Job ID = 9159840 sra ファイルのダウンロード中... Completed: 914460K bytes transferred in 10 seconds (729260K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 14658841 spots for /home/okishinya/chipatlas/results/dm3/SRX749023/SRR1636751.sra Written 14658841 spots total 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: 00:00:01 Multiseed full-index search: 00:30:35 14658841 reads; of these: 14658841 (100.00%) were paired; of these: 2288163 (15.61%) aligned concordantly 0 times 9289114 (63.37%) aligned concordantly exactly 1 time 3081564 (21.02%) aligned concordantly >1 times ---- 2288163 pairs aligned concordantly 0 times; of these: 43792 (1.91%) aligned discordantly 1 time ---- 2244371 pairs aligned 0 times concordantly or discordantly; of these: 4488742 mates make up the pairs; of these: 4150778 (92.47%) aligned 0 times 244243 (5.44%) aligned exactly 1 time 93721 (2.09%) aligned >1 times 85.84% overall alignment rate Time searching: 00:30:36 Overall time: 00:30:36 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1410128 / 12406066 = 0.1137 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, 28 Jun 2017 00:50:10: # Command line: callpeak -t SRX749023.bam -f BAM -g dm -n SRX749023.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749023.10 # format = BAM # ChIP-seq file = ['SRX749023.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, 28 Jun 2017 00:50:10: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:50:10: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:50:10: # Command line: callpeak -t SRX749023.bam -f BAM -g dm -n SRX749023.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749023.05 # format = BAM # ChIP-seq file = ['SRX749023.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, 28 Jun 2017 00:50:10: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:50:10: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:50:10: # Command line: callpeak -t SRX749023.bam -f BAM -g dm -n SRX749023.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749023.20 # format = BAM # ChIP-seq file = ['SRX749023.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, 28 Jun 2017 00:50:10: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:50:10: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:50:16: 1000000 INFO @ Wed, 28 Jun 2017 00:50:16: 1000000 INFO @ Wed, 28 Jun 2017 00:50:16: 1000000 INFO @ Wed, 28 Jun 2017 00:50:22: 2000000 INFO @ Wed, 28 Jun 2017 00:50:22: 2000000 INFO @ Wed, 28 Jun 2017 00:50:22: 2000000 INFO @ Wed, 28 Jun 2017 00:50:27: 3000000 INFO @ Wed, 28 Jun 2017 00:50:28: 3000000 INFO @ Wed, 28 Jun 2017 00:50:28: 3000000 INFO @ Wed, 28 Jun 2017 00:50:33: 4000000 INFO @ Wed, 28 Jun 2017 00:50:34: 4000000 INFO @ Wed, 28 Jun 2017 00:50:34: 4000000 INFO @ Wed, 28 Jun 2017 00:50:39: 5000000 INFO @ Wed, 28 Jun 2017 00:50:39: 5000000 INFO @ Wed, 28 Jun 2017 00:50:39: 5000000 INFO @ Wed, 28 Jun 2017 00:50:45: 6000000 INFO @ Wed, 28 Jun 2017 00:50:45: 6000000 INFO @ Wed, 28 Jun 2017 00:50:45: 6000000 INFO @ Wed, 28 Jun 2017 00:50:51: 7000000 INFO @ Wed, 28 Jun 2017 00:50:51: 7000000 INFO @ Wed, 28 Jun 2017 00:50:51: 7000000 INFO @ Wed, 28 Jun 2017 00:50:56: 8000000 INFO @ Wed, 28 Jun 2017 00:50:57: 8000000 INFO @ Wed, 28 Jun 2017 00:50:57: 8000000 INFO @ Wed, 28 Jun 2017 00:51:02: 9000000 INFO @ Wed, 28 Jun 2017 00:51:03: 9000000 INFO @ Wed, 28 Jun 2017 00:51:03: 9000000 INFO @ Wed, 28 Jun 2017 00:51:08: 10000000 INFO @ Wed, 28 Jun 2017 00:51:09: 10000000 INFO @ Wed, 28 Jun 2017 00:51:09: 10000000 INFO @ Wed, 28 Jun 2017 00:51:14: 11000000 INFO @ Wed, 28 Jun 2017 00:51:15: 11000000 INFO @ Wed, 28 Jun 2017 00:51:15: 11000000 INFO @ Wed, 28 Jun 2017 00:51:19: 12000000 INFO @ Wed, 28 Jun 2017 00:51:21: 12000000 INFO @ Wed, 28 Jun 2017 00:51:21: 12000000 INFO @ Wed, 28 Jun 2017 00:51:25: 13000000 INFO @ Wed, 28 Jun 2017 00:51:27: 13000000 INFO @ Wed, 28 Jun 2017 00:51:27: 13000000 INFO @ Wed, 28 Jun 2017 00:51:31: 14000000 INFO @ Wed, 28 Jun 2017 00:51:32: 14000000 INFO @ Wed, 28 Jun 2017 00:51:32: 14000000 INFO @ Wed, 28 Jun 2017 00:51:37: 15000000 INFO @ Wed, 28 Jun 2017 00:51:38: 15000000 INFO @ Wed, 28 Jun 2017 00:51:38: 15000000 INFO @ Wed, 28 Jun 2017 00:51:42: 16000000 INFO @ Wed, 28 Jun 2017 00:51:44: 16000000 INFO @ Wed, 28 Jun 2017 00:51:46: 16000000 INFO @ Wed, 28 Jun 2017 00:51:48: 17000000 INFO @ Wed, 28 Jun 2017 00:51:51: 17000000 INFO @ Wed, 28 Jun 2017 00:51:52: 17000000 INFO @ Wed, 28 Jun 2017 00:51:54: 18000000 INFO @ Wed, 28 Jun 2017 00:51:57: 18000000 INFO @ Wed, 28 Jun 2017 00:51:59: 18000000 INFO @ Wed, 28 Jun 2017 00:52:00: 19000000 INFO @ Wed, 28 Jun 2017 00:52:03: 19000000 INFO @ Wed, 28 Jun 2017 00:52:05: 19000000 INFO @ Wed, 28 Jun 2017 00:52:05: 20000000 INFO @ Wed, 28 Jun 2017 00:52:10: 20000000 INFO @ Wed, 28 Jun 2017 00:52:11: 20000000 INFO @ Wed, 28 Jun 2017 00:52:11: 21000000 INFO @ Wed, 28 Jun 2017 00:52:16: 21000000 INFO @ Wed, 28 Jun 2017 00:52:17: 22000000 INFO @ Wed, 28 Jun 2017 00:52:17: 21000000 INFO @ Wed, 28 Jun 2017 00:52:19: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:52:19: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:52:19: #1 