Job ID = 11240760 sra ファイルのダウンロード中... Completed: 917593K bytes transferred in 14 seconds (528963K 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 53793738 spots for /home/okishinya/chipatlas/results/dm3/SRX4669044/SRR7817569.sra Written 53793738 spots for /home/okishinya/chipatlas/results/dm3/SRX4669044/SRR7817569.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: 00:16:51 53793738 reads; of these: 53793738 (100.00%) were unpaired; of these: 6804669 (12.65%) aligned 0 times 35375263 (65.76%) aligned exactly 1 time 11613806 (21.59%) aligned >1 times 87.35% overall alignment rate Time searching: 00:16:51 Overall time: 00:16:51 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] 18246991 / 46989069 = 0.3883 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 20:58:28: # Command line: callpeak -t SRX4669044.bam -f BAM -g dm -n SRX4669044.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4669044.20 # format = BAM # ChIP-seq file = ['SRX4669044.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 20:58:28: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:58:28: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:58:28: # Command line: callpeak -t SRX4669044.bam -f BAM -g dm -n SRX4669044.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4669044.10 # format = BAM # ChIP-seq file = ['SRX4669044.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 20:58:28: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:58:28: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:58:28: # Command line: callpeak -t SRX4669044.bam -f BAM -g dm -n SRX4669044.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4669044.05 # format = BAM # ChIP-seq file = ['SRX4669044.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 20:58:28: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:58:28: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:58:38: 1000000 INFO @ Sun, 07 Oct 2018 20:58:38: 1000000 INFO @ Sun, 07 Oct 2018 20:58:38: 1000000 INFO @ Sun, 07 Oct 2018 20:58:47: 2000000 INFO @ Sun, 07 Oct 2018 20:58:47: 2000000 INFO @ Sun, 07 Oct 2018 20:58:48: 2000000 INFO @ Sun, 07 Oct 2018 20:58:57: 3000000 INFO @ Sun, 07 Oct 2018 20:58:57: 3000000 INFO @ Sun, 07 Oct 2018 20:58:57: 3000000 INFO @ Sun, 07 Oct 2018 20:59:06: 4000000 INFO @ Sun, 07 Oct 2018 20:59:06: 4000000 INFO @ Sun, 07 Oct 2018 20:59:07: 4000000 INFO @ Sun, 07 Oct 2018 20:59:16: 5000000 INFO @ Sun, 07 Oct 2018 20:59:16: 5000000 INFO @ Sun, 07 Oct 2018 20:59:16: 5000000 INFO @ Sun, 07 Oct 2018 20:59:25: 6000000 INFO @ Sun, 07 Oct 2018 20:59:25: 6000000 INFO @ Sun, 07 Oct 2018 20:59:26: 6000000 INFO @ Sun, 07 Oct 2018 20:59:35: 7000000 INFO @ Sun, 07 Oct 2018 20:59:35: 7000000 INFO @ Sun, 07 Oct 2018 20:59:35: 7000000 INFO @ Sun, 07 Oct 2018 20:59:44: 8000000 INFO @ Sun, 07 Oct 2018 20:59:44: 8000000 INFO @ Sun, 07 Oct 2018 20:59:45: 8000000 INFO @ Sun, 07 Oct 2018 20:59:54: 9000000 INFO @ Sun, 07 Oct 2018 20:59:54: 9000000 INFO @ Sun, 07 Oct 2018 20:59:55: 9000000 INFO @ Sun, 07 Oct 2018 21:00:03: 10000000 INFO @ Sun, 07 Oct 2018 21:00:03: 10000000 INFO @ Sun, 07 Oct 2018 21:00:04: 10000000 INFO @ Sun, 07 Oct 2018 21:00:13: 11000000 INFO @ Sun, 07 Oct 2018 21:00:13: 11000000 INFO @ Sun, 07 Oct 2018 21:00:14: 11000000 INFO @ Sun, 07 Oct 2018 21:00:23: 12000000 INFO @ Sun, 07 Oct 2018 21:00:23: 12000000 INFO @ Sun, 07 Oct 2018 21:00:23: 12000000 INFO @ Sun, 07 Oct 2018 21:00:32: 13000000 INFO @ Sun, 07 Oct 2018 21:00:32: 13000000 INFO @ Sun, 07 Oct 2018 21:00:33: 13000000 INFO @ Sun, 07 Oct 2018 21:00:42: 14000000 INFO @ Sun, 07 Oct 2018 21:00:42: 14000000 INFO @ Sun, 07 Oct 2018 21:00:42: 14000000 INFO @ Sun, 07 Oct 2018 21:00:51: 15000000 INFO @ Sun, 07 Oct 2018 21:00:51: 15000000 INFO @ Sun, 07 Oct 2018 21:00:52: 15000000 INFO @ Sun, 07 Oct 2018 21:01:00: 16000000 INFO @ Sun, 07 Oct 2018 21:01:01: 16000000 INFO @ Sun, 07 Oct 2018 21:01:01: 16000000 INFO @ Sun, 07 Oct 2018 21:01:10: 17000000 INFO @ Sun, 07 Oct 2018 21:01:10: 17000000 INFO @ Sun, 07 Oct 2018 21:01:11: 17000000 INFO @ Sun, 07 Oct 2018 21:01:19: 18000000 INFO @ Sun, 07 Oct 2018 21:01:19: 18000000 INFO @ Sun, 07 Oct 2018 21:01:21: 18000000 INFO @ Sun, 07 Oct 2018 21:01:29: 19000000 INFO @ Sun, 07 Oct 2018 21:01:29: 19000000 INFO @ Sun, 07 Oct 2018 21:01:31: 19000000 INFO @ Sun, 07 Oct 2018 21:01:38: 20000000 INFO @ Sun, 07 Oct 2018 21:01:39: 20000000 INFO @ Sun, 07 Oct 2018 21:01:41: 20000000 INFO @ Sun, 07 Oct 2018 21:01:48: 21000000 INFO @ Sun, 07 Oct 2018 21:01:49: 21000000 INFO @ Sun, 07 Oct 2018 21:01:50: 21000000 INFO @ Sun, 07 Oct 2018 21:01:58: 22000000 INFO @ Sun, 07 Oct 2018 21:01:58: 22000000 INFO @ Sun, 07 Oct 2018 21:02:00: 22000000 INFO @ Sun, 07 Oct 2018 21:02:08: 23000000 INFO @ Sun, 07 Oct 2018 21:02:08: 23000000 INFO @ Sun, 07 Oct 2018 21:02:10: 23000000 INFO @ Sun, 07 Oct 2018 21:02:18: 24000000 INFO @ Sun, 07 Oct 2018 21:02:18: 24000000 INFO @ Sun, 07 Oct 2018 21:02:20: 24000000 INFO @ Sun, 07 Oct 2018 21:02:28: 25000000 INFO @ Sun, 07 Oct 2018 21:02:28: 25000000 INFO @ Sun, 07 Oct 2018 21:02:30: 25000000 INFO @ Sun, 07 Oct 2018 21:02:38: 26000000 INFO @ Sun, 07 Oct 2018 21:02:38: 26000000 INFO @ Sun, 07 Oct 2018 21:02:40: 26000000 INFO @ Sun, 07 Oct 2018 21:02:47: 27000000 INFO @ Sun, 07 Oct 2018 21:02:48: 27000000 INFO @ Sun, 07 Oct 2018 21:02:49: 27000000 INFO @ Sun, 07 Oct 2018 21:02:57: 28000000 INFO @ Sun, 07 Oct 2018 21:02:57: 28000000 INFO @ Sun, 07 Oct 2018 21:02:59: 28000000 INFO @ Sun, 07 Oct 2018 21:03:04: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 21:03:04: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 21:03:04: #1 total tags in treatment: 28742078 INFO @ Sun, 07 Oct 2018 21:03:04: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:03:04: #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 21:03:04: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 21:03:04: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 21:03:04: #1 total tags in treatment: 28742078 INFO @ Sun, 07 Oct 2018 21:03:04: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:03:04: #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 21:03:05: #1 tags after filtering in treatment: 28742078 INFO @ Sun, 07 Oct 2018 21:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:03:05: #1 finished! INFO @ Sun, 07 Oct 2018 21:03:05: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:03:05: #1 tags after filtering in treatment: 28742078 INFO @ Sun, 07 Oct 2018 21:03:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:03:05: #1 finished! INFO @ Sun, 07 Oct 2018 21:03:05: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:03:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:03:06: #1 tag size is determined as 50 bps INFO @ Sun, 07 Oct 2018 21:03:06: #1 tag size = 50 INFO @ Sun, 07 Oct 2018 21:03:06: #1 total tags in treatment: 28742078 INFO @ Sun, 07 Oct 2018 21:03:06: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 21:03:06: #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 21:03:07: #1 tags after filtering in treatment: 28742078 INFO @ Sun, 07 Oct 2018 21:03:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 21:03:07: #1 finished! INFO @ Sun, 07 Oct 2018 21:03:07: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 21:03:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 