Job ID = 11632675 sra ファイルのダウンロード中... Completed: 976102K bytes transferred in 22 seconds (355338K 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 52351152 spots for /home/okishinya/chipatlas/results/rn6/SRX3360113/SRR6253219.sra Written 52351152 spots for /home/okishinya/chipatlas/results/rn6/SRX3360113/SRR6253219.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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:14:09 52351152 reads; of these: 52351152 (100.00%) were unpaired; of these: 34513251 (65.93%) aligned 0 times 14729186 (28.14%) aligned exactly 1 time 3108715 (5.94%) aligned >1 times 34.07% overall alignment rate Time searching: 00:14:11 Overall time: 00:14:11 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] 8893223 / 17837901 = 0.4986 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 06:30:52: # Command line: callpeak -t SRX3360113.bam -f BAM -g 2.15e9 -n SRX3360113.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360113.05 # format = BAM # ChIP-seq file = ['SRX3360113.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 06:30:52: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:30:52: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:30:52: # Command line: callpeak -t SRX3360113.bam -f BAM -g 2.15e9 -n SRX3360113.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360113.20 # format = BAM # ChIP-seq file = ['SRX3360113.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 06:30:52: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:30:52: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:30:53: # Command line: callpeak -t SRX3360113.bam -f BAM -g 2.15e9 -n SRX3360113.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360113.10 # format = BAM # ChIP-seq file = ['SRX3360113.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 06:30:53: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:30:53: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:30:59: 1000000 INFO @ Fri, 15 Feb 2019 06:30:59: 1000000 INFO @ Fri, 15 Feb 2019 06:30:59: 1000000 INFO @ Fri, 15 Feb 2019 06:31:05: 2000000 INFO @ Fri, 15 Feb 2019 06:31:06: 2000000 INFO @ Fri, 15 Feb 2019 06:31:06: 2000000 INFO @ Fri, 15 Feb 2019 06:31:12: 3000000 INFO @ Fri, 15 Feb 2019 06:31:12: 3000000 INFO @ Fri, 15 Feb 2019 06:31:13: 3000000 INFO @ Fri, 15 Feb 2019 06:31:19: 4000000 INFO @ Fri, 15 Feb 2019 06:31:19: 4000000 INFO @ Fri, 15 Feb 2019 06:31:19: 4000000 INFO @ Fri, 15 Feb 2019 06:31:25: 5000000 INFO @ Fri, 15 Feb 2019 06:31:26: 5000000 INFO @ Fri, 15 Feb 2019 06:31:26: 5000000 INFO @ Fri, 15 Feb 2019 06:31:32: 6000000 INFO @ Fri, 15 Feb 2019 06:31:33: 6000000 INFO @ Fri, 15 Feb 2019 06:31:33: 6000000 INFO @ Fri, 15 Feb 2019 06:31:38: 7000000 INFO @ Fri, 15 Feb 2019 06:31:39: 7000000 INFO @ Fri, 15 Feb 2019 06:31:40: 7000000 INFO @ Fri, 15 Feb 2019 06:31:45: 8000000 INFO @ Fri, 15 Feb 2019 06:31:46: 8000000 INFO @ Fri, 15 Feb 2019 06:31:46: 8000000 INFO @ Fri, 15 Feb 2019 06:31:51: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:31:51: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:31:51: #1 total tags in treatment: 8944678 INFO @ Fri, 15 Feb 2019 06:31:51: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:31:51: #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 06:31:52: #1 tags after filtering in treatment: 8944419 INFO @ Fri, 15 Feb 2019 06:31:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:31:52: #1 finished! INFO @ Fri, 15 Feb 2019 06:31:52: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:31:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:31:53: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:31:53: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:31:53: #1 total tags in treatment: 8944678 INFO @ Fri, 15 Feb 2019 06:31:53: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:31:53: #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 06:31:53: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 06:31:53: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 06:31:53: #1 total tags in treatment: 8944678 INFO @ Fri, 15 Feb 2019 06:31:53: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:31:53: #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 06:31:53: #1 tags after filtering in treatment: 8944419 INFO @ Fri, 15 Feb 2019 06:31:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:31:53: #1 finished! INFO @ Fri, 15 Feb 2019 06:31:53: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:31:53: #1 tags after filtering in treatment: 8944419 INFO @ Fri, 15 Feb 2019 06:31:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:31:53: #1 finished! INFO @ Fri, 15 Feb 2019 06:31:53: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:31:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:31:54: #2 number of paired peaks: 37013 INFO @ Fri, 15 Feb 2019 06:31:54: start model_add_line... INFO @ Fri, 15 Feb 2019 06:31:54: start X-correlation... INFO @ Fri, 15 Feb 2019 06:31:54: end of X-cor INFO @ Fri, 15 Feb 2019 06:31:54: #2 finished! INFO @ Fri, 15 Feb 2019 06:31:54: #2 predicted fragment length is 179 bps INFO @ Fri, 15 Feb 2019 06:31:54: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 15 Feb 2019 06:31:54: #2.2 Generate R script for model : SRX3360113.20_model.r INFO @ Fri, 15 Feb 2019 06:31:54: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:31:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:31:55: #2 number of paired peaks: 37013 INFO @ Fri, 15 Feb 2019 06:31:55: start model_add_line... INFO @ Fri, 15 Feb 2019 06:31:55: #2 number of paired peaks: 37013 INFO @ Fri, 15 Feb 2019 06:31:55: start model_add_line... INFO @ Fri, 15 Feb 2019 06:31:55: start X-correlation... INFO @ Fri, 15 Feb 2019 06:31:55: end of X-cor INFO @ Fri, 15 Feb 2019 06:31:55: #2 finished! INFO @ Fri, 15 Feb 2019 06:31:55: #2 predicted fragment length is 179 bps INFO @ Fri, 15 Feb 2019 06:31:55: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 15 Feb 2019 06:31:55: #2.2 Generate R script for model : SRX3360113.10_model.r INFO @ Fri, 15 Feb 2019 06:31:55: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:31:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:31:56: start X-correlation... INFO @ Fri, 15 Feb 2019 06:31:56: end of X-cor INFO @ Fri, 15 Feb 2019 06:31:56: #2 finished! INFO @ Fri, 15 Feb 2019 06:31:56: #2 predicted fragment length is 179 bps INFO @ Fri, 15 Feb 2019 06:31:56: #2 alternative fragment length(s) may be 179 bps INFO @ Fri, 15 Feb 2019 06:31:56: #2.2 Generate R script for model : SRX3360113.05_model.r INFO @ Fri, 15 Feb 2019 06:31:56: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:31:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:32:17: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:32:18: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:32:19: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:32:30: #4 Write output xls file... SRX3360113.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:32:31: #4 Write peak in narrowPeak format file... SRX3360113.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:32:31: #4 Write summits bed file... SRX3360113.20_summits.bed INFO @ Fri, 15 Feb 2019 06:32:31: Done! pass1 - making usageList (70 chroms): 5 millis pass2 - checking and writing primary data (11301 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:32:33: #4 Write output xls file... SRX3360113.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:32:33: #4 Write peak in narrowPeak format file... SRX3360113.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:32:33: #4 Write summits bed file... SRX3360113.05_summits.bed INFO @ Fri, 15 Feb 2019 06:32:33: Done! pass1 - making usageList (124 chroms): 6 millis pass2 - checking and writing primary data (21434 records, 4 fields): 33 millis INFO @ Fri, 15 Feb 2019 06:32:34: #4 Write output xls file... SRX3360113.10_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:32:34: #4 Write peak in narrowPeak format file... SRX3360113.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:32:34: #4 Write summits bed file... SRX3360113.10_summits.bed INFO @ Fri, 15 Feb 2019 06:32:34: Done! pass1 - making usageList (104 chroms): 6 millis pass2 - checking and writing primary data (17307 records, 4 fields): 26 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。