Job ID = 2640601 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,189,839 reads read : 48,379,678 reads written : 24,189,839 reads 0-length : 24,189,839 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: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:34 24189839 reads; of these: 24189839 (100.00%) were unpaired; of these: 682103 (2.82%) aligned 0 times 17542735 (72.52%) aligned exactly 1 time 5965001 (24.66%) aligned >1 times 97.18% overall alignment rate Time searching: 00:20:38 Overall time: 00:20:38 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 12 files... [bam_rmdupse_core] 16281644 / 23507736 = 0.6926 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:29:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.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 18:29:25: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:29:25: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:29:33: 1000000 INFO @ Sat, 24 Aug 2019 18:29:41: 2000000 INFO @ Sat, 24 Aug 2019 18:29:49: 3000000 INFO @ Sat, 24 Aug 2019 18:29:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.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 18:29:54: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:29:54: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:29:57: 4000000 INFO @ Sat, 24 Aug 2019 18:30:03: 1000000 INFO @ Sat, 24 Aug 2019 18:30:07: 5000000 INFO @ Sat, 24 Aug 2019 18:30:11: 2000000 INFO @ Sat, 24 Aug 2019 18:30:15: 6000000 INFO @ Sat, 24 Aug 2019 18:30:20: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:30:24: 7000000 INFO @ Sat, 24 Aug 2019 18:30:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.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 18:30:24: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:30:24: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:30:25: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:30:25: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:30:25: #1 total tags in treatment: 7226092 INFO @ Sat, 24 Aug 2019 18:30:25: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:30:25: #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 18:30:26: #1 tags after filtering in treatment: 7225897 INFO @ Sat, 24 Aug 2019 18:30:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:30:26: #1 finished! INFO @ Sat, 24 Aug 2019 18:30:26: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:30:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:30:28: 4000000 INFO @ Sat, 24 Aug 2019 18:30:28: #2 number of paired peaks: 42921 INFO @ Sat, 24 Aug 2019 18:30:28: start model_add_line... INFO @ Sat, 24 Aug 2019 18:30:28: start X-correlation... INFO @ Sat, 24 Aug 2019 18:30:28: end of X-cor INFO @ Sat, 24 Aug 2019 18:30:28: #2 finished! INFO @ Sat, 24 Aug 2019 18:30:28: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:30:28: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.05_model.r INFO @ Sat, 24 Aug 2019 18:30:28: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:30:33: 1000000 INFO @ Sat, 24 Aug 2019 18:30:36: 5000000 INFO @ Sat, 24 Aug 2019 18:30:42: 2000000 INFO @ Sat, 24 Aug 2019 18:30:44: 6000000 INFO @ Sat, 24 Aug 2019 18:30:50: 3000000 INFO @ Sat, 24 Aug 2019 18:30:52: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:30:52: 7000000 INFO @ Sat, 24 Aug 2019 18:30:54: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:30:54: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:30:54: #1 total tags in treatment: 7226092 INFO @ Sat, 24 Aug 2019 18:30:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:30:54: #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 18:30:54: #1 tags after filtering in treatment: 7225897 INFO @ Sat, 24 Aug 2019 18:30:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:30:54: #1 finished! INFO @ Sat, 24 Aug 2019 18:30:54: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:30:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:30:57: #2 number of paired peaks: 42921 INFO @ Sat, 24 Aug 2019 18:30:57: start model_add_line... INFO @ Sat, 24 Aug 2019 18:30:57: start X-correlation... INFO @ Sat, 24 Aug 2019 18:30:57: end of X-cor INFO @ Sat, 24 Aug 2019 18:30:57: #2 finished! INFO @ Sat, 24 Aug 2019 18:30:57: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:30:57: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:30:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.10_model.r INFO @ Sat, 24 Aug 2019 18:30:57: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:30:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:30:58: 4000000 INFO @ Sat, 24 Aug 2019 18:31:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:31:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:31:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.05_summits.bed INFO @ Sat, 24 Aug 2019 18:31:04: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (1049 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:31:06: 5000000 INFO @ Sat, 24 Aug 2019 18:31:14: 6000000 INFO @ Sat, 24 Aug 2019 18:31:21: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:31:22: 7000000 INFO @ Sat, 24 Aug 2019 18:31:24: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:31:24: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:31:24: #1 total tags in treatment: 7226092 INFO @ Sat, 24 Aug 2019 18:31:24: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:31:24: #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 18:31:24: #1 tags after filtering in treatment: 7225897 INFO @ Sat, 24 Aug 2019 18:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:31:24: #1 finished! INFO @ Sat, 24 Aug 2019 18:31:24: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:31:27: #2 number of paired peaks: 42921 INFO @ Sat, 24 Aug 2019 18:31:27: start model_add_line... INFO @ Sat, 24 Aug 2019 18:31:27: start X-correlation... INFO @ Sat, 24 Aug 2019 18:31:27: end of X-cor INFO @ Sat, 24 Aug 2019 18:31:27: #2 finished! INFO @ Sat, 24 Aug 2019 18:31:27: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:31:27: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:31:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.20_model.r INFO @ Sat, 24 Aug 2019 18:31:27: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:31:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:31:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:31:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:31:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.10_summits.bed INFO @ Sat, 24 Aug 2019 18:31:32: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (459 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:31:50: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:32:01: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:32:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:32:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375031/SRX5375031.20_summits.bed INFO @ Sat, 24 Aug 2019 18:32:01: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。