Job ID = 2640680 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,332,570 reads read : 10,665,140 reads written : 5,332,570 reads 0-length : 5,332,570 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:00:00 Multiseed full-index search: 00:04:28 5332570 reads; of these: 5332570 (100.00%) were unpaired; of these: 480483 (9.01%) aligned 0 times 3560918 (66.78%) aligned exactly 1 time 1291169 (24.21%) aligned >1 times 90.99% overall alignment rate Time searching: 00:04:29 Overall time: 00:04:29 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] 183062 / 4852087 = 0.0377 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:13:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.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 @ Sat, 24 Aug 2019 18:13:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:13:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:14:02: 1000000 INFO @ Sat, 24 Aug 2019 18:14:09: 2000000 INFO @ Sat, 24 Aug 2019 18:14:15: 3000000 INFO @ Sat, 24 Aug 2019 18:14:21: 4000000 INFO @ Sat, 24 Aug 2019 18:14:26: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:14:26: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:14:26: #1 total tags in treatment: 4669025 INFO @ Sat, 24 Aug 2019 18:14:26: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:14:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:14:26: #1 tags after filtering in treatment: 4668744 INFO @ Sat, 24 Aug 2019 18:14:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:14:26: #1 finished! INFO @ Sat, 24 Aug 2019 18:14:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:14:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.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 @ Sat, 24 Aug 2019 18:14:26: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:14:26: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:14:29: #2 number of paired peaks: 27044 INFO @ Sat, 24 Aug 2019 18:14:29: start model_add_line... INFO @ Sat, 24 Aug 2019 18:14:29: start X-correlation... INFO @ Sat, 24 Aug 2019 18:14:29: end of X-cor INFO @ Sat, 24 Aug 2019 18:14:29: #2 finished! INFO @ Sat, 24 Aug 2019 18:14:29: #2 predicted fragment length is 167 bps INFO @ Sat, 24 Aug 2019 18:14:29: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 24 Aug 2019 18:14:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.05_model.r INFO @ Sat, 24 Aug 2019 18:14:29: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:14:34: 1000000 INFO @ Sat, 24 Aug 2019 18:14:42: 2000000 INFO @ Sat, 24 Aug 2019 18:14:44: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:14:50: 3000000 INFO @ Sat, 24 Aug 2019 18:14:52: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:14:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:14:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.05_summits.bed INFO @ Sat, 24 Aug 2019 18:14:52: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (2655 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:14:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.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 @ Sat, 24 Aug 2019 18:14:56: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:14:56: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:14:58: 4000000 INFO @ Sat, 24 Aug 2019 18:15:03: 1000000 INFO @ Sat, 24 Aug 2019 18:15:03: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:15:03: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:15:03: #1 total tags in treatment: 4669025 INFO @ Sat, 24 Aug 2019 18:15:03: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:15:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:15:03: #1 tags after filtering in treatment: 4668744 INFO @ Sat, 24 Aug 2019 18:15:03: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:15:03: #1 finished! INFO @ Sat, 24 Aug 2019 18:15:03: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:15:03: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:15:07: #2 number of paired peaks: 27044 INFO @ Sat, 24 Aug 2019 18:15:07: start model_add_line... INFO @ Sat, 24 Aug 2019 18:15:07: start X-correlation... INFO @ Sat, 24 Aug 2019 18:15:07: end of X-cor INFO @ Sat, 24 Aug 2019 18:15:07: #2 finished! INFO @ Sat, 24 Aug 2019 18:15:07: #2 predicted fragment length is 167 bps INFO @ Sat, 24 Aug 2019 18:15:07: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 24 Aug 2019 18:15:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.10_model.r INFO @ Sat, 24 Aug 2019 18:15:07: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:15:10: 2000000 INFO @ Sat, 24 Aug 2019 18:15:17: 3000000 INFO @ Sat, 24 Aug 2019 18:15:22: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:15:24: 4000000 INFO @ Sat, 24 Aug 2019 18:15:28: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:15:28: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:15:28: #1 total tags in treatment: 4669025 INFO @ Sat, 24 Aug 2019 18:15:28: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:15:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 18:15:29: #1 tags after filtering in treatment: 4668744 INFO @ Sat, 24 Aug 2019 18:15:29: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:15:29: #1 finished! INFO @ Sat, 24 Aug 2019 18:15:29: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:15:29: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:15:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:15:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.10_summits.bed INFO @ Sat, 24 Aug 2019 18:15:29: Done! pass1 - making usageList (28 chroms): 2 millis pass2 - checking and writing primary data (1297 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:15:32: #2 number of paired peaks: 27044 INFO @ Sat, 24 Aug 2019 18:15:32: start model_add_line... INFO @ Sat, 24 Aug 2019 18:15:32: start X-correlation... INFO @ Sat, 24 Aug 2019 18:15:32: end of X-cor INFO @ Sat, 24 Aug 2019 18:15:32: #2 finished! INFO @ Sat, 24 Aug 2019 18:15:32: #2 predicted fragment length is 167 bps INFO @ Sat, 24 Aug 2019 18:15:32: #2 alternative fragment length(s) may be 167 bps INFO @ Sat, 24 Aug 2019 18:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.20_model.r INFO @ Sat, 24 Aug 2019 18:15:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:15:47: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:15:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:15:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:15:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375044/SRX5375044.20_summits.bed INFO @ Sat, 24 Aug 2019 18:15:54: Done! pass1 - making usageList (23 chroms): 2 millis pass2 - checking and writing primary data (527 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。