Job ID = 10194717 sra ファイルのダウンロード中... Completed: 416292K bytes transferred in 8 seconds (407429K 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 11613355 spots for /home/okishinya/chipatlas/results/rn6/SRX039670/SRR096825.sra Written 11613355 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: 00:18:52 11613355 reads; of these: 11613355 (100.00%) were unpaired; of these: 2328560 (20.05%) aligned 0 times 6615822 (56.97%) aligned exactly 1 time 2668973 (22.98%) aligned >1 times 79.95% overall alignment rate Time searching: 00:18:56 Overall time: 00:18:56 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_rmdupse_core] 995377 / 9284795 = 0.1072 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 19:07:16: # Command line: callpeak -t SRX039670.bam -f BAM -g 2.15e9 -n SRX039670.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX039670.05 # format = BAM # ChIP-seq file = ['SRX039670.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 19:07:16: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:07:16: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:07:16: # Command line: callpeak -t SRX039670.bam -f BAM -g 2.15e9 -n SRX039670.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX039670.10 # format = BAM # ChIP-seq file = ['SRX039670.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 19:07:16: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:07:16: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:07:16: # Command line: callpeak -t SRX039670.bam -f BAM -g 2.15e9 -n SRX039670.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX039670.20 # format = BAM # ChIP-seq file = ['SRX039670.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 19:07:16: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:07:16: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:07:28: 1000000 INFO @ Fri, 10 Nov 2017 19:07:31: 1000000 INFO @ Fri, 10 Nov 2017 19:07:32: 1000000 INFO @ Fri, 10 Nov 2017 19:07:42: 2000000 INFO @ Fri, 10 Nov 2017 19:07:43: 2000000 INFO @ Fri, 10 Nov 2017 19:07:46: 2000000 INFO @ Fri, 10 Nov 2017 19:07:54: 3000000 INFO @ Fri, 10 Nov 2017 19:07:55: 3000000 INFO @ Fri, 10 Nov 2017 19:08:00: 3000000 INFO @ Fri, 10 Nov 2017 19:08:05: 4000000 INFO @ Fri, 10 Nov 2017 19:08:09: 4000000 INFO @ Fri, 10 Nov 2017 19:08:14: 4000000 INFO @ Fri, 10 Nov 2017 19:08:24: 5000000 INFO @ Fri, 10 Nov 2017 19:08:26: 5000000 INFO @ Fri, 10 Nov 2017 19:08:30: 5000000 INFO @ Fri, 10 Nov 2017 19:08:40: 6000000 INFO @ Fri, 10 Nov 2017 19:08:45: 6000000 INFO @ Fri, 10 Nov 2017 19:08:48: 6000000 INFO @ Fri, 10 Nov 2017 19:08:56: 7000000 INFO @ Fri, 10 Nov 2017 19:09:01: 7000000 INFO @ Fri, 10 Nov 2017 19:09:09: 7000000 INFO @ Fri, 10 Nov 2017 19:09:11: 8000000 INFO @ Fri, 10 Nov 2017 19:09:15: 8000000 INFO @ Fri, 10 Nov 2017 19:09:16: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 19:09:16: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 19:09:16: #1 total tags in treatment: 8289418 INFO @ Fri, 10 Nov 2017 19:09:16: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:09:16: #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 19:09:16: #1 tags after filtering in treatment: 8289213 INFO @ Fri, 10 Nov 2017 19:09:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:09:16: #1 finished! INFO @ Fri, 10 Nov 2017 19:09:16: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:09:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:09:19: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 19:09:19: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 19:09:19: #1 total tags in treatment: 8289418 INFO @ Fri, 10 Nov 2017 19:09:19: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:09:19: #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 19:09:20: #2 number of paired peaks: 38876 INFO @ Fri, 10 Nov 2017 19:09:20: start model_add_line... INFO @ Fri, 10 Nov 2017 19:09:20: start X-correlation... INFO @ Fri, 10 Nov 2017 19:09:20: end of X-cor INFO @ Fri, 10 Nov 2017 19:09:20: #2 finished! INFO @ Fri, 10 Nov 2017 19:09:20: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Nov 2017 19:09:20: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Nov 2017 19:09:20: #2.2 Generate R script for model : SRX039670.10_model.r INFO @ Fri, 10 Nov 2017 19:09:20: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:09:20: #1 tags after filtering in treatment: 8289213 INFO @ Fri, 10 Nov 2017 19:09:20: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:09:20: #1 finished! INFO @ Fri, 10 Nov 2017 19:09:20: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:09:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:09:20: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:09:23: #2 number of paired peaks: 38876 INFO @ Fri, 10 Nov 2017 19:09:23: start model_add_line... INFO @ Fri, 10 Nov 2017 19:09:24: start X-correlation... INFO @ Fri, 10 Nov 2017 19:09:24: end of X-cor INFO @ Fri, 10 Nov 2017 19:09:24: #2 finished! INFO @ Fri, 10 Nov 2017 19:09:24: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Nov 2017 19:09:24: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Nov 2017 19:09:24: #2.2 Generate R script for model : SRX039670.05_model.r INFO @ Fri, 10 Nov 2017 19:09:24: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:09:24: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:09:31: 8000000 INFO @ Fri, 10 Nov 2017 19:09:37: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 19:09:37: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 19:09:37: #1 total tags in treatment: 8289418 INFO @ Fri, 10 Nov 2017 19:09:37: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:09:37: #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 19:09:37: #1 tags after filtering in treatment: 8289213 INFO @ Fri, 10 Nov 2017 19:09:37: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:09:37: #1 finished! INFO @ Fri, 10 Nov 2017 19:09:37: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:09:37: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:09:40: #2 number of paired peaks: 38876 INFO @ Fri, 10 Nov 2017 19:09:40: start model_add_line... INFO @ Fri, 10 Nov 2017 19:09:41: start X-correlation... INFO @ Fri, 10 Nov 2017 19:09:41: end of X-cor INFO @ Fri, 10 Nov 2017 19:09:41: #2 finished! INFO @ Fri, 10 Nov 2017 19:09:41: #2 predicted fragment length is 156 bps INFO @ Fri, 10 Nov 2017 19:09:41: #2 alternative fragment length(s) may be 156 bps INFO @ Fri, 10 Nov 2017 19:09:41: #2.2 Generate R script for model : SRX039670.20_model.r INFO @ Fri, 10 Nov 2017 19:09:41: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:09:41: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:09:47: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:09:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:10:03: #4 Write output xls file... SRX039670.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:10:03: #4 Write peak in narrowPeak format file... SRX039670.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:10:03: #4 Write summits bed file... SRX039670.10_summits.bed INFO @ Fri, 10 Nov 2017 19:10:03: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (618 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:10:05: #4 Write output xls file... SRX039670.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:10:05: #4 Write peak in narrowPeak format file... SRX039670.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:10:05: #4 Write summits bed file... SRX039670.05_summits.bed INFO @ Fri, 10 Nov 2017 19:10:05: Done! pass1 - making usageList (62 chroms): 3 millis pass2 - checking and writing primary data (2854 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:10:07: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:10:22: #4 Write output xls file... SRX039670.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:10:22: #4 Write peak in narrowPeak format file... SRX039670.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:10:22: #4 Write summits bed file... SRX039670.20_summits.bed INFO @ Fri, 10 Nov 2017 19:10:22: Done! pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (208 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。