Job ID = 10194774 sra ファイルのダウンロード中... Completed: 503532K bytes transferred in 6 seconds (603263K 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... Written 22051737 spots for /home/okishinya/chipatlas/results/rn6/SRX1774907/SRR3544936.sra Written 22051737 spots total 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:16:30 22051737 reads; of these: 22051737 (100.00%) were unpaired; of these: 887739 (4.03%) aligned 0 times 16414516 (74.44%) aligned exactly 1 time 4749482 (21.54%) aligned >1 times 95.97% overall alignment rate Time searching: 00:16:34 Overall time: 00:16:34 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 3081149 / 21163998 = 0.1456 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, 10 Nov 2017 17:01:17: # Command line: callpeak -t SRX1774907.bam -f BAM -g 2.15e9 -n SRX1774907.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774907.10 # format = BAM # ChIP-seq file = ['SRX1774907.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 17:01:17: # Command line: callpeak -t SRX1774907.bam -f BAM -g 2.15e9 -n SRX1774907.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774907.20 # format = BAM # ChIP-seq file = ['SRX1774907.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 17:01:17: # Command line: callpeak -t SRX1774907.bam -f BAM -g 2.15e9 -n SRX1774907.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774907.05 # format = BAM # ChIP-seq file = ['SRX1774907.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 17:01:17: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:01:17: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:01:17: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:01:17: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:01:17: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:01:17: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:01:24: 1000000 INFO @ Fri, 10 Nov 2017 17:01:24: 1000000 INFO @ Fri, 10 Nov 2017 17:01:24: 1000000 INFO @ Fri, 10 Nov 2017 17:01:31: 2000000 INFO @ Fri, 10 Nov 2017 17:01:31: 2000000 INFO @ Fri, 10 Nov 2017 17:01:31: 2000000 INFO @ Fri, 10 Nov 2017 17:01:39: 3000000 INFO @ Fri, 10 Nov 2017 17:01:39: 3000000 INFO @ Fri, 10 Nov 2017 17:01:39: 3000000 INFO @ Fri, 10 Nov 2017 17:01:46: 4000000 INFO @ Fri, 10 Nov 2017 17:01:46: 4000000 INFO @ Fri, 10 Nov 2017 17:01:46: 4000000 INFO @ Fri, 10 Nov 2017 17:01:53: 5000000 INFO @ Fri, 10 Nov 2017 17:01:53: 5000000 INFO @ Fri, 10 Nov 2017 17:01:54: 5000000 INFO @ Fri, 10 Nov 2017 17:02:01: 6000000 INFO @ Fri, 10 Nov 2017 17:02:01: 6000000 INFO @ Fri, 10 Nov 2017 17:02:02: 6000000 INFO @ Fri, 10 Nov 2017 17:02:08: 7000000 INFO @ Fri, 10 Nov 2017 17:02:09: 7000000 INFO @ Fri, 10 Nov 2017 17:02:09: 7000000 INFO @ Fri, 10 Nov 2017 17:02:15: 8000000 INFO @ Fri, 10 Nov 2017 17:02:16: 8000000 INFO @ Fri, 10 Nov 2017 17:02:17: 8000000 INFO @ Fri, 10 Nov 2017 17:02:23: 9000000 INFO @ Fri, 10 Nov 2017 17:02:24: 9000000 INFO @ Fri, 10 Nov 2017 17:02:25: 9000000 INFO @ Fri, 10 Nov 2017 17:02:31: 10000000 INFO @ Fri, 10 Nov 2017 17:02:32: 10000000 INFO @ Fri, 10 Nov 2017 17:02:33: 10000000 INFO @ Fri, 10 Nov 2017 17:02:38: 11000000 INFO @ Fri, 10 Nov 2017 17:02:40: 11000000 INFO @ Fri, 10 Nov 2017 17:02:41: 11000000 INFO @ Fri, 10 Nov 2017 17:02:46: 12000000 INFO @ Fri, 10 Nov 2017 17:02:48: 12000000 INFO @ Fri, 10 Nov 2017 17:02:48: 12000000 INFO @ Fri, 10 Nov 2017 17:02:53: 13000000 INFO @ Fri, 10 Nov 2017 17:02:55: 13000000 INFO @ Fri, 10 Nov 2017 17:02:56: 13000000 INFO @ Fri, 10 Nov 2017 17:03:01: 14000000 INFO @ Fri, 10 Nov 2017 17:03:03: 14000000 INFO @ Fri, 10 Nov 2017 17:03:04: 14000000 INFO @ Fri, 10 Nov 2017 17:03:09: 15000000 INFO @ Fri, 10 Nov 2017 17:03:11: 15000000 INFO @ Fri, 10 Nov 2017 17:03:12: 15000000 INFO @ Fri, 10 Nov 2017 17:03:17: 16000000 INFO @ Fri, 10 Nov 2017 17:03:19: 16000000 INFO @ Fri, 10 Nov 2017 17:03:20: 16000000 INFO @ Fri, 10 Nov 2017 17:03:25: 17000000 INFO @ Fri, 10 Nov 2017 17:03:28: 17000000 INFO @ Fri, 10 Nov 2017 17:03:28: 17000000 INFO @ Fri, 10 Nov 2017 17:03:33: 18000000 INFO @ Fri, 10 Nov 2017 17:03:34: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:03:34: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:03:34: #1 total tags in treatment: 18082849 INFO @ Fri, 10 Nov 2017 17:03:34: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:03:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:03:34: #1 tags after filtering in treatment: 18082672 INFO @ Fri, 10 Nov 2017 17:03:34: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:03:34: #1 finished! INFO @ Fri, 10 Nov 2017 17:03:34: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:03:34: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:03:35: 18000000 INFO @ Fri, 10 Nov 2017 