Job ID = 11632727 sra ファイルのダウンロード中... Completed: 474889K bytes transferred in 7 seconds (520778K 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 24675454 spots for /home/okishinya/chipatlas/results/rn6/SRX4497197/SRR7633467.sra Written 24675454 spots for /home/okishinya/chipatlas/results/rn6/SRX4497197/SRR7633467.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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:37 24675454 reads; of these: 24675454 (100.00%) were unpaired; of these: 861568 (3.49%) aligned 0 times 17558605 (71.16%) aligned exactly 1 time 6255281 (25.35%) aligned >1 times 96.51% overall alignment rate Time searching: 00:18:42 Overall time: 00:18:43 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] 4196257 / 23813886 = 0.1762 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, 15 Feb 2019 07:23:22: # Command line: callpeak -t SRX4497197.bam -f BAM -g 2.15e9 -n SRX4497197.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4497197.10 # format = BAM # ChIP-seq file = ['SRX4497197.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, 15 Feb 2019 07:23:22: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:23:22: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:23:22: # Command line: callpeak -t SRX4497197.bam -f BAM -g 2.15e9 -n SRX4497197.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4497197.20 # format = BAM # ChIP-seq file = ['SRX4497197.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, 15 Feb 2019 07:23:22: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:23:22: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:23:22: # Command line: callpeak -t SRX4497197.bam -f BAM -g 2.15e9 -n SRX4497197.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4497197.05 # format = BAM # ChIP-seq file = ['SRX4497197.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, 15 Feb 2019 07:23:22: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:23:22: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:23:28: 1000000 INFO @ Fri, 15 Feb 2019 07:23:28: 1000000 INFO @ Fri, 15 Feb 2019 07:23:28: 1000000 INFO @ Fri, 15 Feb 2019 07:23:34: 2000000 INFO @ Fri, 15 Feb 2019 07:23:34: 2000000 INFO @ Fri, 15 Feb 2019 07:23:34: 2000000 INFO @ Fri, 15 Feb 2019 07:23:39: 3000000 INFO @ Fri, 15 Feb 2019 07:23:40: 3000000 INFO @ Fri, 15 Feb 2019 07:23:40: 3000000 INFO @ Fri, 15 Feb 2019 07:23:45: 4000000 INFO @ Fri, 15 Feb 2019 07:23:46: 4000000 INFO @ Fri, 15 Feb 2019 07:23:46: 4000000 INFO @ Fri, 15 Feb 2019 07:23:51: 5000000 INFO @ Fri, 15 Feb 2019 07:23:52: 5000000 INFO @ Fri, 15 Feb 2019 07:23:52: 5000000 INFO @ Fri, 15 Feb 2019 07:23:57: 6000000 INFO @ Fri, 15 Feb 2019 07:23:59: 6000000 INFO @ Fri, 15 Feb 2019 07:23:59: 6000000 INFO @ Fri, 15 Feb 2019 07:24:03: 7000000 INFO @ Fri, 15 Feb 2019 07:24:05: 7000000 INFO @ Fri, 15 Feb 2019 07:24:05: 7000000 INFO @ Fri, 15 Feb 2019 07:24:09: 8000000 INFO @ Fri, 15 Feb 2019 07:24:11: 8000000 INFO @ Fri, 15 Feb 2019 07:24:11: 8000000 INFO @ Fri, 15 Feb 2019 07:24:15: 9000000 INFO @ Fri, 15 Feb 2019 07:24:17: 9000000 INFO @ Fri, 15 Feb 2019 07:24:17: 9000000 INFO @ Fri, 15 Feb 2019 07:24:21: 10000000 INFO @ Fri, 15 Feb 2019 07:24:23: 10000000 INFO @ Fri, 15 Feb 2019 07:24:24: 10000000 INFO @ Fri, 15 Feb 2019 07:24:27: 11000000 INFO @ Fri, 15 Feb 2019 07:24:29: 11000000 INFO @ Fri, 15 Feb 2019 07:24:30: 11000000 INFO @ Fri, 15 Feb 2019 07:24:33: 12000000 INFO @ Fri, 15 Feb 2019 07:24:36: 12000000 INFO @ Fri, 15 Feb 2019 07:24:36: 12000000 INFO @ Fri, 15 Feb 2019 07:24:39: 13000000 INFO @ Fri, 15 Feb 2019 07:24:42: 13000000 INFO @ Fri, 15 Feb 2019 07:24:43: 13000000 INFO @ Fri, 15 Feb 2019 07:24:45: 14000000 INFO @ Fri, 15 Feb 2019 07:24:48: 14000000 INFO @ Fri, 15 Feb 2019 07:24:49: 14000000 INFO @ Fri, 15 Feb 2019 07:24:50: 15000000 INFO @ Fri, 15 Feb 2019 07:24:55: 15000000 INFO @ Fri, 15 Feb 2019 07:24:55: 15000000 INFO @ Fri, 15 Feb 2019 07:24:56: 16000000 INFO @ Fri, 15 Feb 2019 07:25:01: 16000000 INFO @ Fri, 15 Feb 2019 07:25:02: 16000000 INFO @ Fri, 15 Feb 2019 07:25:02: 17000000 INFO @ Fri, 15 Feb 2019 07:25:07: 17000000 INFO @ Fri, 15 Feb 2019 07:25:08: 18000000 INFO @ Fri, 15 Feb 2019 07:25:08: 17000000 INFO @ Fri, 15 Feb 2019 07:25:14: 18000000 INFO @ Fri, 15 Feb 2019 07:25:14: 19000000 INFO @ Fri, 15 Feb 2019 07:25:15: 18000000 INFO @ Fri, 15 Feb 2019 07:25:18: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:25:18: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:25:18: #1 total tags in treatment: 19617629 INFO @ Fri, 15 Feb 2019 07:25:18: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:25:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:25:19: #1 tags after filtering in treatment: 19617504 INFO @ Fri, 15 Feb 2019 07:25:19: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:25:19: #1 finished! INFO @ Fri, 15 Feb 2019 