Job ID = 10609116 sra ファイルのダウンロード中... Completed: 441170K bytes transferred in 56 seconds (64099K 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 20762234 spots for /home/okishinya/chipatlas/results/dm3/SRX3011254/SRR5834731.sra Written 20762234 spots for /home/okishinya/chipatlas/results/dm3/SRX3011254/SRR5834731.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: 00:03:59 20762234 reads; of these: 20762234 (100.00%) were unpaired; of these: 244327 (1.18%) aligned 0 times 20024019 (96.44%) aligned exactly 1 time 493888 (2.38%) aligned >1 times 98.82% overall alignment rate Time searching: 00:03:59 Overall time: 00:03:59 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_rmdupse_core] 2596520 / 20517907 = 0.1265 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 07:12:22: # Command line: callpeak -t SRX3011254.bam -f BAM -g dm -n SRX3011254.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011254.05 # format = BAM # ChIP-seq file = ['SRX3011254.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 07:12:22: # Command line: callpeak -t SRX3011254.bam -f BAM -g dm -n SRX3011254.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011254.20 # format = BAM # ChIP-seq file = ['SRX3011254.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 07:12:22: # Command line: callpeak -t SRX3011254.bam -f BAM -g dm -n SRX3011254.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011254.10 # format = BAM # ChIP-seq file = ['SRX3011254.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 07:12:22: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:22: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:22: #1 read tag files... INFO @ Fri, 04 May 2018 07:12:22: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:22: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:22: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:12:28: 1000000 INFO @ Fri, 04 May 2018 07:12:28: 1000000 INFO @ Fri, 04 May 2018 07:12:29: 1000000 INFO @ Fri, 04 May 2018 07:12:35: 2000000 INFO @ Fri, 04 May 2018 07:12:35: 2000000 INFO @ Fri, 04 May 2018 07:12:36: 2000000 INFO @ Fri, 04 May 2018 07:12:42: 3000000 INFO @ Fri, 04 May 2018 07:12:42: 3000000 INFO @ Fri, 04 May 2018 07:12:42: 3000000 INFO @ Fri, 04 May 2018 07:12:48: 4000000 INFO @ Fri, 04 May 2018 07:12:49: 4000000 INFO @ Fri, 04 May 2018 07:12:49: 4000000 INFO @ Fri, 04 May 2018 07:12:55: 5000000 INFO @ Fri, 04 May 2018 07:12:56: 5000000 INFO @ Fri, 04 May 2018 07:12:56: 5000000 INFO @ Fri, 04 May 2018 07:13:01: 6000000 INFO @ Fri, 04 May 2018 07:13:03: 6000000 INFO @ Fri, 04 May 2018 07:13:03: 6000000 INFO @ Fri, 04 May 2018 07:13:08: 7000000 INFO @ Fri, 04 May 2018 07:13:10: 7000000 INFO @ Fri, 04 May 2018 07:13:10: 7000000 INFO @ Fri, 04 May 2018 07:13:15: 8000000 INFO @ Fri, 04 May 2018 07:13:16: 8000000 INFO @ Fri, 04 May 2018 07:13:17: 8000000 INFO @ Fri, 04 May 2018 07:13:22: 9000000 INFO @ Fri, 04 May 2018 07:13:23: 9000000 INFO @ Fri, 04 May 2018 07:13:23: 9000000 INFO @ Fri, 04 May 2018 07:13:28: 10000000 INFO @ Fri, 04 May 2018 07:13:30: 10000000 INFO @ Fri, 04 May 2018 07:13:31: 10000000 INFO @ Fri, 04 May 2018 07:13:36: 11000000 INFO @ Fri, 04 May 2018 07:13:36: 11000000 INFO @ Fri, 04 May 2018 07:13:38: 11000000 INFO @ Fri, 04 May 2018 07:13:42: 12000000 INFO @ Fri, 04 May 2018 07:13:43: 12000000 INFO @ Fri, 04 May 2018 07:13:45: 12000000 INFO @ Fri, 04 May 2018 07:13:49: 13000000 INFO @ Fri, 04 May 2018 07:13:50: 13000000 INFO @ Fri, 04 May 2018 07:13:52: 13000000 INFO @ Fri, 04 May 2018 07:13:55: 14000000 INFO @ Fri, 04 May 2018 07:13:57: 14000000 INFO @ Fri, 04 May 2018 07:13:59: 14000000 INFO @ Fri, 04 May 2018 07:14:02: 15000000 INFO @ Fri, 04 May 2018 07:14:04: 15000000 INFO @ Fri, 04 May 2018 07:14:05: 15000000 INFO @ Fri, 04 May 2018 07:14:08: 16000000 INFO @ Fri, 04 May 2018 07:14:10: 16000000 INFO @ Fri, 04 May 2018 07:14:12: 16000000 INFO @ Fri, 04 May 2018 07:14:15: 17000000 INFO @ Fri, 04 May 2018 07:14:17: 17000000 INFO @ Fri, 04 May 2018 07:14:19: 17000000 INFO @ Fri, 04 May 2018 07:14:21: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:14:21: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:14:21: #1 total tags in treatment: 17921387 INFO @ Fri, 04 May 2018 07:14:21: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:14:21: #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 07:14:22: #1 tags after filtering in treatment: 17921387 INFO @ Fri, 04 May 2018 07:14:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:14:22: #1 finished! INFO @ Fri, 04 May 2018 07:14:22: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:14:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:14:23: #2 