 30 Jan 2019 17:09:23: 14000000 INFO @ Wed, 30 Jan 2019 17:09:23: 14000000 INFO @ Wed, 30 Jan 2019 17:09:24: 14000000 INFO @ Wed, 30 Jan 2019 17:09:30: 15000000 INFO @ Wed, 30 Jan 2019 17:09:31: 15000000 INFO @ Wed, 30 Jan 2019 17:09:31: 15000000 INFO @ Wed, 30 Jan 2019 17:09:37: 16000000 INFO @ Wed, 30 Jan 2019 17:09:38: 16000000 INFO @ Wed, 30 Jan 2019 17:09:39: 16000000 INFO @ Wed, 30 Jan 2019 17:09:44: 17000000 INFO @ Wed, 30 Jan 2019 17:09:45: 17000000 INFO @ Wed, 30 Jan 2019 17:09:46: 17000000 INFO @ Wed, 30 Jan 2019 17:09:51: 18000000 INFO @ Wed, 30 Jan 2019 17:09:52: 18000000 INFO @ Wed, 30 Jan 2019 17:09:53: 18000000 INFO @ Wed, 30 Jan 2019 17:09:58: 19000000 INFO @ Wed, 30 Jan 2019 17:09:59: 19000000 INFO @ Wed, 30 Jan 2019 17:10:00: 19000000 INFO @ Wed, 30 Jan 2019 17:10:05: 20000000 INFO @ Wed, 30 Jan 2019 17:10:06: 20000000 INFO @ Wed, 30 Jan 2019 17:10:07: 20000000 INFO @ Wed, 30 Jan 2019 17:10:12: 21000000 INFO @ Wed, 30 Jan 2019 17:10:12: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:10:12: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:10:12: #1 total tags in treatment: 21030567 INFO @ Wed, 30 Jan 2019 17:10:12: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:10:12: #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 17:10:13: #1 tags after filtering in treatment: 21030567 INFO @ Wed, 30 Jan 2019 17:10:13: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:10:13: #1 finished! INFO @ Wed, 30 Jan 2019 17:10:13: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:10:13: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:10:13: 21000000 INFO @ Wed, 30 Jan 2019 17:10:13: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:10:13: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:10:13: #1 total tags in treatment: 21030567 INFO @ Wed, 30 Jan 2019 17:10:13: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:10:13: #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 17:10:14: #1 tags after filtering in treatment: 21030567 INFO @ Wed, 30 Jan 2019 17:10:14: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:10:14: #1 finished! INFO @ Wed, 30 Jan 2019 17:10:14: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:10:14: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:10:14: #2 number of paired peaks: 953 WARNING @ Wed, 30 Jan 2019 17:10:14: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Wed, 30 Jan 2019 17:10:14: start model_add_line... INFO @ Wed, 30 Jan 2019 17:10:14: 21000000 INFO @ Wed, 30 Jan 2019 17:10:14: start X-correlation... INFO @ Wed, 30 Jan 2019 17:10:14: end of X-cor INFO @ Wed, 30 Jan 2019 17:10:14: #2 finished! INFO @ Wed, 30 Jan 2019 17:10:14: #2 predicted fragment length is 126 bps INFO @ Wed, 30 Jan 2019 17:10:14: #2 alternative fragment length(s) may be 4,126 bps INFO @ Wed, 30 Jan 2019 17:10:14: #2.2 Generate R script for model : SRX4664660.10_model.r INFO @ Wed, 30 Jan 2019 17:10:14: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:10:14: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:10:15: #1 tag size is determined as 50 bps INFO @ Wed, 30 Jan 2019 17:10:15: #1 tag size = 50 INFO @ Wed, 30 Jan 2019 17:10:15: #1 total tags in treatment: 21030567 INFO @ Wed, 30 Jan 2019 17:10:15: #1 user defined the maximum tags... INFO @ Wed, 30 Jan 2019 17:10:15: #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 17:10:15: #1 tags after filtering in treatment: 21030567 INFO @ Wed, 30 Jan 2019 17:10:15: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 30 Jan 2019 17:10:15: #1 finished! INFO @ Wed, 30 Jan 2019 17:10:15: #2 Build Peak Model... INFO @ Wed, 30 Jan 2019 17:10:15: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 30 Jan 2019 17:10:15: #2 number of paired peaks: 953 WARNING @ Wed, 30 Jan 2019 17:10:15: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Wed, 30 Jan 2019 17:10:15: start model_add_line... INFO @ Wed, 30 Jan 2019 17:10:16: start X-correlation... INFO @ Wed, 30 Jan 2019 17:10:16: end of X-cor INFO @ Wed, 30 Jan 2019 17:10:16: #2 finished! INFO @ Wed, 30 Jan 2019 17:10:16: #2 predicted fragment length is 126 bps INFO @ Wed, 30 Jan 2019 17:10:16: #2 alternative fragment length(s) may be 4,126 bps INFO @ Wed, 30 Jan 2019 17:10:16: #2.2 Generate R script for model : SRX4664660.20_model.r INFO @ Wed, 30 Jan 2019 17:10:16: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:10:16: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:10:17: #2 number of paired peaks: 953 WARNING @ Wed, 30 Jan 2019 17:10:17: Fewer paired peaks (953) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 953 pairs to build model! INFO @ Wed, 30 Jan 2019 17:10:17: start model_add_line... INFO @ Wed, 30 Jan 2019 17:10:17: start X-correlation... INFO @ Wed, 30 Jan 2019 17:10:17: end of X-cor INFO @ Wed, 30 Jan 2019 17:10:17: #2 finished! INFO @ Wed, 30 Jan 2019 17:10:17: #2 predicted fragment length is 126 bps INFO @ Wed, 30 Jan 2019 17:10:17: #2 alternative fragment length(s) may be 4,126 bps INFO @ Wed, 30 Jan 2019 17:10:17: #2.2 Generate R script for model : SRX4664660.05_model.r INFO @ Wed, 30 Jan 2019 17:10:17: #3 Call peaks... INFO @ Wed, 30 Jan 2019 17:10:17: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 30 Jan 2019 17:10:59: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:10:59: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:11:02: #3 Call peaks for each chromosome... INFO @ Wed, 30 Jan 2019 17:11:23: #4 Write output xls file... SRX4664660.10_peaks.xls INFO @ Wed, 30 Jan 2019 17:11:23: #4 Write peak in narrowPeak format file... SRX4664660.10_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:11:23: #4 Write summits bed file... SRX4664660.10_summits.bed INFO @ Wed, 30 Jan 2019 17:11:23: #4 Write output xls file... SRX4664660.20_peaks.xls INFO @ Wed, 30 Jan 2019 17:11:23: Done! INFO @ Wed, 30 Jan 2019 17:11:23: #4 Write peak in narrowPeak format file... SRX4664660.20_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:11:23: #4 Write summits bed file... SRX4664660.20_summits.bed INFO @ Wed, 30 Jan 2019 17:11:23: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3504 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (2257 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 30 Jan 2019 17:11:25: #4 Write output xls file... SRX4664660.05_peaks.xls INFO @ Wed, 30 Jan 2019 17:11:25: #4 Write peak in narrowPeak format file... SRX4664660.05_peaks.narrowPeak INFO @ Wed, 30 Jan 2019 17:11:25: #4 Write summits bed file... SRX4664660.05_summits.bed INFO @ Wed, 30 Jan 2019 17:11:25: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5603 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。