Job ID = 10609090 sra ファイルのダウンロード中... Completed: 551389K bytes transferred in 42 seconds (105913K 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 26713838 spots for /home/okishinya/chipatlas/results/dm3/SRX3011228/SRR5834705.sra Written 26713838 spots for /home/okishinya/chipatlas/results/dm3/SRX3011228/SRR5834705.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: 00:05:01 26713838 reads; of these: 26713838 (100.00%) were unpaired; of these: 306719 (1.15%) aligned 0 times 25870431 (96.84%) aligned exactly 1 time 536688 (2.01%) aligned >1 times 98.85% overall alignment rate Time searching: 00:05:02 Overall time: 00:05:02 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] 6628338 / 26407119 = 0.2510 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 07:14:20: # Command line: callpeak -t SRX3011228.bam -f BAM -g dm -n SRX3011228.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3011228.20 # format = BAM # ChIP-seq file = ['SRX3011228.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 07:14:20: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:20: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:20: # Command line: callpeak -t SRX3011228.bam -f BAM -g dm -n SRX3011228.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3011228.05 # format = BAM # ChIP-seq file = ['SRX3011228.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 07:14:20: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:20: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:20: # Command line: callpeak -t SRX3011228.bam -f BAM -g dm -n SRX3011228.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3011228.10 # format = BAM # ChIP-seq file = ['SRX3011228.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 07:14:20: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:20: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:27: 1000000 INFO @ Fri, 04 May 2018 07:14:27: 1000000 INFO @ Fri, 04 May 2018 07:14:27: 1000000 INFO @ Fri, 04 May 2018 07:14:34: 2000000 INFO @ Fri, 04 May 2018 07:14:34: 2000000 INFO @ Fri, 04 May 2018 07:14:34: 2000000 INFO @ Fri, 04 May 2018 07:14:40: 3000000 INFO @ Fri, 04 May 2018 07:14:41: 3000000 INFO @ Fri, 04 May 2018 07:14:41: 3000000 INFO @ Fri, 04 May 2018 07:14:47: 4000000 INFO @ Fri, 04 May 2018 07:14:48: 4000000 INFO @ Fri, 04 May 2018 07:14:48: 4000000 INFO @ Fri, 04 May 2018 07:14:54: 5000000 INFO @ Fri, 04 May 2018 07:14:55: 5000000 INFO @ Fri, 04 May 2018 07:14:55: 5000000 INFO @ Fri, 04 May 2018 07:15:00: 6000000 INFO @ Fri, 04 May 2018 07:15:02: 6000000 INFO @ Fri, 04 May 2018 07:15:02: 6000000 INFO @ Fri, 04 May 2018 07:15:07: 7000000 INFO @ Fri, 04 May 2018 07:15:08: 7000000 INFO @ Fri, 04 May 2018 07:15:09: 7000000 INFO @ Fri, 04 May 2018 07:15:14: 8000000 INFO @ Fri, 04 May 2018 07:15:15: 8000000 INFO @ Fri, 04 May 2018 07:15:16: 8000000 INFO @ Fri, 04 May 2018 07:15:20: 9000000 INFO @ Fri, 04 May 2018 07:15:22: 9000000 INFO @ Fri, 04 May 2018 07:15:23: 9000000 INFO @ Fri, 04 May 2018 07:15:27: 10000000 INFO @ Fri, 04 May 2018 07:15:29: 10000000 INFO @ Fri, 04 May 2018 07:15:29: 10000000 INFO @ Fri, 04 May 2018 07:15:34: 11000000 INFO @ Fri, 04 May 2018 07:15:36: 11000000 INFO @ Fri, 04 May 2018 07:15:36: 11000000 INFO @ Fri, 04 May 2018 07:15:41: 12000000 INFO @ Fri, 04 May 2018 07:15:43: 12000000 INFO @ Fri, 04 May 2018 07:15:43: 12000000 INFO @ Fri, 04 May 2018 07:15:48: 13000000 INFO @ Fri, 04 May 2018 07:15:50: 13000000 INFO @ Fri, 04 May 2018 07:15:50: 13000000 INFO @ Fri, 04 May 2018 07:15:55: 14000000 INFO @ Fri, 04 May 2018 07:15:57: 14000000 INFO @ Fri, 04 May 2018 07:15:57: 14000000 INFO @ Fri, 04 May 2018 07:16:03: 15000000 INFO @ Fri, 04 May 2018 07:16:04: 15000000 INFO @ Fri, 04 May 2018 07:16:04: 15000000 INFO @ Fri, 04 May 2018 07:16:10: 16000000 INFO @ Fri, 04 May 2018 07:16:11: 16000000 INFO @ Fri, 04 May 2018 07:16:11: 16000000 INFO @ Fri, 04 May 2018 07:16:17: 17000000 INFO @ Fri, 04 May 2018 07:16:18: 17000000 INFO @ Fri, 04 May 2018 07:16:18: 17000000 INFO @ Fri, 04 May 2018 07:16:24: 18000000 INFO @ Fri, 04 May 2018 07:16:24: 18000000 INFO @ Fri, 04 May 2018 07:16:24: 18000000 INFO @ Fri, 04 May 2018 07:16:31: 19000000 INFO @ Fri, 04 May 2018 07:16:31: 19000000 INFO @ Fri, 04 May 2018 07:16:31: 19000000 INFO @ Fri, 04 May 2018 07:16:36: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:16:36: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:16:36: #1 total tags in treatment: 19778781 INFO @ Fri, 04 May 2018 07:16:36: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:36: #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 