Job ID = 2003632 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,721,817 reads read : 17,721,817 reads written : 17,721,817 spots read : 15,021,781 reads read : 15,021,781 reads written : 15,021,781 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: 00:37:02 32743598 reads; of these: 32743598 (100.00%) were unpaired; of these: 8583122 (26.21%) aligned 0 times 17456100 (53.31%) aligned exactly 1 time 6704376 (20.48%) aligned >1 times 73.79% overall alignment rate Time searching: 00:37:07 Overall time: 00:37:07 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] 3844457 / 24160476 = 0.1591 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 13:57:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.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 13:57:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:57:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:57:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.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 13:57:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:57:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:57:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.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 13:57:27: #1 read tag files... INFO @ Fri, 05 Jul 2019 13:57:27: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 13:57:34: 1000000 INFO @ Fri, 05 Jul 2019 13:57:35: 1000000 INFO @ Fri, 05 Jul 2019 13:57:36: 1000000 INFO @ Fri, 05 Jul 2019 13:57:43: 2000000 INFO @ Fri, 05 Jul 2019 13:57:44: 2000000 INFO @ Fri, 05 Jul 2019 13:57:45: 2000000 INFO @ Fri, 05 Jul 2019 13:57:51: 3000000 INFO @ Fri, 05 Jul 2019 13:57:53: 3000000 INFO @ Fri, 05 Jul 2019 13:57:54: 3000000 INFO @ Fri, 05 Jul 2019 13:58:00: 4000000 INFO @ Fri, 05 Jul 2019 13:58:02: 4000000 INFO @ Fri, 05 Jul 2019 13:58:02: 4000000 INFO @ Fri, 05 Jul 2019 13:58:09: 5000000 INFO @ Fri, 05 Jul 2019 13:58:11: 5000000 INFO @ Fri, 05 Jul 2019 13:58:11: 5000000 INFO @ Fri, 05 Jul 2019 13:58:17: 6000000 INFO @ Fri, 05 Jul 2019 13:58:20: 6000000 INFO @ Fri, 05 Jul 2019 13:58:20: 6000000 INFO @ Fri, 05 Jul 2019 13:58:26: 7000000 INFO @ Fri, 05 Jul 2019 13:58:29: 7000000 INFO @ Fri, 05 Jul 2019 13:58:29: 7000000 INFO @ Fri, 05 Jul 2019 13:58:35: 8000000 INFO @ Fri, 05 Jul 2019 13:58:37: 8000000 INFO @ Fri, 05 Jul 2019 13:58:37: 8000000 INFO @ Fri, 05 Jul 2019 13:58:43: 9000000 INFO @ Fri, 05 Jul 2019 13:58:46: 9000000 INFO @ Fri, 05 Jul 2019 13:58:46: 9000000 INFO @ Fri, 05 Jul 2019 13:58:52: 10000000 INFO @ Fri, 05 Jul 2019 13:58:55: 10000000 INFO @ Fri, 05 Jul 2019 13:58:55: 10000000 INFO @ Fri, 05 Jul 2019 13:59:01: 11000000 INFO @ Fri, 05 Jul 2019 13:59:04: 11000000 INFO @ Fri, 05 Jul 2019 13:59:04: 11000000 INFO @ Fri, 05 Jul 2019 13:59:10: 12000000 INFO @ Fri, 05 Jul 2019 13:59:14: 12000000 INFO @ Fri, 05 Jul 2019 13:59:14: 12000000 INFO @ Fri, 05 Jul 2019 13:59:23: 13000000 INFO @ Fri, 05 Jul 2019 13:59:23: 13000000 INFO @ Fri, 05 Jul 2019 13:59:23: 13000000 INFO @ Fri, 05 Jul 2019 13:59:32: 14000000 INFO @ Fri, 05 Jul 2019 13:59:32: 14000000 INFO @ Fri, 05 Jul 2019 13:59:32: 14000000 INFO @ Fri, 05 Jul 2019 13:59:41: 15000000 INFO @ Fri, 05 Jul 2019 13:59:41: 15000000 INFO @ Fri, 05 Jul 2019 13:59:41: 15000000 INFO @ Fri, 05 Jul 2019 13:59:50: 16000000 INFO @ Fri, 05 Jul 2019 13:59:50: 16000000 INFO @ Fri, 05 Jul 2019 13:59:50: 16000000 INFO @ Fri, 05 Jul 2019 13:59:58: 17000000 INFO @ Fri, 05 Jul 2019 13:59:59: 17000000 INFO @ Fri, 05 Jul 2019 13:59:59: 17000000 INFO @ Fri, 05 Jul 2019 14:00:07: 18000000 INFO @ Fri, 05 Jul 2019 14:00:07: 18000000 INFO @ Fri, 05 Jul 2019 14:00:07: 18000000 INFO @ Fri, 05 Jul 2019 14:00:16: 19000000 INFO @ Fri, 05 Jul 2019 14:00:16: 19000000 INFO @ Fri, 05 Jul 2019 14:00:16: 19000000 INFO @ Fri, 05 Jul 2019 14:00:25: 20000000 INFO @ Fri, 05 Jul 2019 14:00:25: 20000000 INFO @ Fri, 05 Jul 2019 14:00:25: 20000000 INFO @ Fri, 05 Jul 2019 14:00:30: #1 tag size is determined as 55 bps INFO @ Fri, 05 Jul 2019 14:00:30: #1 tag size = 55 INFO @ Fri, 05 Jul 2019 14:00:30: #1 total tags in treatment: 20316019 INFO @ Fri, 05 Jul 2019 14:00:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:00:30: #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 