Job ID = 2590078 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 36,072,847 reads read : 36,072,847 reads written : 36,072,847 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:51 36072847 reads; of these: 36072847 (100.00%) were unpaired; of these: 1319324 (3.66%) aligned 0 times 31090543 (86.19%) aligned exactly 1 time 3662980 (10.15%) aligned >1 times 96.34% overall alignment rate Time searching: 00:07:51 Overall time: 00:07:51 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 12956184 / 34753523 = 0.3728 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 @ Mon, 12 Aug 2019 20:00:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 20:00:14: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:00:14: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:00:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 20:00:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:00:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:00:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Mon, 12 Aug 2019 20:00:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:00:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:00:22: 1000000 INFO @ Mon, 12 Aug 2019 20:00:24: 1000000 INFO @ Mon, 12 Aug 2019 20:00:24: 1000000 INFO @ Mon, 12 Aug 2019 20:00:30: 2000000 INFO @ Mon, 12 Aug 2019 20:00:32: 2000000 INFO @ Mon, 12 Aug 2019 20:00:33: 2000000 INFO @ Mon, 12 Aug 2019 20:00:38: 3000000 INFO @ Mon, 12 Aug 2019 20:00:40: 3000000 INFO @ Mon, 12 Aug 2019 20:00:41: 3000000 INFO @ Mon, 12 Aug 2019 20:00:47: 4000000 INFO @ Mon, 12 Aug 2019 20:00:49: 4000000 INFO @ Mon, 12 Aug 2019 20:00:50: 4000000 INFO @ Mon, 12 Aug 2019 20:00:55: 5000000 INFO @ Mon, 12 Aug 2019 20:00:57: 5000000 INFO @ Mon, 12 Aug 2019 20:00:58: 5000000 INFO @ Mon, 12 Aug 2019 20:01:04: 6000000 INFO @ Mon, 12 Aug 2019 20:01:06: 6000000 INFO @ Mon, 12 Aug 2019 20:01:07: 6000000 INFO @ Mon, 12 Aug 2019 20:01:12: 7000000 INFO @ Mon, 12 Aug 2019 20:01:14: 7000000 INFO @ Mon, 12 Aug 2019 20:01:15: 7000000 INFO @ Mon, 12 Aug 2019 20:01:21: 8000000 INFO @ Mon, 12 Aug 2019 20:01:23: 8000000 INFO @ Mon, 12 Aug 2019 20:01:24: 8000000 INFO @ Mon, 12 Aug 2019 20:01:29: 9000000 INFO @ Mon, 12 Aug 2019 20:01:31: 9000000 INFO @ Mon, 12 Aug 2019 20:01:33: 9000000 INFO @ Mon, 12 Aug 2019 20:01:37: 10000000 INFO @ Mon, 12 Aug 2019 20:01:39: 10000000 INFO @ Mon, 12 Aug 2019 20:01:41: 10000000 INFO @ Mon, 12 Aug 2019 20:01:46: 11000000 INFO @ Mon, 12 Aug 2019 20:01:48: 11000000 INFO @ Mon, 12 Aug 2019 20:01:50: 11000000 INFO @ Mon, 12 Aug 2019 20:01:54: 12000000 INFO @ Mon, 12 Aug 2019 20:01:56: 12000000 INFO @ Mon, 12 Aug 2019 20:01:59: 12000000 INFO @ Mon, 12 Aug 2019 20:02:03: 13000000 INFO @ Mon, 12 Aug 2019 20:02:05: 13000000 INFO @ Mon, 12 Aug 2019 20:02:07: 13000000 INFO @ Mon, 12 Aug 2019 20:02:11: 14000000 INFO @ Mon, 12 Aug 2019 20:02:13: 14000000 INFO @ Mon, 12 Aug 2019 20:02:16: 14000000 INFO @ Mon, 12 Aug 2019 20:02:19: 15000000 INFO @ Mon, 12 Aug 2019 20:02:21: 15000000 INFO @ Mon, 12 Aug 2019 20:02:24: 15000000 INFO @ Mon, 12 Aug 2019 20:02:28: 16000000 INFO @ Mon, 12 Aug 2019 20:02:30: 16000000 INFO @ Mon, 12 Aug 2019 20:02:33: 16000000 INFO @ Mon, 12 Aug 2019 20:02:36: 17000000 INFO @ Mon, 12 Aug 2019 20:02:38: 17000000 INFO @ Mon, 12 Aug 2019 20:02:41: 17000000 INFO @ Mon, 12 Aug 2019 20:02:44: 18000000 INFO @ Mon, 12 Aug 2019 20:02:46: 18000000 INFO @ Mon, 12 Aug 2019 20:02:50: 18000000 INFO @ Mon, 12 Aug 2019 20:02:52: 19000000 INFO @ Mon, 12 Aug 2019 20:02:54: 19000000 INFO @ Mon, 12 Aug 2019 20:02:58: 19000000 INFO @ Mon, 12 Aug 2019 20:03:01: 20000000 INFO @ Mon, 12 Aug 2019 20:03:03: 20000000 INFO @ Mon, 12 Aug 2019 20:03:07: 20000000 INFO @ Mon, 12 Aug 2019 20:03:09: 21000000 