Job ID = 2161337 sra ファイルのダウンロード中... Completed: 402154K bytes transferred in 6 seconds (489831K bits/sec), in 1 file, 2 directories. % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 0 0 0 0 0 0 0 0 --:--:-- --:--:-- --:--:-- 0 100 36122 0 36122 0 0 48373 0 --:--:-- --:--:-- --:--:-- 65084 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 8228465 spots for /home/okishinya/chipatlas/results/dm3/SRX019952/SRR042282.sra Written 8228465 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: 00:00:00 Multiseed full-index search: 00:12:41 8228465 reads; of these: 8228465 (100.00%) were paired; of these: 1800198 (21.88%) aligned concordantly 0 times 4847023 (58.91%) aligned concordantly exactly 1 time 1581244 (19.22%) aligned concordantly >1 times ---- 1800198 pairs aligned concordantly 0 times; of these: 76590 (4.25%) aligned discordantly 1 time ---- 1723608 pairs aligned 0 times concordantly or discordantly; of these: 3447216 mates make up the pairs; of these: 2637623 (76.51%) aligned 0 times 583193 (16.92%) aligned exactly 1 time 226400 (6.57%) aligned >1 times 83.97% overall alignment rate Time searching: 00:12:41 Overall time: 00:12:41 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_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] 139940 / 6464578 = 0.0216 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 @ Tue, 21 Apr 2015 12:40:07: # Command line: callpeak -t SRX019952.bam -f BAM -g dm -n SRX019952.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX019952.20 # format = BAM # ChIP-seq file = ['SRX019952.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 INFO @ Tue, 21 Apr 2015 12:40:07: # Command line: callpeak -t SRX019952.bam -f BAM -g dm -n SRX019952.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX019952.05 # format = BAM # ChIP-seq file = ['SRX019952.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 INFO @ Tue, 21 Apr 2015 12:40:07: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:07: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:07: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:07: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:07: # Command line: callpeak -t SRX019952.bam -f BAM -g dm -n SRX019952.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX019952.10 # format = BAM # ChIP-seq file = ['SRX019952.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 INFO @ Tue, 21 Apr 2015 12:40:07: #1 read tag files... INFO @ Tue, 21 Apr 2015 12:40:07: #1 read treatment tags... INFO @ Tue, 21 Apr 2015 12:40:12: 1000000 INFO @ Tue, 21 Apr 2015 12:40:12: 1000000 INFO @ Tue, 21 Apr 2015 12:40:12: 1000000 INFO @ Tue, 21 Apr 2015 12:40:18: 2000000 INFO @ Tue, 21 Apr 2015 12:40:18: 2000000 INFO @ Tue, 21 Apr 2015 12:40:18: 2000000 INFO @ Tue, 21 Apr 2015 12:40:24: 3000000 INFO @ Tue, 21 Apr 2015 12:40:24: 3000000 INFO @ Tue, 21 Apr 2015 12:40:24: 3000000 INFO @ Tue, 21 Apr 2015 12:40:29: 4000000 INFO @ Tue, 21 Apr 2015 12:40:30: 4000000 INFO @ Tue, 21 Apr 2015 12:40:30: 4000000 INFO @ Tue, 21 Apr 2015 12:40:35: 5000000 INFO @ Tue, 21 Apr 2015 12:40:36: 5000000 INFO @ Tue, 21 Apr 2015 12:40:36: 5000000 INFO @ Tue, 21 Apr 2015 12:40:41: 6000000 INFO @ Tue, 21 Apr 2015 12:40:42: 6000000 INFO @ Tue, 21 Apr 2015 12:40:42: 6000000 INFO @ Tue, 21 Apr 2015 12:40:46: 7000000 INFO @ Tue, 21 Apr 2015 12:40:48: 7000000 INFO @ Tue, 21 Apr 2015 12:40:49: 7000000 INFO @ Tue, 21 Apr 2015 12:40:52: 8000000 INFO @ Tue, 21 Apr 2015 12:40:55: 8000000 INFO @ Tue, 21 Apr 2015 12:40:55: 8000000 INFO @ Tue, 21 Apr 2015 12:40:58: 9000000 INFO @ Tue, 21 Apr 2015 12:41:01: 9000000 INFO @ Tue, 21 Apr 2015 12:41:01: 9000000 INFO @ Tue, 21 Apr 2015 12:41:03: 10000000 INFO @ Tue, 21 Apr 2015 12:41:07: 10000000 INFO @ Tue, 21 Apr 2015 12:41:07: 10000000 INFO @ Tue, 21 Apr 2015 12:41:09: 11000000 INFO @ Tue, 21 Apr 2015 12:41:13: 11000000 INFO @ Tue, 21 Apr 2015 12:41:13: 11000000 INFO @ Tue, 21 Apr 2015 12:41:15: 12000000 INFO @ Tue, 21 Apr 2015 12:41:19: 12000000 INFO @ Tue, 21 Apr 2015 12:41:20: 12000000 INFO @ Tue, 21 Apr 2015 12:41:21: 13000000 INFO @ Tue, 21 Apr 2015 12:41:24: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:41:24: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:41:24: #1 total tags in treatment: 6288752 INFO @ Tue, 21 Apr 2015 12:41:24: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:41:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:41:25: #1 tags after filtering in treatment: 5836365 INFO @ Tue, 21 Apr 2015 12:41:25: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 21 Apr 2015 12:41:25: #1 finished! INFO @ Tue, 21 Apr 2015 12:41:25: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:41:26: 13000000 INFO @ Tue, 21 Apr 2015 12:41:26: 13000000 INFO @ Tue, 21 Apr 2015 12:41:26: #2 number of paired peaks: 386 WARNING @ Tue, 21 Apr 2015 12:41:26: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 21 Apr 2015 12:41:26: start model_add_line... INFO @ Tue, 21 Apr 2015 12:41:27: start X-correlation... INFO @ Tue, 21 Apr 2015 12:41:27: end of X-cor INFO @ Tue, 21 Apr 2015 12:41:27: #2 finished! INFO @ Tue, 21 Apr 2015 12:41:27: #2 predicted fragment length is 85 bps INFO @ Tue, 21 Apr 2015 12:41:27: #2 alternative fragment length(s) may be 85 bps INFO @ Tue, 21 Apr 2015 12:41:27: #2.2 Generate R script for model : SRX019952.10_model.r INFO @ Tue, 21 Apr 2015 12:41:27: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:41:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:41:29: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:41:29: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:41:29: #1 total tags in treatment: 6288752 INFO @ Tue, 21 Apr 2015 12:41:29: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:41:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:41:29: #1 tag size is determined as 35 bps INFO @ Tue, 21 Apr 2015 12:41:29: #1 tag size = 35 INFO @ Tue, 21 Apr 2015 12:41:29: #1 total tags in treatment: 6288752 INFO @ Tue, 21 Apr 2015 12:41:29: #1 user defined the maximum tags... INFO @ Tue, 21 Apr 2015 12:41:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 21 Apr 2015 12:41:30: #1 tags after filtering in treatment: 5836365 INFO @ Tue, 21 Apr 2015 12:41:30: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 21 Apr 2015 12:41:30: #1 finished! INFO @ Tue, 21 Apr 2015 12:41:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:41:30: #1 tags after filtering in treatment: 5836365 INFO @ Tue, 21 Apr 2015 12:41:30: #1 Redundant rate of treatment: 0.07 INFO @ Tue, 21 Apr 2015 12:41:30: #1 finished! INFO @ Tue, 21 Apr 2015 12:41:30: #2 Build Peak Model... INFO @ Tue, 21 Apr 2015 12:41:31: #2 number of paired peaks: 386 WARNING @ Tue, 21 Apr 2015 12:41:31: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 21 Apr 2015 12:41:31: start model_add_line... INFO @ Tue, 21 Apr 2015 12:41:31: #2 number of paired peaks: 386 WARNING @ Tue, 21 Apr 2015 12:41:31: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Tue, 21 Apr 2015 12:41:31: start model_add_line... INFO @ Tue, 21 Apr 2015 12:41:33: start X-correlation... INFO @ Tue, 21 Apr 2015 12:41:33: end of X-cor INFO @ Tue, 21 Apr 2015 12:41:33: #2 finished! INFO @ Tue, 21 Apr 2015 12:41:33: #2 predicted fragment length is 85 bps INFO @ Tue, 21 Apr 2015 12:41:33: #2 alternative fragment length(s) may be 85 bps INFO @ Tue, 21 Apr 2015 12:41:33: #2.2 Generate R script for model : SRX019952.05_model.r INFO @ Tue, 21 Apr 2015 12:41:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:41:33: start X-correlation... INFO @ Tue, 21 Apr 2015 12:41:33: end of X-cor INFO @ Tue, 21 Apr 2015 12:41:33: #2 finished! INFO @ Tue, 21 Apr 2015 12:41:33: #2 predicted fragment length is 85 bps INFO @ Tue, 21 Apr 2015 12:41:33: #2 alternative fragment length(s) may be 85 bps INFO @ Tue, 21 Apr 2015 12:41:33: #2.2 Generate R script for model : SRX019952.20_model.r INFO @ Tue, 21 Apr 2015 12:41:33: #3 Call peaks... INFO @ Tue, 21 Apr 2015 12:41:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 21 Apr 2015 12:42:00: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:42:05: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:42:06: #3 Call peaks for each chromosome... INFO @ Tue, 21 Apr 2015 12:42:23: #4 Write output xls file... SRX019952.10_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:23: #4 Write peak in narrowPeak format file... SRX019952.10_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:23: #4 Write summits bed file... SRX019952.10_summits.bed INFO @ Tue, 21 Apr 2015 12:42:23: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (445 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:42:28: #4 Write output xls file... SRX019952.20_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:28: #4 Write peak in narrowPeak format file... SRX019952.20_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:28: #4 Write summits bed file... SRX019952.20_summits.bed INFO @ Tue, 21 Apr 2015 12:42:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (155 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 21 Apr 2015 12:42:30: #4 Write output xls file... SRX019952.05_peaks.xls INFO @ Tue, 21 Apr 2015 12:42:31: #4 Write peak in narrowPeak format file... SRX019952.05_peaks.narrowPeak INFO @ Tue, 21 Apr 2015 12:42:31: #4 Write summits bed file... SRX019952.05_summits.bed INFO @ Tue, 21 Apr 2015 12:42:31: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1168 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。