Job ID = 10608883 sra ファイルのダウンロード中... Completed: 483288K bytes transferred in 22 seconds (179746K 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 17562011 spots for /home/okishinya/chipatlas/results/rn6/SRX3145022/SRR5989257.sra Written 17562011 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:51 17562011 reads; of these: 17562011 (100.00%) were unpaired; of these: 413611 (2.36%) aligned 0 times 11687799 (66.55%) aligned exactly 1 time 5460601 (31.09%) aligned >1 times 97.64% overall alignment rate Time searching: 00:11:54 Overall time: 00:11:54 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] 1051273 / 17148400 = 0.0613 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 @ Thu, 03 May 2018 22:39:03: # Command line: callpeak -t SRX3145022.bam -f BAM -g 2.15e9 -n SRX3145022.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3145022.20 # format = BAM # ChIP-seq file = ['SRX3145022.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 @ Thu, 03 May 2018 22:39:03: #1 read tag files... INFO @ Thu, 03 May 2018 22:39:03: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:39:03: # Command line: callpeak -t SRX3145022.bam -f BAM -g 2.15e9 -n SRX3145022.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3145022.10 # format = BAM # ChIP-seq file = ['SRX3145022.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 @ Thu, 03 May 2018 22:39:03: #1 read tag files... INFO @ Thu, 03 May 2018 22:39:03: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:39:03: # Command line: callpeak -t SRX3145022.bam -f BAM -g 2.15e9 -n SRX3145022.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3145022.05 # format = BAM # ChIP-seq file = ['SRX3145022.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 @ Thu, 03 May 2018 22:39:03: #1 read tag files... INFO @ Thu, 03 May 2018 22:39:03: #1 read treatment tags... INFO @ Thu, 03 May 2018 22:39:10: 1000000 INFO @ Thu, 03 May 2018 22:39:10: 1000000 INFO @ Thu, 03 May 2018 22:39:10: 1000000 INFO @ Thu, 03 May 2018 22:39:17: 2000000 INFO @ Thu, 03 May 2018 22:39:18: 2000000 INFO @ Thu, 03 May 2018 22:39:18: 2000000 INFO @ Thu, 03 May 2018 22:39:24: 3000000 INFO @ Thu, 03 May 2018 22:39:25: 3000000 INFO @ Thu, 03 May 2018 22:39:25: 3000000 INFO @ Thu, 03 May 2018 22:39:31: 4000000 INFO @ Thu, 03 May 2018 22:39:33: 4000000 INFO @ Thu, 03 May 2018 22:39:33: 4000000 INFO @ Thu, 03 May 2018 22:39:38: 5000000 INFO @ Thu, 03 May 2018 22:39:40: 5000000 INFO @ Thu, 03 May 2018 22:39:40: 5000000 INFO @ Thu, 03 May 2018 22:39:45: 6000000 INFO @ Thu, 03 May 2018 22:39:47: 6000000 INFO @ Thu, 03 May 2018 22:39:47: 6000000 INFO @ Thu, 03 May 2018 22:39:52: 7000000 INFO @ Thu, 03 May 2018 22:39:55: 7000000 INFO @ Thu, 03 May 2018 22:39:55: 7000000 INFO @ Thu, 03 May 2018 22:39:58: 8000000 INFO @ Thu, 03 May 2018 22:40:02: 8000000 INFO @ Thu, 03 May 2018 22:40:02: 8000000 INFO @ Thu, 03 May 2018 22:40:05: 9000000 INFO @ Thu, 03 May 2018 22:40:09: 9000000 INFO @ Thu, 03 May 2018 22:40:09: 9000000 INFO @ Thu, 03 May 2018 22:40:12: 10000000 INFO @ Thu, 03 May 2018 22:40:17: 10000000 INFO @ Thu, 03 May 2018 22:40:17: 10000000 INFO @ Thu, 03 May 2018 22:40:19: 11000000 INFO @ Thu, 03 May 2018 22:40:24: 11000000 INFO @ Thu, 03 May 2018 22:40:24: 11000000 INFO @ Thu, 03 May 2018 22:40:26: 12000000 INFO @ Thu, 03 May 2018 22:40:31: 12000000 INFO @ Thu, 03 May 2018 22:40:31: 12000000 INFO @ Thu, 03 May 2018 22:40:33: 13000000 INFO @ Thu, 03 May 2018 22:40:39: 13000000 INFO @ Thu, 03 May 2018 22:40:39: 13000000 INFO @ Thu, 03 May 2018 22:40:40: 14000000 INFO @ Thu, 03 May 2018 22:40:46: 14000000 INFO @ Thu, 03 May 2018 22:40:46: 14000000 INFO @ Thu, 03 May 2018 22:40:47: 15000000 INFO @ Thu, 03 May 2018 22:40:53: 15000000 INFO @ Thu, 03 May 2018 22:40:53: 15000000 INFO @ Thu, 03 May 2018 22:40:54: 16000000 INFO @ Thu, 03 May 2018 22:40:55: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:40:55: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:40:55: #1 total tags in treatment: 16097127 INFO @ Thu, 03 May 2018 22:40:55: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:40:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:40:55: #1 tags after filtering in treatment: 16096973 INFO @ Thu, 03 May 2018 22:40:55: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:40:55: #1 finished! INFO @ Thu, 03 May 2018 22:40:55: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:40:55: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:40:59: #2 number of paired peaks: 43263 INFO @ Thu, 03 May 2018 22:40:59: start model_add_line... INFO @ Thu, 03 May 2018 22:40:59: start X-correlation... INFO @ Thu, 03 May 2018 