Job ID = 2001670 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,833,263 reads read : 12,833,263 reads written : 12,833,263 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: 00:05:40 12833263 reads; of these: 12833263 (100.00%) were unpaired; of these: 274357 (2.14%) aligned 0 times 8527805 (66.45%) aligned exactly 1 time 4031101 (31.41%) aligned >1 times 97.86% overall alignment rate Time searching: 00:05:41 Overall time: 00:05:41 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] 442927 / 12558906 = 0.0353 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, 05 Jul 2019 08:01:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.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, 05 Jul 2019 08:01:02: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:01:02: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.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, 05 Jul 2019 08:01:03: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:01:03: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.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, 05 Jul 2019 08:01:04: #1 read tag files... INFO @ Fri, 05 Jul 2019 08:01:04: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 08:01:09: 1000000 INFO @ Fri, 05 Jul 2019 08:01:11: 1000000 INFO @ Fri, 05 Jul 2019 08:01:11: 1000000 INFO @ Fri, 05 Jul 2019 08:01:16: 2000000 INFO @ Fri, 05 Jul 2019 08:01:17: 2000000 INFO @ Fri, 05 Jul 2019 08:01:20: 2000000 INFO @ Fri, 05 Jul 2019 08:01:23: 3000000 INFO @ Fri, 05 Jul 2019 08:01:24: 3000000 INFO @ Fri, 05 Jul 2019 08:01:28: 3000000 INFO @ Fri, 05 Jul 2019 08:01:29: 4000000 INFO @ Fri, 05 Jul 2019 08:01:30: 4000000 INFO @ Fri, 05 Jul 2019 08:01:36: 5000000 INFO @ Fri, 05 Jul 2019 08:01:37: 4000000 INFO @ Fri, 05 Jul 2019 08:01:37: 5000000 INFO @ Fri, 05 Jul 2019 08:01:42: 6000000 INFO @ Fri, 05 Jul 2019 08:01:44: 6000000 INFO @ Fri, 05 Jul 2019 08:01:45: 5000000 INFO @ Fri, 05 Jul 2019 08:01:49: 7000000 INFO @ Fri, 05 Jul 2019 08:01:51: 7000000 INFO @ Fri, 05 Jul 2019 08:01:54: 6000000 INFO @ Fri, 05 Jul 2019 08:01:55: 8000000 INFO @ Fri, 05 Jul 2019 08:01:57: 8000000 INFO @ Fri, 05 Jul 2019 08:02:02: 9000000 INFO @ Fri, 05 Jul 2019 08:02:02: 7000000 INFO @ Fri, 05 Jul 2019 08:02:04: 9000000 INFO @ Fri, 05 Jul 2019 08:02:08: 10000000 INFO @ Fri, 05 Jul 2019 08:02:11: 10000000 INFO @ Fri, 05 Jul 2019 08:02:11: 8000000 INFO @ Fri, 05 Jul 2019 08:02:15: 11000000 INFO @ Fri, 05 Jul 2019 08:02:17: 11000000 INFO @ Fri, 05 Jul 2019 08:02:19: 9000000 INFO @ Fri, 05 Jul 2019 08:02:22: 12000000 INFO @ Fri, 05 Jul 2019 08:02:23: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:02:23: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:02:23: #1 total tags in treatment: 12115979 INFO @ Fri, 05 Jul 2019 08:02:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:02:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 08:02:23: #1 tags after filtering in treatment: 12115809 INFO @ Fri, 05 Jul 2019 08:02:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:02:23: #1 finished! INFO @ Fri, 05 Jul 2019 08:02:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:02:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:02:24: 12000000 INFO @ Fri, 05 Jul 2019 08:02:25: #2 number of paired peaks: 10877 INFO @ Fri, 05 Jul 2019 08:02:25: start model_add_line... INFO @ Fri, 05 Jul 2019 08:02:25: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:02:25: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:02:25: #1 total tags in treatment: 12115979 INFO @ Fri, 05 Jul 2019 08:02:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:02:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 08:02:25: start X-correlation... INFO @ Fri, 05 Jul 2019 08:02:25: end of X-cor INFO @ Fri, 05 Jul 2019 08:02:25: #2 finished! INFO @ Fri, 05 Jul 2019 08:02:25: #2 predicted fragment length is 96 bps INFO @ Fri, 05 Jul 2019 08:02:25: #2 alternative fragment length(s) may be 96 bps INFO @ Fri, 05 Jul 2019 