Job ID = 10609119 sra ファイルのダウンロード中... Completed: 641062K bytes transferred in 51 seconds (102376K 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 30637517 spots for /home/okishinya/chipatlas/results/dm3/SRX3011257/SRR5834734.sra Written 30637517 spots for /home/okishinya/chipatlas/results/dm3/SRX3011257/SRR5834734.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:40 30637517 reads; of these: 30637517 (100.00%) were unpaired; of these: 360233 (1.18%) aligned 0 times 29529573 (96.38%) aligned exactly 1 time 747711 (2.44%) aligned >1 times 98.82% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 5824301 / 30277284 = 0.1924 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 07:16:54: # Command line: callpeak -t SRX3011257.bam -f BAM -g dm -n SRX3011257.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011257.05 # format = BAM # ChIP-seq file = ['SRX3011257.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 07:16:54: #1 read tag files... INFO @ Fri, 04 May 2018 07:16:54: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:16:54: # Command line: callpeak -t SRX3011257.bam -f BAM -g dm -n SRX3011257.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011257.10 # format = BAM # ChIP-seq file = ['SRX3011257.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 07:16:54: #1 read tag files... INFO @ Fri, 04 May 2018 07:16:54: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:16:54: # Command line: callpeak -t SRX3011257.bam -f BAM -g dm -n SRX3011257.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011257.20 # format = BAM # ChIP-seq file = ['SRX3011257.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 07:16:54: #1 read tag files... INFO @ Fri, 04 May 2018 07:16:54: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:17:01: 1000000 INFO @ Fri, 04 May 2018 07:17:01: 1000000 INFO @ Fri, 04 May 2018 07:17:01: 1000000 INFO @ Fri, 04 May 2018 07:17:07: 2000000 INFO @ Fri, 04 May 2018 07:17:07: 2000000 INFO @ Fri, 04 May 2018 07:17:08: 2000000 INFO @ Fri, 04 May 2018 07:17:14: 3000000 INFO @ Fri, 04 May 2018 07:17:14: 3000000 INFO @ Fri, 04 May 2018 07:17:15: 3000000 INFO @ Fri, 04 May 2018 07:17:20: 4000000 INFO @ Fri, 04 May 2018 07:17:21: 4000000 INFO @ Fri, 04 May 2018 07:17:22: 4000000 INFO @ Fri, 04 May 2018 07:17:26: 5000000 INFO @ Fri, 04 May 2018 07:17:27: 5000000 INFO @ Fri, 04 May 2018 07:17:29: 5000000 INFO @ Fri, 04 May 2018 07:17:33: 6000000 INFO @ Fri, 04 May 2018 07:17:34: 6000000 INFO @ Fri, 04 May 2018 07:17:36: 6000000 INFO @ Fri, 04 May 2018 07:17:39: 7000000 INFO @ Fri, 04 May 2018 07:17:40: 7000000 INFO @ Fri, 04 May 2018 07:17:43: 7000000 INFO @ Fri, 04 May 2018 07:17:45: 8000000 INFO @ Fri, 04 May 2018 07:17:47: 8000000 INFO @ Fri, 04 May 2018 07:17:51: 8000000 INFO @ Fri, 04 May 2018 07:17:51: 9000000 INFO @ Fri, 04 May 2018 07:17:54: 9000000 INFO @ Fri, 04 May 2018 07:17:58: 9000000 INFO @ Fri, 04 May 2018 07:17:58: 10000000 INFO @ Fri, 04 May 2018 07:18:00: 10000000 INFO @ Fri, 04 May 2018 07:18:04: 11000000 INFO @ Fri, 04 May 2018 07:18:05: 10000000 INFO @ Fri, 04 May 2018 07:18:07: 11000000 INFO @ Fri, 04 May 2018 07:18:10: 12000000 INFO @ Fri, 04 May 2018 07:18:12: 11000000 INFO @ Fri, 04 May 2018 07:18:14: 12000000 INFO @ Fri, 04 May 2018 07:18:16: 13000000 INFO @ Fri, 04 May 2018 07:18:19: 12000000 INFO @ Fri, 04 May 2018 07:18:20: 13000000 INFO @ Fri, 04 May 2018 07:18:23: 14000000 INFO @ Fri, 04 May 2018 07:18:26: 13000000 INFO @ Fri, 04 May 2018 07:18:27: 14000000 INFO @ Fri, 04 May 2018 07:18:29: 15000000 INFO @ Fri, 04 May 2018 07:18:33: 14000000 INFO @ Fri, 04 May 2018 07:18:33: 15000000 INFO @ Fri, 04 May 2018 07:18:35: 16000000 INFO @ Fri, 04 May 2018 07:18:40: 16000000 INFO @ Fri, 04 May 2018 07:18:40: 15000000 INFO @ Fri, 04 May 2018 07:18:41: 17000000 INFO @ Fri, 04 May 2018 07:18:47: 17000000 INFO @ Fri, 04 May 2018 07:18:47: 16000000 INFO @ Fri, 04 May 2018 07:18:48: 18000000 INFO @ Fri, 04 May 2018 07:18:53: 18000000 INFO @ Fri, 04 May 2018 07:18:54: 19000000 INFO @ Fri, 04 May 2018 07:18:54: 17000000 INFO @ Fri, 04 May 2018 07:19:00: 19000000 INFO @ Fri, 04 May 2018 07:19:00: 20000000 INFO @ Fri, 04 May 2018 07:19:01: 18000000 INFO @ Fri, 04 May 2018 07:19:06: 21000000 INFO @ Fri, 04 May 2018 07:19:07: 20000000 INFO @ Fri, 04 May 2018 07:19:09: 19000000 INFO @ Fri, 04 May 2018 07:19:13: 22000000 INFO @ Fri, 04 May 2018 07:19:13: 21000000 INFO @ Fri, 04 May 2018 07:19:16: 20000000 INFO @ Fri, 04 May 2018 07:19:19: 23000000 INFO @ Fri, 04 May 2018 07:19:20: 22000000 INFO @ Fri, 04 May 2018 07:19:23: 21000000 INFO @ Fri, 04 May 2018 07:19:25: 24000000 INFO @ Fri, 04 May 2018 07:19:27: 23000000 INFO @ Fri, 04 May 2018 07:19:28: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:19:28: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:19:28: #1 total tags in treatment: 24452983 INFO @ Fri, 04 May 2018 07:19:28: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:19:28: #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 07:19:29: #1 tags after filtering in treatment: 24452983 INFO @ Fri, 04 May 2018 07:19:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:19:29: #1 finished! INFO @ Fri, 04 May 