22:40:59: end of X-cor INFO @ Thu, 03 May 2018 22:40:59: #2 finished! INFO @ Thu, 03 May 2018 22:40:59: #2 predicted fragment length is 268 bps INFO @ Thu, 03 May 2018 22:40:59: #2 alternative fragment length(s) may be 268 bps INFO @ Thu, 03 May 2018 22:40:59: #2.2 Generate R script for model : SRX3145022.05_model.r INFO @ Thu, 03 May 2018 22:40:59: #3 Call peaks... INFO @ Thu, 03 May 2018 22:40:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:41:00: 16000000 INFO @ Thu, 03 May 2018 22:41:00: 16000000 INFO @ Thu, 03 May 2018 22:41:01: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:41:01: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:41:01: #1 total tags in treatment: 16097127 INFO @ Thu, 03 May 2018 22:41:01: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:41:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:41:01: #1 tag size is determined as 51 bps INFO @ Thu, 03 May 2018 22:41:01: #1 tag size = 51 INFO @ Thu, 03 May 2018 22:41:01: #1 total tags in treatment: 16097127 INFO @ Thu, 03 May 2018 22:41:01: #1 user defined the maximum tags... INFO @ Thu, 03 May 2018 22:41:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 03 May 2018 22:41:01: #1 tags after filtering in treatment: 16096973 INFO @ Thu, 03 May 2018 22:41:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:41:01: #1 finished! INFO @ Thu, 03 May 2018 22:41:01: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:41:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:41:01: #1 tags after filtering in treatment: 16096973 INFO @ Thu, 03 May 2018 22:41:01: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 03 May 2018 22:41:01: #1 finished! INFO @ Thu, 03 May 2018 22:41:01: #2 Build Peak Model... INFO @ Thu, 03 May 2018 22:41:01: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 03 May 2018 22:41:04: #2 number of paired peaks: 43263 INFO @ Thu, 03 May 2018 22:41:04: start model_add_line... INFO @ Thu, 03 May 2018 22:41:04: #2 number of paired peaks: 43263 INFO @ Thu, 03 May 2018 22:41:04: start model_add_line... INFO @ Thu, 03 May 2018 22:41:04: start X-correlation... INFO @ Thu, 03 May 2018 22:41:04: end of X-cor INFO @ Thu, 03 May 2018 22:41:04: #2 finished! INFO @ Thu, 03 May 2018 22:41:04: #2 predicted fragment length is 268 bps INFO @ Thu, 03 May 2018 22:41:04: #2 alternative fragment length(s) may be 268 bps INFO @ Thu, 03 May 2018 22:41:04: #2.2 Generate R script for model : SRX3145022.10_model.r INFO @ Thu, 03 May 2018 22:41:04: #3 Call peaks... INFO @ Thu, 03 May 2018 22:41:04: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:41:05: start X-correlation... INFO @ Thu, 03 May 2018 22:41:05: end of X-cor INFO @ Thu, 03 May 2018 22:41:05: #2 finished! INFO @ Thu, 03 May 2018 22:41:05: #2 predicted fragment length is 268 bps INFO @ Thu, 03 May 2018 22:41:05: #2 alternative fragment length(s) may be 268 bps INFO @ Thu, 03 May 2018 22:41:05: #2.2 Generate R script for model : SRX3145022.20_model.r INFO @ Thu, 03 May 2018 22:41:05: #3 Call peaks... INFO @ Thu, 03 May 2018 22:41:05: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 03 May 2018 22:41:42: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:41:46: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:41:47: #3 Call peaks for each chromosome... INFO @ Thu, 03 May 2018 22:42:05: #4 Write output xls file... SRX3145022.05_peaks.xls INFO @ Thu, 03 May 2018 22:42:05: #4 Write peak in narrowPeak format file... SRX3145022.05_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:42:05: #4 Write summits bed file... SRX3145022.05_summits.bed INFO @ Thu, 03 May 2018 22:42:05: Done! pass1 - making usageList (105 chroms): 4 millis pass2 - checking and writing primary data (16293 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:42:10: #4 Write output xls file... SRX3145022.10_peaks.xls INFO @ Thu, 03 May 2018 22:42:10: #4 Write peak in narrowPeak format file... SRX3145022.10_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:42:10: #4 Write summits bed file... SRX3145022.10_summits.bed INFO @ Thu, 03 May 2018 22:42:10: Done! pass1 - making usageList (65 chroms): 2 millis pass2 - checking and writing primary data (9222 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 03 May 2018 22:42:12: #4 Write output xls file... SRX3145022.20_peaks.xls INFO @ Thu, 03 May 2018 22:42:12: #4 Write peak in narrowPeak format file... SRX3145022.20_peaks.narrowPeak INFO @ Thu, 03 May 2018 22:42:12: #4 Write summits bed file... SRX3145022.20_summits.bed INFO @ Thu, 03 May 2018 22:42:12: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1566 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。