number of paired peaks: 164 WARNING @ Fri, 04 May 2018 07:14:23: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 04 May 2018 07:14:23: start model_add_line... INFO @ Fri, 04 May 2018 07:14:23: start X-correlation... INFO @ Fri, 04 May 2018 07:14:23: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:14:23: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:14:23: #1 total tags in treatment: 17921387 INFO @ Fri, 04 May 2018 07:14:23: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:14:23: #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 07:14:23: end of X-cor INFO @ Fri, 04 May 2018 07:14:23: #2 finished! INFO @ Fri, 04 May 2018 07:14:23: #2 predicted fragment length is 175 bps INFO @ Fri, 04 May 2018 07:14:23: #2 alternative fragment length(s) may be 3,161,175,194,208 bps INFO @ Fri, 04 May 2018 07:14:23: #2.2 Generate R script for model : SRX3011254.20_model.r INFO @ Fri, 04 May 2018 07:14:23: #3 Call peaks... INFO @ Fri, 04 May 2018 07:14:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:14:24: #1 tags after filtering in treatment: 17921387 INFO @ Fri, 04 May 2018 07:14:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:14:24: #1 finished! INFO @ Fri, 04 May 2018 07:14:24: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:14:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:14:25: #2 number of paired peaks: 164 WARNING @ Fri, 04 May 2018 07:14:25: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 04 May 2018 07:14:25: start model_add_line... INFO @ Fri, 04 May 2018 07:14:25: start X-correlation... INFO @ Fri, 04 May 2018 07:14:25: end of X-cor INFO @ Fri, 04 May 2018 07:14:25: #2 finished! INFO @ Fri, 04 May 2018 07:14:25: #2 predicted fragment length is 175 bps INFO @ Fri, 04 May 2018 07:14:25: #2 alternative fragment length(s) may be 3,161,175,194,208 bps INFO @ Fri, 04 May 2018 07:14:25: #2.2 Generate R script for model : SRX3011254.05_model.r INFO @ Fri, 04 May 2018 07:14:25: #3 Call peaks... INFO @ Fri, 04 May 2018 07:14:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:14:25: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:14:25: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:14:25: #1 total tags in treatment: 17921387 INFO @ Fri, 04 May 2018 07:14:25: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:14:25: #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 07:14:26: #1 tags after filtering in treatment: 17921387 INFO @ Fri, 04 May 2018 07:14:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:14:26: #1 finished! INFO @ Fri, 04 May 2018 07:14:26: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:14:27: #2 number of paired peaks: 164 WARNING @ Fri, 04 May 2018 07:14:27: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 04 May 2018 07:14:27: start model_add_line... INFO @ Fri, 04 May 2018 07:14:27: start X-correlation... INFO @ Fri, 04 May 2018 07:14:27: end of X-cor INFO @ Fri, 04 May 2018 07:14:27: #2 finished! INFO @ Fri, 04 May 2018 07:14:27: #2 predicted fragment length is 175 bps INFO @ Fri, 04 May 2018 07:14:27: #2 alternative fragment length(s) may be 3,161,175,194,208 bps INFO @ Fri, 04 May 2018 07:14:27: #2.2 Generate R script for model : SRX3011254.10_model.r INFO @ Fri, 04 May 2018 07:14:27: #3 Call peaks... INFO @ Fri, 04 May 2018 07:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:03: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:06: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:08: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:25: #4 Write output xls file... SRX3011254.05_peaks.xls INFO @ Fri, 04 May 2018 07:15:25: #4 Write peak in narrowPeak format file... SRX3011254.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:25: #4 Write summits bed file... SRX3011254.05_summits.bed INFO @ Fri, 04 May 2018 07:15:25: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3052 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:15:29: #4 Write output xls file... SRX3011254.20_peaks.xls INFO @ Fri, 04 May 2018 07:15:29: #4 Write peak in narrowPeak format file... SRX3011254.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:29: #4 Write summits bed file... SRX3011254.20_summits.bed INFO @ Fri, 04 May 2018 07:15:29: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (42 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:15:29: #4 Write output xls file... SRX3011254.10_peaks.xls INFO @ Fri, 04 May 2018 07:15:29: #4 Write peak in narrowPeak format file... SRX3011254.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:29: #4 Write summits bed file... SRX3011254.10_summits.bed INFO @ Fri, 04 May 2018 07:15:29: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。