Job ID = 10609122 sra ファイルのダウンロード中... Completed: 572084K bytes transferred in 49 seconds (94950K 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... 2018-05-03T22:00:32 fastq-dump.2.9.0 int: no error - skipping the cache-tee completely Read 37493028 spots for /home/okishinya/chipatlas/results/dm3/SRX3011267/SRR5834743.sra Written 37493028 spots for /home/okishinya/chipatlas/results/dm3/SRX3011267/SRR5834743.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: 00:09:05 37493028 reads; of these: 37493028 (100.00%) were unpaired; of these: 6171803 (16.46%) aligned 0 times 23840251 (63.59%) aligned exactly 1 time 7480974 (19.95%) aligned >1 times 83.54% overall alignment rate Time searching: 00:09:05 Overall time: 00:09:05 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] 8279286 / 31321225 = 0.2643 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 @ Fri, 04 May 2018 07:19:22: # Command line: callpeak -t SRX3011267.bam -f BAM -g dm -n SRX3011267.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011267.10 # format = BAM # ChIP-seq file = ['SRX3011267.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 @ Fri, 04 May 2018 07:19:22: #1 read tag files... INFO @ Fri, 04 May 2018 07:19:22: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:19:22: # Command line: callpeak -t SRX3011267.bam -f BAM -g dm -n SRX3011267.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011267.05 # format = BAM # ChIP-seq file = ['SRX3011267.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 @ Fri, 04 May 2018 07:19:22: #1 read tag files... INFO @ Fri, 04 May 2018 07:19:22: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:19:22: # Command line: callpeak -t SRX3011267.bam -f BAM -g dm -n SRX3011267.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011267.20 # format = BAM # ChIP-seq file = ['SRX3011267.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 @ Fri, 04 May 2018 07:19:22: #1 read tag files... INFO @ Fri, 04 May 2018 07:19:22: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:19:28: 1000000 INFO @ Fri, 04 May 2018 07:19:28: 1000000 INFO @ Fri, 04 May 2018 07:19:28: 1000000 INFO @ Fri, 04 May 2018 07:19:34: 2000000 INFO @ Fri, 04 May 2018 07:19:34: 2000000 INFO @ Fri, 04 May 2018 07:19:35: 2000000 INFO @ Fri, 04 May 2018 07:19:40: 3000000 INFO @ Fri, 04 May 2018 07:19:41: 3000000 INFO @ Fri, 04 May 2018 07:19:42: 3000000 INFO @ Fri, 04 May 2018 07:19:46: 4000000 INFO @ Fri, 04 May 2018 07:19:47: 4000000 INFO @ Fri, 04 May 2018 07:19:49: 4000000 INFO @ Fri, 04 May 2018 07:19:53: 5000000 INFO @ Fri, 04 May 2018 07:19:54: 5000000 INFO @ Fri, 04 May 2018 07:19:56: 5000000 INFO @ Fri, 04 May 2018 07:19:59: 6000000 INFO @ Fri, 04 May 2018 07:20:01: 6000000 INFO @ Fri, 04 May 2018 07:20:03: 6000000 INFO @ Fri, 04 May 2018 07:20:06: 7000000 INFO @ Fri, 04 May 2018 07:20:07: 7000000 INFO @ Fri, 04 May 2018 07:20:10: 7000000 INFO @ Fri, 04 May 2018 07:20:12: 8000000 INFO @ Fri, 04 May 2018 07:20:14: 8000000 INFO @ Fri, 04 May 2018 07:20:16: 8000000 INFO @ Fri, 04 May 2018 07:20:19: 9000000 INFO @ Fri, 04 May 2018 07:20:21: 9000000 INFO @ Fri, 04 May 2018 07:20:23: 9000000 INFO @ Fri, 04 May 2018 07:20:25: 10000000 INFO @ Fri, 04 May 2018 07:20:27: 10000000 INFO @ Fri, 04 May 2018 07:20:30: 10000000 INFO @ Fri, 04 May 2018 07:20:31: 11000000 INFO @ Fri, 04 May 2018 07:20:33: 11000000 INFO @ Fri, 04 May 2018 07:20:36: 11000000 INFO @ Fri, 04 May 2018 07:20:37: 12000000 INFO @ Fri, 04 May 2018 