08:02:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.10_model.r INFO @ Fri, 05 Jul 2019 08:02:25: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:02:25: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:02:25: #1 tags after filtering in treatment: 12115809 INFO @ Fri, 05 Jul 2019 08:02:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:02:25: #1 finished! INFO @ Fri, 05 Jul 2019 08:02:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:02:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:02:27: #2 number of paired peaks: 10877 INFO @ Fri, 05 Jul 2019 08:02:27: start model_add_line... INFO @ Fri, 05 Jul 2019 08:02:27: 10000000 INFO @ Fri, 05 Jul 2019 08:02:27: start X-correlation... INFO @ Fri, 05 Jul 2019 08:02:27: end of X-cor INFO @ Fri, 05 Jul 2019 08:02:27: #2 finished! INFO @ Fri, 05 Jul 2019 08:02:27: #2 predicted fragment length is 96 bps INFO @ Fri, 05 Jul 2019 08:02:27: #2 alternative fragment length(s) may be 96 bps INFO @ Fri, 05 Jul 2019 08:02:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.20_model.r INFO @ Fri, 05 Jul 2019 08:02:28: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:02:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:02:36: 11000000 INFO @ Fri, 05 Jul 2019 08:02:44: 12000000 INFO @ Fri, 05 Jul 2019 08:02:45: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 08:02:45: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 08:02:45: #1 total tags in treatment: 12115979 INFO @ Fri, 05 Jul 2019 08:02:45: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 08:02:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 08:02:45: #1 tags after filtering in treatment: 12115809 INFO @ Fri, 05 Jul 2019 08:02:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 08:02:45: #1 finished! INFO @ Fri, 05 Jul 2019 08:02:45: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 08:02:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 08:02:47: #2 number of paired peaks: 10877 INFO @ Fri, 05 Jul 2019 08:02:47: start model_add_line... INFO @ Fri, 05 Jul 2019 08:02:47: start X-correlation... INFO @ Fri, 05 Jul 2019 08:02:47: end of X-cor INFO @ Fri, 05 Jul 2019 08:02:47: #2 finished! INFO @ Fri, 05 Jul 2019 08:02:47: #2 predicted fragment length is 96 bps INFO @ Fri, 05 Jul 2019 08:02:47: #2 alternative fragment length(s) may be 96 bps INFO @ Fri, 05 Jul 2019 08:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.05_model.r INFO @ Fri, 05 Jul 2019 08:02:47: #3 Call peaks... INFO @ Fri, 05 Jul 2019 08:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 08:03:03: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:03:06: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:03:22: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.10_peaks.xls INFO @ Fri, 05 Jul 2019 08:03:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:03:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.10_summits.bed INFO @ Fri, 05 Jul 2019 08:03:22: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (459 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:03:25: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.20_peaks.xls INFO @ Fri, 05 Jul 2019 08:03:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:03:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.20_summits.bed INFO @ Fri, 05 Jul 2019 08:03:25: Done! pass1 - making usageList (24 chroms): 2 millis pass2 - checking and writing primary data (129 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 08:03:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 08:03:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.05_peaks.xls INFO @ Fri, 05 Jul 2019 08:03:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 08:03:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101985/ERX101985.05_summits.bed INFO @ Fri, 05 Jul 2019 08:03:45: Done! pass1 - making usageList (54 chroms): 2 millis pass2 - checking and writing primary data (1456 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。