17:03:36: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:03:36: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:03:36: #1 total tags in treatment: 18082849 INFO @ Fri, 10 Nov 2017 17:03:36: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:03:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:03:36: 18000000 INFO @ Fri, 10 Nov 2017 17:03:37: #1 tags after filtering in treatment: 18082672 INFO @ Fri, 10 Nov 2017 17:03:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:03:37: #1 finished! INFO @ Fri, 10 Nov 2017 17:03:37: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:03:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:03:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:03:37: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:03:37: #1 total tags in treatment: 18082849 INFO @ Fri, 10 Nov 2017 17:03:37: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:03:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 17:03:37: #2 number of paired peaks: 32321 INFO @ Fri, 10 Nov 2017 17:03:37: start model_add_line... INFO @ Fri, 10 Nov 2017 17:03:37: start X-correlation... INFO @ Fri, 10 Nov 2017 17:03:37: end of X-cor INFO @ Fri, 10 Nov 2017 17:03:37: #2 finished! INFO @ Fri, 10 Nov 2017 17:03:37: #2 predicted fragment length is 171 bps INFO @ Fri, 10 Nov 2017 17:03:37: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 10 Nov 2017 17:03:37: #2.2 Generate R script for model : SRX1774907.05_model.r INFO @ Fri, 10 Nov 2017 17:03:37: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:03:37: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:03:38: #1 tags after filtering in treatment: 18082672 INFO @ Fri, 10 Nov 2017 17:03:38: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:03:38: #1 finished! INFO @ Fri, 10 Nov 2017 17:03:38: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:03:38: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:03:39: #2 number of paired peaks: 32321 INFO @ Fri, 10 Nov 2017 17:03:39: start model_add_line... INFO @ Fri, 10 Nov 2017 17:03:40: start X-correlation... INFO @ Fri, 10 Nov 2017 17:03:40: end of X-cor INFO @ Fri, 10 Nov 2017 17:03:40: #2 finished! INFO @ Fri, 10 Nov 2017 17:03:40: #2 predicted fragment length is 171 bps INFO @ Fri, 10 Nov 2017 17:03:40: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 10 Nov 2017 17:03:40: #2.2 Generate R script for model : SRX1774907.10_model.r INFO @ Fri, 10 Nov 2017 17:03:40: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:03:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:03:40: #2 number of paired peaks: 32321 INFO @ Fri, 10 Nov 2017 17:03:40: start model_add_line... INFO @ Fri, 10 Nov 2017 17:03:41: start X-correlation... INFO @ Fri, 10 Nov 2017 17:03:41: end of X-cor INFO @ Fri, 10 Nov 2017 17:03:41: #2 finished! INFO @ Fri, 10 Nov 2017 17:03:41: #2 predicted fragment length is 171 bps INFO @ Fri, 10 Nov 2017 17:03:41: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 10 Nov 2017 17:03:41: #2.2 Generate R script for model : SRX1774907.20_model.r INFO @ Fri, 10 Nov 2017 17:03:41: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:03:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:04:22: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:04:26: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:04:28: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:04:49: #4 Write output xls file... SRX1774907.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:04:49: #4 Write peak in narrowPeak format file... SRX1774907.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:04:49: #4 Write summits bed file... SRX1774907.05_summits.bed INFO @ Fri, 10 Nov 2017 17:04:49: Done! pass1 - making usageList (72 chroms): 3 millis pass2 - checking and writing primary data (17602 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:04:53: #4 Write output xls file... SRX1774907.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:04:53: #4 Write peak in narrowPeak format file... SRX1774907.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:04:53: #4 Write summits bed file... SRX1774907.10_summits.bed INFO @ Fri, 10 Nov 2017 17:04:53: Done! pass1 - making usageList (53 chroms): 3 millis pass2 - checking and writing primary data (8678 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:04:54: #4 Write output xls file... SRX1774907.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:04:54: #4 Write peak in narrowPeak format file... SRX1774907.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:04:54: #4 Write summits bed file... SRX1774907.20_summits.bed INFO @ Fri, 10 Nov 2017 17:04:54: Done! pass1 - making usageList (37 chroms): 1 millis pass2 - checking and writing primary data (3376 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。