07:25:19: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:25:19: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:25:21: 19000000 INFO @ Fri, 15 Feb 2019 07:25:22: #2 number of paired peaks: 26760 INFO @ Fri, 15 Feb 2019 07:25:22: start model_add_line... INFO @ Fri, 15 Feb 2019 07:25:22: start X-correlation... INFO @ Fri, 15 Feb 2019 07:25:22: end of X-cor INFO @ Fri, 15 Feb 2019 07:25:22: #2 finished! INFO @ Fri, 15 Feb 2019 07:25:22: #2 predicted fragment length is 262 bps INFO @ Fri, 15 Feb 2019 07:25:22: #2 alternative fragment length(s) may be 262 bps INFO @ Fri, 15 Feb 2019 07:25:22: #2.2 Generate R script for model : SRX4497197.05_model.r INFO @ Fri, 15 Feb 2019 07:25:22: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:25:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:25:23: 19000000 INFO @ Fri, 15 Feb 2019 07:25:25: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:25:25: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:25:25: #1 total tags in treatment: 19617629 INFO @ Fri, 15 Feb 2019 07:25:25: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:25:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:25:26: #1 tags after filtering in treatment: 19617504 INFO @ Fri, 15 Feb 2019 07:25:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:25:26: #1 finished! INFO @ Fri, 15 Feb 2019 07:25:26: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:25:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:25:27: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:25:27: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:25:27: #1 total tags in treatment: 19617629 INFO @ Fri, 15 Feb 2019 07:25:27: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:25:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:25:28: #1 tags after filtering in treatment: 19617504 INFO @ Fri, 15 Feb 2019 07:25:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:25:28: #1 finished! INFO @ Fri, 15 Feb 2019 07:25:28: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:25:29: #2 number of paired peaks: 26760 INFO @ Fri, 15 Feb 2019 07:25:29: start model_add_line... INFO @ Fri, 15 Feb 2019 07:25:29: start X-correlation... INFO @ Fri, 15 Feb 2019 07:25:29: end of X-cor INFO @ Fri, 15 Feb 2019 07:25:29: #2 finished! INFO @ Fri, 15 Feb 2019 07:25:29: #2 predicted fragment length is 262 bps INFO @ Fri, 15 Feb 2019 07:25:29: #2 alternative fragment length(s) may be 262 bps INFO @ Fri, 15 Feb 2019 07:25:29: #2.2 Generate R script for model : SRX4497197.20_model.r INFO @ Fri, 15 Feb 2019 07:25:29: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:25:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:25:31: #2 number of paired peaks: 26760 INFO @ Fri, 15 Feb 2019 07:25:31: start model_add_line... INFO @ Fri, 15 Feb 2019 07:25:31: start X-correlation... INFO @ Fri, 15 Feb 2019 07:25:31: end of X-cor INFO @ Fri, 15 Feb 2019 07:25:31: #2 finished! INFO @ Fri, 15 Feb 2019 07:25:31: #2 predicted fragment length is 262 bps INFO @ Fri, 15 Feb 2019 07:25:31: #2 alternative fragment length(s) may be 262 bps INFO @ Fri, 15 Feb 2019 07:25:31: #2.2 Generate R script for model : SRX4497197.10_model.r INFO @ Fri, 15 Feb 2019 07:25:31: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:25:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:26:12: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:26:18: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:26:25: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:26:41: #4 Write output xls file... SRX4497197.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:26:41: #4 Write peak in narrowPeak format file... SRX4497197.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:26:41: #4 Write summits bed file... SRX4497197.05_summits.bed INFO @ Fri, 15 Feb 2019 07:26:41: Done! pass1 - making usageList (48 chroms): 9 millis pass2 - checking and writing primary data (945 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:26:47: #4 Write output xls file... SRX4497197.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:26:47: #4 Write peak in narrowPeak format file... SRX4497197.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:26:47: #4 Write summits bed file... SRX4497197.20_summits.bed INFO @ Fri, 15 Feb 2019 07:26:47: Done! pass1 - making usageList (29 chroms): 8 millis pass2 - checking and writing primary data (240 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:26:53: #4 Write output xls file... SRX4497197.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:26:53: #4 Write peak in narrowPeak format file... SRX4497197.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:26:54: #4 Write summits bed file... SRX4497197.10_summits.bed INFO @ Fri, 15 Feb 2019 07:26:54: Done! pass1 - making usageList (41 chroms): 8 millis pass2 - checking and writing primary data (515 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。