14:00:30: #1 tag size is determined as 55 bps INFO @ Fri, 05 Jul 2019 14:00:30: #1 tag size = 55 INFO @ Fri, 05 Jul 2019 14:00:30: #1 total tags in treatment: 20316019 INFO @ Fri, 05 Jul 2019 14:00:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:00:30: #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 14:00:30: #1 tag size is determined as 55 bps INFO @ Fri, 05 Jul 2019 14:00:30: #1 tag size = 55 INFO @ Fri, 05 Jul 2019 14:00:30: #1 total tags in treatment: 20316019 INFO @ Fri, 05 Jul 2019 14:00:30: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:00:30: #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 14:00:30: #1 tags after filtering in treatment: 20315906 INFO @ Fri, 05 Jul 2019 14:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:00:30: #1 finished! INFO @ Fri, 05 Jul 2019 14:00:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:00:30: #1 tags after filtering in treatment: 20315906 INFO @ Fri, 05 Jul 2019 14:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:00:30: #1 finished! INFO @ Fri, 05 Jul 2019 14:00:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:00:30: #1 tags after filtering in treatment: 20315906 INFO @ Fri, 05 Jul 2019 14:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:00:30: #1 finished! INFO @ Fri, 05 Jul 2019 14:00:30: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:00:33: #2 number of paired peaks: 5891 INFO @ Fri, 05 Jul 2019 14:00:33: start model_add_line... INFO @ Fri, 05 Jul 2019 14:00:33: #2 number of paired peaks: 5891 INFO @ Fri, 05 Jul 2019 14:00:33: start model_add_line... INFO @ Fri, 05 Jul 2019 14:00:33: #2 number of paired peaks: 5891 INFO @ Fri, 05 Jul 2019 14:00:33: start model_add_line... INFO @ Fri, 05 Jul 2019 14:00:33: start X-correlation... INFO @ Fri, 05 Jul 2019 14:00:33: end of X-cor INFO @ Fri, 05 Jul 2019 14:00:33: #2 finished! INFO @ Fri, 05 Jul 2019 14:00:33: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 14:00:33: #2 alternative fragment length(s) may be 131,217 bps INFO @ Fri, 05 Jul 2019 14:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.05_model.r INFO @ Fri, 05 Jul 2019 14:00:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:00:33: start X-correlation... INFO @ Fri, 05 Jul 2019 14:00:33: end of X-cor INFO @ Fri, 05 Jul 2019 14:00:33: #2 finished! INFO @ Fri, 05 Jul 2019 14:00:33: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 14:00:33: #2 alternative fragment length(s) may be 131,217 bps INFO @ Fri, 05 Jul 2019 14:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.20_model.r INFO @ Fri, 05 Jul 2019 14:00:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:00:33: start X-correlation... INFO @ Fri, 05 Jul 2019 14:00:33: end of X-cor INFO @ Fri, 05 Jul 2019 14:00:33: #2 finished! INFO @ Fri, 05 Jul 2019 14:00:33: #2 predicted fragment length is 131 bps INFO @ Fri, 05 Jul 2019 14:00:33: #2 alternative fragment length(s) may be 131,217 bps INFO @ Fri, 05 Jul 2019 14:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.10_model.r INFO @ Fri, 05 Jul 2019 14:00:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:01:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:01:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:01:38: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:02:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:02:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:02:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.20_summits.bed INFO @ Fri, 05 Jul 2019 14:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:02:12: Done! INFO @ Fri, 05 Jul 2019 14:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.10_summits.bed INFO @ Fri, 05 Jul 2019 14:02:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:02:12: Done! INFO @ Fri, 05 Jul 2019 14:02:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204154/SRX204154.05_summits.bed INFO @ Fri, 05 Jul 2019 14:02:12: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (307 records, 4 fields): 3 millis pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (725 records, 4 fields): 6 millis pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1732 records, 4 fields): 7 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。