07:20:39: 12000000 INFO @ Fri, 04 May 2018 07:20:42: 12000000 INFO @ Fri, 04 May 2018 07:20:43: 13000000 INFO @ Fri, 04 May 2018 07:20:46: 13000000 INFO @ Fri, 04 May 2018 07:20:48: 13000000 INFO @ Fri, 04 May 2018 07:20:49: 14000000 INFO @ Fri, 04 May 2018 07:20:52: 14000000 INFO @ Fri, 04 May 2018 07:20:54: 14000000 INFO @ Fri, 04 May 2018 07:20:55: 15000000 INFO @ Fri, 04 May 2018 07:20:58: 15000000 INFO @ Fri, 04 May 2018 07:21:01: 15000000 INFO @ Fri, 04 May 2018 07:21:01: 16000000 INFO @ Fri, 04 May 2018 07:21:04: 16000000 INFO @ Fri, 04 May 2018 07:21:07: 16000000 INFO @ Fri, 04 May 2018 07:21:07: 17000000 INFO @ Fri, 04 May 2018 07:21:10: 17000000 INFO @ Fri, 04 May 2018 07:21:13: 17000000 INFO @ Fri, 04 May 2018 07:21:13: 18000000 INFO @ Fri, 04 May 2018 07:21:17: 18000000 INFO @ Fri, 04 May 2018 07:21:19: 18000000 INFO @ Fri, 04 May 2018 07:21:19: 19000000 INFO @ Fri, 04 May 2018 07:21:23: 19000000 INFO @ Fri, 04 May 2018 07:21:25: 20000000 INFO @ Fri, 04 May 2018 07:21:25: 19000000 INFO @ Fri, 04 May 2018 07:21:29: 20000000 INFO @ Fri, 04 May 2018 07:21:31: 21000000 INFO @ Fri, 04 May 2018 07:21:32: 20000000 INFO @ Fri, 04 May 2018 07:21:35: 21000000 INFO @ Fri, 04 May 2018 07:21:37: 22000000 INFO @ Fri, 04 May 2018 07:21:38: 21000000 INFO @ Fri, 04 May 2018 07:21:41: 22000000 INFO @ Fri, 04 May 2018 07:21:43: 23000000 INFO @ Fri, 04 May 2018 07:21:43: #1 tag size is determined as 40 bps INFO @ Fri, 04 May 2018 07:21:43: #1 tag size = 40 INFO @ Fri, 04 May 2018 07:21:43: #1 total tags in treatment: 23041939 INFO @ Fri, 04 May 2018 07:21:43: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:21:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:21:44: #1 tags after filtering in treatment: 23041939 INFO @ Fri, 04 May 2018 07:21:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:21:44: #1 finished! INFO @ Fri, 04 May 2018 07:21:44: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:21:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:21:44: 22000000 INFO @ Fri, 04 May 2018 07:21:45: #2 number of paired peaks: 521 WARNING @ Fri, 04 May 2018 07:21:45: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Fri, 04 May 2018 07:21:45: start model_add_line... INFO @ Fri, 04 May 2018 07:21:46: start X-correlation... INFO @ Fri, 04 May 2018 07:21:46: end of X-cor INFO @ Fri, 04 May 2018 07:21:46: #2 finished! INFO @ Fri, 04 May 2018 07:21:46: #2 predicted fragment length is 121 bps INFO @ Fri, 04 May 2018 07:21:46: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 04 May 2018 07:21:46: #2.2 Generate R script for model : SRX3011267.05_model.r INFO @ Fri, 04 May 2018 07:21:46: #3 Call peaks... INFO @ Fri, 04 May 2018 07:21:46: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:21:47: 23000000 INFO @ Fri, 04 May 2018 07:21:48: #1 tag size is determined as 40 bps INFO @ Fri, 04 May 2018 07:21:48: #1 tag size = 40 INFO @ Fri, 04 May 2018 07:21:48: #1 total tags in treatment: 23041939 INFO @ Fri, 04 May 2018 07:21:48: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:21:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:21:48: #1 tags after filtering in treatment: 23041939 INFO @ Fri, 04 May 2018 07:21:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:21:48: #1 finished! INFO @ Fri, 04 May 2018 07:21:48: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:21:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:21:50: #2 number of paired peaks: 521 WARNING @ Fri, 04 May 2018 