Job ID = 10487616 sra ファイルのダウンロード中... Completed: 704696K bytes transferred in 14 seconds (394538K 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 18631904 spots for /home/okishinya/chipatlas/results/rn6/SRX3358572/SRR6251631.sra Written 18631904 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:21:11 18631904 reads; of these: 18631904 (100.00%) were unpaired; of these: 753892 (4.05%) aligned 0 times 15846871 (85.05%) aligned exactly 1 time 2031141 (10.90%) aligned >1 times 95.95% overall alignment rate Time searching: 00:21:13 Overall time: 00:21:13 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 8 files... [bam_rmdupse_core] 1124674 / 17878012 = 0.0629 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 @ Sun, 18 Mar 2018 10:44:47: # Command line: callpeak -t SRX3358572.bam -f BAM -g 2.15e9 -n SRX3358572.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3358572.05 # format = BAM # ChIP-seq file = ['SRX3358572.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 @ Sun, 18 Mar 2018 10:44:47: # Command line: callpeak -t SRX3358572.bam -f BAM -g 2.15e9 -n SRX3358572.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3358572.20 # format = BAM # ChIP-seq file = ['SRX3358572.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 @ Sun, 18 Mar 2018 10:44:47: # Command line: callpeak -t SRX3358572.bam -f BAM -g 2.15e9 -n SRX3358572.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3358572.10 # format = BAM # ChIP-seq file = ['SRX3358572.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 @ Sun, 18 Mar 2018 10:44:47: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:44:47: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:44:47: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:44:47: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:44:47: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:44:47: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:44:54: 1000000 INFO @ Sun, 18 Mar 2018 10:44:54: 1000000 INFO @ Sun, 18 Mar 2018 10:44:54: 1000000 INFO @ Sun, 18 Mar 2018 10:45:00: 2000000 INFO @ Sun, 18 Mar 2018 10:45:00: 2000000 INFO @ Sun, 18 Mar 2018 10:45:01: 2000000 INFO @ Sun, 18 Mar 2018 10:45:07: 3000000 INFO @ Sun, 18 Mar 2018 10:45:07: 3000000 INFO @ Sun, 18 Mar 2018 10:45:07: 3000000 INFO @ Sun, 18 Mar 2018 10:45:14: 4000000 INFO @ Sun, 18 Mar 2018 10:45:14: 4000000 INFO @ Sun, 18 Mar 2018 10:45:14: 4000000 INFO @ Sun, 18 Mar 2018 10:45:20: 5000000 INFO @ Sun, 18 Mar 2018 10:45:20: 5000000 INFO @ Sun, 18 Mar 2018 10:45:21: 5000000 INFO @ Sun, 18 Mar 2018 10:45:27: 6000000 INFO @ Sun, 18 Mar 2018 10:45:27: 6000000 INFO @ Sun, 18 Mar 2018 10:45:27: 6000000 INFO @ Sun, 18 Mar 2018 10:45:34: 7000000 INFO @ Sun, 18 Mar 2018 10:45:34: 7000000 INFO @ Sun, 18 Mar 2018 10:45:34: 7000000 INFO @ Sun, 18 Mar 2018 10:45:41: 8000000 INFO @ Sun, 18 Mar 2018 10:45:41: 8000000 INFO @ Sun, 18 Mar 2018 10:45:41: 8000000 INFO @ Sun, 18 Mar 2018 10:45:47: 9000000 INFO @ Sun, 18 Mar 2018 10:45:47: 9000000 INFO @ Sun, 18 Mar 2018 10:45:48: 9000000 INFO @ Sun, 18 Mar 2018 10:45:54: 10000000 INFO @ Sun, 18 Mar 2018 10:45:54: 10000000 INFO @ Sun, 18 Mar 2018 10:45:55: 10000000 INFO @ Sun, 18 Mar 2018 10:46:00: 11000000 INFO @ Sun, 18 Mar 2018 10:46:01: 11000000 INFO @ Sun, 18 Mar 2018 10:46:01: 11000000 INFO @ Sun, 18 Mar 2018 10:46:07: 12000000 INFO @ Sun, 18 Mar 2018 10:46:08: 12000000 INFO @ Sun, 18 Mar 2018 10:46:08: 12000000 INFO @ Sun, 18 Mar 2018 10:46:13: 13000000 INFO @ Sun, 18 Mar 2018 10:46:14: 13000000 INFO @ Sun, 18 Mar 2018 10:46:15: 13000000 INFO @ Sun, 18 Mar 2018 10:46:20: 14000000 INFO @ Sun, 18 Mar 2018 10:46:21: 14000000 INFO @ Sun, 18 Mar 2018 10:46:22: 14000000 INFO @ Sun, 18 Mar 2018 10:46:26: 15000000 INFO @ Sun, 18 Mar 2018 10:46:28: 15000000 INFO @ Sun, 18 Mar 2018 10:46:29: 15000000 INFO @ Sun, 18 Mar 2018 10:46:33: 16000000 INFO @ Sun, 18 Mar 2018 10:46:35: 16000000 INFO @ Sun, 18 Mar 2018 10:46:36: 16000000 INFO @ Sun, 18 Mar 2018 10:46:38: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:46:38: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:46:38: #1 total tags in treatment: 16753338 INFO @ Sun, 18 Mar 2018 10:46:38: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:46:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 10:46:39: #1 tags after filtering in treatment: 16753067 INFO @ Sun, 18 Mar 2018 10:46:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:46:39: #1 finished! INFO @ Sun, 18 Mar 2018 10:46:39: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:46:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:46:40: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:46:40: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:46:40: #1 total tags in treatment: 16753338 INFO @ Sun, 18 Mar 2018 10:46:40: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:46:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 10:46:41: #1 tags after filtering in treatment: 16753067 INFO @ Sun, 18 Mar 2018 10:46:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:46:41: #1 finished! INFO @ Sun, 18 Mar 2018 10:46:41: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:46:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:46:41: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:46:41: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:46:41: #1 total tags in treatment: 16753338 INFO @ Sun, 18 Mar 2018 10:46:41: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:46:41: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 10:46:42: #1 tags after filtering in treatment: 16753067 INFO @ Sun, 18 Mar 2018 10:46:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:46:42: #1 finished! INFO @ Sun, 18 Mar 2018 10:46:42: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:46:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:46:44: #2 number of paired peaks: 93266 INFO @ Sun, 18 Mar 2018 10:46:44: start model_add_line... INFO @ Sun, 18 Mar 2018 10:46:44: start X-correlation... INFO @ Sun, 18 Mar 2018 10:46:44: end of X-cor INFO @ Sun, 18 Mar 2018 10:46:44: #2 finished! INFO @ Sun, 18 Mar 2018 10:46:44: #2 predicted fragment length is 182 bps INFO @ Sun, 18 Mar 2018 10:46:44: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 18 Mar 2018 10:46:44: #2.2 Generate R script for model : SRX3358572.10_model.r INFO @ Sun, 18 Mar 2018 10:46:44: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:46:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:46:46: #2 number of paired peaks: 93266 INFO @ Sun, 18 Mar 2018 10:46:46: start model_add_line... INFO @ Sun, 18 Mar 2018 10:46:46: start X-correlation... INFO @ Sun, 18 Mar 2018 10:46:46: end of X-cor INFO @ Sun, 18 Mar 2018 10:46:46: #2 finished! INFO @ Sun, 18 Mar 2018 10:46:46: #2 predicted fragment length is 182 bps INFO @ Sun, 18 Mar 2018 10:46:46: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 18 Mar 2018 10:46:46: #2.2 Generate R script for model : SRX3358572.20_model.r INFO @ Sun, 18 Mar 2018 10:46:46: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:46:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:46:47: #2 number of paired peaks: 93266 INFO @ Sun, 18 Mar 2018 10:46:47: start model_add_line... INFO @ Sun, 18 Mar 2018 10:46:47: start X-correlation... INFO @ Sun, 18 Mar 2018 10:46:47: end of X-cor INFO @ Sun, 18 Mar 2018 10:46:47: #2 finished! INFO @ Sun, 18 Mar 2018 10:46:47: #2 predicted fragment length is 182 bps INFO @ Sun, 18 Mar 2018 10:46:47: #2 alternative fragment length(s) may be 182 bps INFO @ Sun, 18 Mar 2018 10:46:47: #2.2 Generate R script for model : SRX3358572.05_model.r INFO @ Sun, 18 Mar 2018 10:46:47: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:47:27: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:47:33: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:47:33: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:47:54: #4 Write output xls file... SRX3358572.10_peaks.xls INFO @ Sun, 18 Mar 2018 10:47:54: #4 Write peak in narrowPeak format file... SRX3358572.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:47:55: #4 Write summits bed file... SRX3358572.10_summits.bed INFO @ Sun, 18 Mar 2018 10:47:55: Done! pass1 - making usageList (89 chroms): 6 millis pass2 - checking and writing primary data (26455 records, 4 fields): 33 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 10:48:01: #4 Write output xls file... SRX3358572.20_peaks.xls INFO @ Sun, 18 Mar 2018 10:48:01: #4 Write peak in narrowPeak format file... SRX3358572.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:48:01: #4 Write summits bed file... SRX3358572.20_summits.bed INFO @ Sun, 18 Mar 2018 10:48:02: Done! pass1 - making usageList (56 chroms): 4 millis pass2 - checking and writing primary data (13217 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 10:48:03: #4 Write output xls file... SRX3358572.05_peaks.xls INFO @ Sun, 18 Mar 2018 10:48:03: #4 Write peak in narrowPeak format file... SRX3358572.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:48:04: #4 Write summits bed file... SRX3358572.05_summits.bed INFO @ Sun, 18 Mar 2018 10:48:04: Done! pass1 - making usageList (113 chroms): 8 millis pass2 - checking and writing primary data (40109 records, 4 fields): 50 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。