total tags in treatment: 10961207 INFO @ Wed, 28 Jun 2017 00:52:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:52:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:52:19: #1 tags after filtering in treatment: 10383882 INFO @ Wed, 28 Jun 2017 00:52:19: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:52:19: #1 finished! INFO @ Wed, 28 Jun 2017 00:52:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:52:20: #2 number of paired peaks: 517 WARNING @ Wed, 28 Jun 2017 00:52:20: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Wed, 28 Jun 2017 00:52:20: start model_add_line... INFO @ Wed, 28 Jun 2017 00:52:20: start X-correlation... INFO @ Wed, 28 Jun 2017 00:52:20: end of X-cor INFO @ Wed, 28 Jun 2017 00:52:20: #2 finished! INFO @ Wed, 28 Jun 2017 00:52:20: #2 predicted fragment length is 146 bps INFO @ Wed, 28 Jun 2017 00:52:20: #2 alternative fragment length(s) may be 146 bps INFO @ Wed, 28 Jun 2017 00:52:20: #2.2 Generate R script for model : SRX749023.20_model.r INFO @ Wed, 28 Jun 2017 00:52:20: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:52:22: 22000000 INFO @ Wed, 28 Jun 2017 00:52:24: 22000000 INFO @ Wed, 28 Jun 2017 00:52:24: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:52:24: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:52:24: #1 total tags in treatment: 10961207 INFO @ Wed, 28 Jun 2017 00:52:24: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:52:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:52:25: #1 tags after filtering in treatment: 10383882 INFO @ Wed, 28 Jun 2017 00:52:25: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:52:25: #1 finished! INFO @ Wed, 28 Jun 2017 00:52:25: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:52:25: #2 number of paired peaks: 517 WARNING @ Wed, 28 Jun 2017 00:52:25: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Wed, 28 Jun 2017 00:52:25: start model_add_line... INFO @ Wed, 28 Jun 2017 00:52:26: start X-correlation... INFO @ Wed, 28 Jun 2017 00:52:26: end of X-cor INFO @ Wed, 28 Jun 2017 00:52:26: #2 finished! INFO @ Wed, 28 Jun 2017 00:52:26: #2 predicted fragment length is 146 bps INFO @ Wed, 28 Jun 2017 00:52:26: #2 alternative fragment length(s) may be 146 bps INFO @ Wed, 28 Jun 2017 00:52:26: #2.2 Generate R script for model : SRX749023.05_model.r INFO @ Wed, 28 Jun 2017 00:52:26: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:52:26: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:52:26: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:52:26: #1 total tags in treatment: 10961207 INFO @ Wed, 28 Jun 2017 00:52:26: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:52:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 00:52:26: #1 tags after filtering in treatment: 10383882 INFO @ Wed, 28 Jun 2017 00:52:26: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:52:26: #1 finished! INFO @ Wed, 28 Jun 2017 00:52:26: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:52:27: #2 number of paired peaks: 517 WARNING @ Wed, 28 Jun 2017 00:52:27: Fewer paired peaks (517) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 517 pairs to build model! INFO @ Wed, 28 Jun 2017 00:52:27: start model_add_line... INFO @ Wed, 28 Jun 2017 00:52:27: start X-correlation... INFO @ Wed, 28 Jun 2017 00:52:27: end of X-cor INFO @ Wed, 28 Jun 2017 00:52:27: #2 finished! INFO @ Wed, 28 Jun 2017 00:52:27: #2 predicted fragment length is 146 bps INFO @ Wed, 28 Jun 2017 00:52:27: #2 alternative fragment length(s) may be 146 bps INFO @ Wed, 28 Jun 2017 00:52:27: #2.2 Generate R script for model : SRX749023.10_model.r INFO @ Wed, 28 Jun 2017 00:52:27: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:52:44: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:52:49: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:52:52: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:52:57: #4 Write output xls file... SRX749023.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:52:57: #4 Write peak in narrowPeak format file... SRX749023.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:52:57: #4 Write summits bed file... SRX749023.20_summits.bed INFO @ Wed, 28 Jun 2017 00:52:57: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1431 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:53:03: #4 Write output xls file... SRX749023.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:53:03: #4 Write peak in narrowPeak format file... SRX749023.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:53:03: #4 Write summits bed file... SRX749023.05_summits.bed INFO @ Wed, 28 Jun 2017 00:53:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4071 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:53:05: #4 Write output xls file... SRX749023.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:53:05: #4 Write peak in narrowPeak format file... SRX749023.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:53:05: #4 Write summits bed file... SRX749023.10_summits.bed INFO @ Wed, 28 Jun 2017 00:53:05: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2617 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。