07:21:50: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Fri, 04 May 2018 07:21:50: start model_add_line... INFO @ Fri, 04 May 2018 07:21:50: start X-correlation... INFO @ Fri, 04 May 2018 07:21:50: end of X-cor INFO @ Fri, 04 May 2018 07:21:50: #2 finished! INFO @ Fri, 04 May 2018 07:21:50: #2 predicted fragment length is 121 bps INFO @ Fri, 04 May 2018 07:21:50: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 04 May 2018 07:21:50: #2.2 Generate R script for model : SRX3011267.10_model.r INFO @ Fri, 04 May 2018 07:21:50: #3 Call peaks... INFO @ Fri, 04 May 2018 07:21:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:21:50: 23000000 INFO @ Fri, 04 May 2018 07:21:51: #1 tag size is determined as 40 bps INFO @ Fri, 04 May 2018 07:21:51: #1 tag size = 40 INFO @ Fri, 04 May 2018 07:21:51: #1 total tags in treatment: 23041939 INFO @ Fri, 04 May 2018 07:21:51: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:21:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:21:51: #1 tags after filtering in treatment: 23041939 INFO @ Fri, 04 May 2018 07:21:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:21:51: #1 finished! INFO @ Fri, 04 May 2018 07:21:51: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:21:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:21:53: #2 number of paired peaks: 521 WARNING @ Fri, 04 May 2018 07:21:53: Fewer paired peaks (521) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 521 pairs to build model! INFO @ Fri, 04 May 2018 07:21:53: start model_add_line... INFO @ Fri, 04 May 2018 07:21:53: start X-correlation... INFO @ Fri, 04 May 2018 07:21:53: end of X-cor INFO @ Fri, 04 May 2018 07:21:53: #2 finished! INFO @ Fri, 04 May 2018 07:21:53: #2 predicted fragment length is 121 bps INFO @ Fri, 04 May 2018 07:21:53: #2 alternative fragment length(s) may be 121 bps INFO @ Fri, 04 May 2018 07:21:53: #2.2 Generate R script for model : SRX3011267.20_model.r INFO @ Fri, 04 May 2018 07:21:53: #3 Call peaks... INFO @ Fri, 04 May 2018 07:21:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:22:38: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:22:39: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:22:41: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:23:05: #4 Write output xls file... SRX3011267.05_peaks.xls INFO @ Fri, 04 May 2018 07:23:05: #4 Write peak in narrowPeak format file... SRX3011267.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:23:05: #4 Write summits bed file... SRX3011267.05_summits.bed INFO @ Fri, 04 May 2018 07:23:05: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (12678 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:23:06: #4 Write output xls file... SRX3011267.10_peaks.xls INFO @ Fri, 04 May 2018 07:23:06: #4 Write peak in narrowPeak format file... SRX3011267.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:23:06: #4 Write summits bed file... SRX3011267.10_summits.bed INFO @ Fri, 04 May 2018 07:23:06: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (7922 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:23:09: #4 Write output xls file... SRX3011267.20_peaks.xls INFO @ Fri, 04 May 2018 07:23:09: #4 Write peak in narrowPeak format file... SRX3011267.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:23:09: #4 Write summits bed file... SRX3011267.20_summits.bed INFO @ Fri, 04 May 2018 07:23:09: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3550 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。