Job ID = 11632677 sra ファイルのダウンロード中... Completed: 790313K bytes transferred in 18 seconds (347799K 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 45125026 spots for /home/okishinya/chipatlas/results/rn6/SRX3360115/SRR6253221.sra Written 45125026 spots for /home/okishinya/chipatlas/results/rn6/SRX3360115/SRR6253221.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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:24:32 45125026 reads; of these: 45125026 (100.00%) were unpaired; of these: 14010878 (31.05%) aligned 0 times 23581749 (52.26%) aligned exactly 1 time 7532399 (16.69%) aligned >1 times 68.95% overall alignment rate Time searching: 00:24:36 Overall time: 00:24:36 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 16 files... [bam_rmdupse_core] 8186371 / 31114148 = 0.2631 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 06:04:40: # Command line: callpeak -t SRX3360115.bam -f BAM -g 2.15e9 -n SRX3360115.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360115.20 # format = BAM # ChIP-seq file = ['SRX3360115.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 06:04:40: # Command line: callpeak -t SRX3360115.bam -f BAM -g 2.15e9 -n SRX3360115.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360115.05 # format = BAM # ChIP-seq file = ['SRX3360115.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 06:04:40: # Command line: callpeak -t SRX3360115.bam -f BAM -g 2.15e9 -n SRX3360115.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360115.10 # format = BAM # ChIP-seq file = ['SRX3360115.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 06:04:40: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:04:40: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:04:40: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:04:40: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:04:40: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:04:40: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:04:46: 1000000 INFO @ Fri, 15 Feb 2019 06:04:46: 1000000 INFO @ Fri, 15 Feb 2019 06:04:46: 1000000 INFO @ Fri, 15 Feb 2019 06:04:52: 2000000 INFO @ Fri, 15 Feb 2019 06:04:52: 2000000 INFO @ Fri, 15 Feb 2019 06:04:52: 2000000 INFO @ Fri, 15 Feb 2019 06:04:58: 3000000 INFO @ Fri, 15 Feb 2019 06:04:58: 3000000 INFO @ Fri, 15 Feb 2019 06:04:59: 3000000 INFO @ Fri, 15 Feb 2019 06:05:04: 4000000 INFO @ Fri, 15 Feb 2019 06:05:04: 4000000 INFO @ Fri, 15 Feb 2019 06:05:05: 4000000 INFO @ Fri, 15 Feb 2019 06:05:10: 5000000 INFO @ Fri, 15 Feb 2019 06:05:10: 5000000 INFO @ Fri, 15 Feb 2019 06:05:11: 5000000 INFO @ Fri, 15 Feb 2019 06:05:16: 6000000 INFO @ Fri, 15 Feb 2019 06:05:16: 6000000 INFO @ Fri, 15 Feb 2019 06:05:17: 6000000 INFO @ Fri, 15 Feb 2019 06:05:22: 7000000 INFO @ Fri, 15 Feb 2019 06:05:23: 7000000 INFO @ Fri, 15 Feb 2019 06:05:23: 7000000 INFO @ Fri, 15 Feb 2019 06:05:28: 8000000 INFO @ Fri, 15 Feb 2019 06:05:29: 8000000 INFO @ Fri, 15 Feb 2019 06:05:29: 8000000 INFO @ Fri, 15 Feb 2019 06:05:34: 9000000 INFO @ Fri, 15 Feb 2019 06:05:35: 9000000 INFO @ Fri, 15 Feb 2019 06:05:36: 9000000 INFO @ Fri, 15 Feb 2019 06:05:40: 10000000 INFO @ Fri, 15 Feb 2019 06:05:41: 10000000 INFO @ Fri, 15 Feb 2019 06:05:42: 10000000 INFO @ Fri, 15 Feb 2019 06:05:46: 11000000 INFO @ Fri, 15 Feb 2019 06:05:47: 11000000 INFO @ Fri, 15 Feb 2019 06:05:48: 11000000 INFO @ Fri, 15 Feb 2019 06:05:53: 12000000 INFO @ Fri, 15 Feb 2019 06:05:54: 12000000 INFO @ Fri, 15 Feb 2019 06:05:54: 12000000 INFO @ Fri, 15 Feb 2019 06:06:00: 13000000 INFO @ Fri, 15 Feb 2019 06:06:00: 13000000 INFO @ Fri, 15 Feb 2019 06:06:01: 13000000 INFO @ Fri, 15 Feb 2019 06:06:07: 14000000 INFO @ Fri, 15 Feb 2019 06:06:07: 14000000 INFO @ Fri, 15 Feb 2019 06:06:08: 14000000 INFO @ Fri, 15 Feb 2019 06:06:13: 15000000 INFO @ Fri, 15 Feb 2019 06:06:14: 15000000 INFO @ Fri, 15 Feb 2019 06:06:15: 15000000 INFO @ Fri, 15 Feb 2019 06:06:19: 16000000 INFO @ Fri, 15 Feb 2019 06:06:20: 16000000 INFO @ Fri, 15 Feb 2019 06:06:22: 16000000 INFO @ Fri, 15 Feb 2019 06:06:25: 17000000 INFO @ Fri, 15 Feb 2019 06:06:27: 17000000 INFO @ Fri, 15 Feb 2019 06:06:28: 17000000 INFO @ Fri, 15 Feb 2019 06:06:31: 18000000 INFO @ Fri, 15 Feb 2019 06:06:33: 18000000 INFO @ Fri, 15 Feb 2019 06:06:34: 18000000 INFO @ Fri, 15 Feb 2019 06:06:38: 19000000 INFO @ Fri, 15 Feb 2019 06:06:40: 19000000 INFO @ Fri, 15 Feb 2019 06:06:40: 19000000 INFO @ Fri, 15 Feb 2019 06:06:44: 20000000 INFO @ Fri, 15 Feb 2019 06:06:46: 20000000 INFO @ Fri, 15 Feb 2019 06:06:46: 20000000 INFO @ Fri, 15 Feb 2019 06:06:51: 21000000 INFO @ Fri, 15 Feb 2019 06:06:52: 21000000 INFO @ Fri, 15 Feb 2019 06:06:53: 21000000 INFO @ Fri, 15 Feb 2019 06:06:57: 22000000 INFO @ Fri, 15 Feb 2019 06:06:58: 22000000 INFO @ Fri, 15 Feb 2019 06:06:59: 22000000 INFO @ Fri, 15 Feb 2019 06:07:03: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:07:03: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:07:03: #1 total tags in treatment: 22927777 INFO @ Fri, 15 Feb 2019 06:07:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:07:03: #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 06:07:04: #1 tags after filtering in treatment: 22927633 INFO @ Fri, 15 Feb 2019 06:07:04: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:07:04: #1 finished! INFO @ Fri, 15 Feb 2019 06:07:04: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:07:04: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:07:05: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:07:05: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:07:05: #1 total tags in treatment: 22927777 INFO @ Fri, 15 Feb 2019 06:07:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:07:05: #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 06:07:05: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:07:05: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:07:05: #1 total tags in treatment: 22927777 INFO @ Fri, 15 Feb 2019 06:07:05: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:07:05: #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 06:07:05: #1 tags after filtering in treatment: 22927633 INFO @ Fri, 15 Feb 2019 06:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:07:05: #1 finished! INFO @ Fri, 15 Feb 2019 06:07:05: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:07:06: #1 tags after filtering in treatment: 22927633 INFO @ Fri, 15 Feb 2019 06:07:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:07:06: #1 finished! INFO @ Fri, 15 Feb 2019 06:07:06: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:07:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:07:08: #2 number of paired peaks: 43701 INFO @ Fri, 15 Feb 2019 06:07:08: start model_add_line... INFO @ Fri, 15 Feb 2019 06:07:08: start X-correlation... INFO @ Fri, 15 Feb 2019 06:07:08: end of X-cor INFO @ Fri, 15 Feb 2019 06:07:08: #2 finished! INFO @ Fri, 15 Feb 2019 06:07:08: #2 predicted fragment length is 166 bps INFO @ Fri, 15 Feb 2019 06:07:08: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 15 Feb 2019 06:07:08: #2.2 Generate R script for model : SRX3360115.05_model.r INFO @ Fri, 15 Feb 2019 06:07:08: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:07:08: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:07:09: #2 number of paired peaks: 43701 INFO @ Fri, 15 Feb 2019 06:07:09: start model_add_line... INFO @ Fri, 15 Feb 2019 06:07:10: start X-correlation... INFO @ Fri, 15 Feb 2019 06:07:10: end of X-cor INFO @ Fri, 15 Feb 2019 06:07:10: #2 finished! INFO @ Fri, 15 Feb 2019 06:07:10: #2 predicted fragment length is 166 bps INFO @ Fri, 15 Feb 2019 06:07:10: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 15 Feb 2019 06:07:10: #2.2 Generate R script for model : SRX3360115.10_model.r INFO @ Fri, 15 Feb 2019 06:07:10: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:07:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:07:10: #2 number of paired peaks: 43701 INFO @ Fri, 15 Feb 2019 06:07:10: start model_add_line... INFO @ Fri, 15 Feb 2019 06:07:10: start X-correlation... INFO @ Fri, 15 Feb 2019 06:07:10: end of X-cor INFO @ Fri, 15 Feb 2019 06:07:10: #2 finished! INFO @ Fri, 15 Feb 2019 06:07:10: #2 predicted fragment length is 166 bps INFO @ Fri, 15 Feb 2019 06:07:10: #2 alternative fragment length(s) may be 166 bps INFO @ Fri, 15 Feb 2019 06:07:10: #2.2 Generate R script for model : SRX3360115.20_model.r INFO @ Fri, 15 Feb 2019 06:07:10: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:07:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:08:07: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:08:08: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:08:11: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:08:42: #4 Write output xls file... SRX3360115.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:08:43: #4 Write peak in narrowPeak format file... SRX3360115.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:08:43: #4 Write summits bed file... SRX3360115.10_summits.bed INFO @ Fri, 15 Feb 2019 06:08:43: Done! pass1 - making usageList (120 chroms): 8 millis pass2 - checking and writing primary data (19778 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:08:43: #4 Write output xls file... SRX3360115.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:08:43: #4 Write peak in narrowPeak format file... SRX3360115.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:08:44: #4 Write summits bed file... SRX3360115.05_summits.bed INFO @ Fri, 15 Feb 2019 06:08:44: Done! pass1 - making usageList (139 chroms): 9 millis pass2 - checking and writing primary data (23675 records, 4 fields): 38 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:08:50: #4 Write output xls file... SRX3360115.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:08:50: #4 Write peak in narrowPeak format file... SRX3360115.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:08:50: #4 Write summits bed file... SRX3360115.20_summits.bed INFO @ Fri, 15 Feb 2019 06:08:50: Done! pass1 - making usageList (95 chroms): 9 millis pass2 - checking and writing primary data (14336 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。