21:03:07: #2 number of paired peaks: 524 WARNING @ Sun, 07 Oct 2018 21:03:07: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sun, 07 Oct 2018 21:03:07: start model_add_line... INFO @ Sun, 07 Oct 2018 21:03:07: #2 number of paired peaks: 524 WARNING @ Sun, 07 Oct 2018 21:03:07: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sun, 07 Oct 2018 21:03:07: start model_add_line... INFO @ Sun, 07 Oct 2018 21:03:07: start X-correlation... INFO @ Sun, 07 Oct 2018 21:03:07: end of X-cor INFO @ Sun, 07 Oct 2018 21:03:07: #2 finished! INFO @ Sun, 07 Oct 2018 21:03:07: #2 predicted fragment length is 117 bps INFO @ Sun, 07 Oct 2018 21:03:07: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sun, 07 Oct 2018 21:03:07: #2.2 Generate R script for model : SRX4669044.20_model.r INFO @ Sun, 07 Oct 2018 21:03:07: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:03:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:03:07: start X-correlation... INFO @ Sun, 07 Oct 2018 21:03:07: end of X-cor INFO @ Sun, 07 Oct 2018 21:03:07: #2 finished! INFO @ Sun, 07 Oct 2018 21:03:07: #2 predicted fragment length is 117 bps INFO @ Sun, 07 Oct 2018 21:03:07: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sun, 07 Oct 2018 21:03:07: #2.2 Generate R script for model : SRX4669044.10_model.r INFO @ Sun, 07 Oct 2018 21:03:07: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:03:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:03:09: #2 number of paired peaks: 524 WARNING @ Sun, 07 Oct 2018 21:03:09: Fewer paired peaks (524) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 524 pairs to build model! INFO @ Sun, 07 Oct 2018 21:03:09: start model_add_line... INFO @ Sun, 07 Oct 2018 21:03:09: start X-correlation... INFO @ Sun, 07 Oct 2018 21:03:09: end of X-cor INFO @ Sun, 07 Oct 2018 21:03:09: #2 finished! INFO @ Sun, 07 Oct 2018 21:03:09: #2 predicted fragment length is 117 bps INFO @ Sun, 07 Oct 2018 21:03:09: #2 alternative fragment length(s) may be 4,117 bps INFO @ Sun, 07 Oct 2018 21:03:09: #2.2 Generate R script for model : SRX4669044.05_model.r INFO @ Sun, 07 Oct 2018 21:03:09: #3 Call peaks... INFO @ Sun, 07 Oct 2018 21:03:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 21:04:13: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:04:17: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:04:18: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 21:04:46: #4 Write output xls file... SRX4669044.10_peaks.xls INFO @ Sun, 07 Oct 2018 21:04:46: #4 Write peak in narrowPeak format file... SRX4669044.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:04:46: #4 Write summits bed file... SRX4669044.10_summits.bed INFO @ Sun, 07 Oct 2018 21:04:46: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10076 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 21:04:49: #4 Write output xls file... SRX4669044.20_peaks.xls INFO @ Sun, 07 Oct 2018 21:04:49: #4 Write peak in narrowPeak format file... SRX4669044.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:04:49: #4 Write summits bed file... SRX4669044.20_summits.bed INFO @ Sun, 07 Oct 2018 21:04:49: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4825 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 21:04:50: #4 Write output xls file... SRX4669044.05_peaks.xls INFO @ Sun, 07 Oct 2018 21:04:50: #4 Write peak in narrowPeak format file... SRX4669044.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 21:04:50: #4 Write summits bed file... SRX4669044.05_summits.bed INFO @ Sun, 07 Oct 2018 21:04:51: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (15684 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。