2018 07:19:29: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:19:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:19:30: 22000000 INFO @ Fri, 04 May 2018 07:19:31: #2 number of paired peaks: 109 WARNING @ Fri, 04 May 2018 07:19:31: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Fri, 04 May 2018 07:19:31: start model_add_line... INFO @ Fri, 04 May 2018 07:19:31: start X-correlation... INFO @ Fri, 04 May 2018 07:19:31: end of X-cor INFO @ Fri, 04 May 2018 07:19:31: #2 finished! INFO @ Fri, 04 May 2018 07:19:31: #2 predicted fragment length is 131 bps INFO @ Fri, 04 May 2018 07:19:31: #2 alternative fragment length(s) may be 4,131,148,167 bps INFO @ Fri, 04 May 2018 07:19:31: #2.2 Generate R script for model : SRX3011257.05_model.r INFO @ Fri, 04 May 2018 07:19:31: #3 Call peaks... INFO @ Fri, 04 May 2018 07:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:19:34: 24000000 INFO @ Fri, 04 May 2018 07:19:37: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:19:37: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:19:37: #1 total tags in treatment: 24452983 INFO @ Fri, 04 May 2018 07:19:37: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:19:37: #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 07:19:37: 23000000 INFO @ Fri, 04 May 2018 07:19:38: #1 tags after filtering in treatment: 24452983 INFO @ Fri, 04 May 2018 07:19:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:19:38: #1 finished! INFO @ Fri, 04 May 2018 07:19:38: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:19:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:19:39: #2 number of paired peaks: 109 WARNING @ Fri, 04 May 2018 07:19:39: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Fri, 04 May 2018 07:19:39: start model_add_line... INFO @ Fri, 04 May 2018 07:19:39: start X-correlation... INFO @ Fri, 04 May 2018 07:19:39: end of X-cor INFO @ Fri, 04 May 2018 07:19:39: #2 finished! INFO @ Fri, 04 May 2018 07:19:39: #2 predicted fragment length is 131 bps INFO @ Fri, 04 May 2018 07:19:39: #2 alternative fragment length(s) may be 4,131,148,167 bps INFO @ Fri, 04 May 2018 07:19:39: #2.2 Generate R script for model : SRX3011257.10_model.r INFO @ Fri, 04 May 2018 07:19:39: #3 Call peaks... INFO @ Fri, 04 May 2018 07:19:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:19:44: 24000000 INFO @ Fri, 04 May 2018 07:19:47: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:19:47: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:19:47: #1 total tags in treatment: 24452983 INFO @ Fri, 04 May 2018 07:19:47: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:19:47: #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 07:19:48: #1 tags after filtering in treatment: 24452983 INFO @ Fri, 04 May 2018 07:19:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:19:48: #1 finished! INFO @ Fri, 04 May 2018 07:19:48: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:19:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:19:49: #2 number of paired peaks: 109 WARNING @ Fri, 04 May 2018 07:19:49: Fewer paired peaks (109) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 109 pairs to build model! INFO @ Fri, 04 May 2018 07:19:49: start model_add_line... INFO @ Fri, 04 May 2018 07:19:50: start X-correlation... INFO @ Fri, 04 May 2018 07:19:50: end of X-cor INFO @ Fri, 04 May 2018 07:19:50: #2 finished! INFO @ Fri, 04 May 2018 07:19:50: #2 predicted fragment length is 131 bps INFO @ Fri, 04 May 2018 07:19:50: #2 alternative fragment length(s) may be 4,131,148,167 bps INFO @ Fri, 04 May 2018 07:19:50: #2.2 Generate R script for model : SRX3011257.20_model.r INFO @ Fri, 04 May 2018 07:19:50: #3 Call peaks... INFO @ Fri, 04 May 2018 07:19:50: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:20:22: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:20:28: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:20:42: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:20:47: #4 Write output xls file... SRX3011257.05_peaks.xls INFO @ Fri, 04 May 2018 07:20:47: #4 Write peak in narrowPeak format file... SRX3011257.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:20:47: #4 Write summits bed file... SRX3011257.05_summits.bed INFO @ Fri, 04 May 2018 07:20:47: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4560 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:20:53: #4 Write output xls file... SRX3011257.10_peaks.xls INFO @ Fri, 04 May 2018 07:20:53: #4 Write peak in narrowPeak format file... SRX3011257.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:20:53: #4 Write summits bed file... SRX3011257.10_summits.bed INFO @ Fri, 04 May 2018 07:20:53: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (978 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:21:06: #4 Write output xls file... SRX3011257.20_peaks.xls INFO @ Fri, 04 May 2018 07:21:06: #4 Write peak in narrowPeak format file... SRX3011257.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:21:06: #4 Write summits bed file... SRX3011257.20_summits.bed INFO @ Fri, 04 May 2018 07:21:06: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (82 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。