07:16:36: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:16:36: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:16:36: #1 total tags in treatment: 19778781 INFO @ Fri, 04 May 2018 07:16:36: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:36: #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 07:16:36: #1 tag size is determined as 50 bps INFO @ Fri, 04 May 2018 07:16:36: #1 tag size = 50 INFO @ Fri, 04 May 2018 07:16:36: #1 total tags in treatment: 19778781 INFO @ Fri, 04 May 2018 07:16:36: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:16:36: #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 07:16:37: #1 tags after filtering in treatment: 19778781 INFO @ Fri, 04 May 2018 07:16:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:37: #1 finished! INFO @ Fri, 04 May 2018 07:16:37: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:37: #1 tags after filtering in treatment: 19778781 INFO @ Fri, 04 May 2018 07:16:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:37: #1 finished! INFO @ Fri, 04 May 2018 07:16:37: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:37: #1 tags after filtering in treatment: 19778781 INFO @ Fri, 04 May 2018 07:16:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 04 May 2018 07:16:37: #1 finished! INFO @ Fri, 04 May 2018 07:16:37: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:16:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:16:38: #2 number of paired peaks: 1668 INFO @ Fri, 04 May 2018 07:16:38: start model_add_line... INFO @ Fri, 04 May 2018 07:16:38: #2 number of paired peaks: 1668 INFO @ Fri, 04 May 2018 07:16:38: start model_add_line... INFO @ Fri, 04 May 2018 07:16:38: #2 number of paired peaks: 1668 INFO @ Fri, 04 May 2018 07:16:38: start model_add_line... INFO @ Fri, 04 May 2018 07:16:39: start X-correlation... INFO @ Fri, 04 May 2018 07:16:39: end of X-cor INFO @ Fri, 04 May 2018 07:16:39: #2 finished! INFO @ Fri, 04 May 2018 07:16:39: #2 predicted fragment length is 245 bps INFO @ Fri, 04 May 2018 07:16:39: #2 alternative fragment length(s) may be 245 bps INFO @ Fri, 04 May 2018 07:16:39: #2.2 Generate R script for model : SRX3011228.10_model.r INFO @ Fri, 04 May 2018 07:16:39: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:39: start X-correlation... INFO @ Fri, 04 May 2018 07:16:39: end of X-cor INFO @ Fri, 04 May 2018 07:16:39: #2 finished! INFO @ Fri, 04 May 2018 07:16:39: #2 predicted fragment length is 245 bps INFO @ Fri, 04 May 2018 07:16:39: #2 alternative fragment length(s) may be 245 bps INFO @ Fri, 04 May 2018 07:16:39: #2.2 Generate R script for model : SRX3011228.20_model.r INFO @ Fri, 04 May 2018 07:16:39: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:16:39: start X-correlation... INFO @ Fri, 04 May 2018 07:16:39: end of X-cor INFO @ Fri, 04 May 2018 07:16:39: #2 finished! INFO @ Fri, 04 May 2018 07:16:39: #2 predicted fragment length is 245 bps INFO @ Fri, 04 May 2018 07:16:39: #2 alternative fragment length(s) may be 245 bps INFO @ Fri, 04 May 2018 07:16:39: #2.2 Generate R script for model : SRX3011228.05_model.r INFO @ Fri, 04 May 2018 07:16:39: #3 Call peaks... INFO @ Fri, 04 May 2018 07:16:39: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:17:39: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:17:39: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:17:40: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:18:04: #4 Write output xls file... SRX3011228.10_peaks.xls INFO @ Fri, 04 May 2018 07:18:04: #4 Write peak in narrowPeak format file... SRX3011228.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:04: #4 Write summits bed file... SRX3011228.10_summits.bed INFO @ Fri, 04 May 2018 07:18:04: #4 Write output xls file... SRX3011228.20_peaks.xls INFO @ Fri, 04 May 2018 07:18:04: Done! INFO @ Fri, 04 May 2018 07:18:04: #4 Write peak in narrowPeak format file... SRX3011228.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:04: #4 Write summits bed file... SRX3011228.20_summits.bed INFO @ Fri, 04 May 2018 07:18:04: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8670 records, 4 fields): 11 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4808 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:18:07: #4 Write output xls file... SRX3011228.05_peaks.xls INFO @ Fri, 04 May 2018 07:18:07: #4 Write peak in narrowPeak format file... SRX3011228.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:18:07: #4 Write summits bed file... SRX3011228.05_summits.bed INFO @ Fri, 04 May 2018 07:18:07: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (12530 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。