INFO @ Mon, 12 Aug 2019 20:03:11: 21000000 INFO @ Mon, 12 Aug 2019 20:03:15: 21000000 INFO @ Mon, 12 Aug 2019 20:03:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:03:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:03:16: #1 total tags in treatment: 21797339 INFO @ Mon, 12 Aug 2019 20:03:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:03:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:03:17: #1 tags after filtering in treatment: 21797339 INFO @ Mon, 12 Aug 2019 20:03:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:03:17: #1 finished! INFO @ Mon, 12 Aug 2019 20:03:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:03:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:03:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:03:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:03:18: #1 total tags in treatment: 21797339 INFO @ Mon, 12 Aug 2019 20:03:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:03:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:03:18: #1 tags after filtering in treatment: 21797339 INFO @ Mon, 12 Aug 2019 20:03:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:03:18: #1 finished! INFO @ Mon, 12 Aug 2019 20:03:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:03:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:03:19: #2 number of paired peaks: 1462 INFO @ Mon, 12 Aug 2019 20:03:19: start model_add_line... INFO @ Mon, 12 Aug 2019 20:03:19: start X-correlation... INFO @ Mon, 12 Aug 2019 20:03:19: end of X-cor INFO @ Mon, 12 Aug 2019 20:03:19: #2 finished! INFO @ Mon, 12 Aug 2019 20:03:19: #2 predicted fragment length is 133 bps INFO @ Mon, 12 Aug 2019 20:03:19: #2 alternative fragment length(s) may be 2,133,148 bps INFO @ Mon, 12 Aug 2019 20:03:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.05_model.r INFO @ Mon, 12 Aug 2019 20:03:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:03:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:03:20: #2 number of paired peaks: 1462 INFO @ Mon, 12 Aug 2019 20:03:20: start model_add_line... INFO @ Mon, 12 Aug 2019 20:03:21: start X-correlation... INFO @ Mon, 12 Aug 2019 20:03:21: end of X-cor INFO @ Mon, 12 Aug 2019 20:03:21: #2 finished! INFO @ Mon, 12 Aug 2019 20:03:21: #2 predicted fragment length is 133 bps INFO @ Mon, 12 Aug 2019 20:03:21: #2 alternative fragment length(s) may be 2,133,148 bps INFO @ Mon, 12 Aug 2019 20:03:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.10_model.r INFO @ Mon, 12 Aug 2019 20:03:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:03:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:03:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:03:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:03:22: #1 total tags in treatment: 21797339 INFO @ Mon, 12 Aug 2019 20:03:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:03:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:03:23: #1 tags after filtering in treatment: 21797339 INFO @ Mon, 12 Aug 2019 20:03:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:03:23: #1 finished! INFO @ Mon, 12 Aug 2019 20:03:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:03:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:03:25: #2 number of paired peaks: 1462 INFO @ Mon, 12 Aug 2019 20:03:25: start model_add_line... INFO @ Mon, 12 Aug 2019 20:03:25: start X-correlation... INFO @ Mon, 12 Aug 2019 20:03:25: end of X-cor INFO @ Mon, 12 Aug 2019 20:03:25: #2 finished! INFO @ Mon, 12 Aug 2019 20:03:25: #2 predicted fragment length is 133 bps INFO @ Mon, 12 Aug 2019 20:03:25: #2 alternative fragment length(s) may be 2,133,148 bps INFO @ Mon, 12 Aug 2019 20:03:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.20_model.r INFO @ Mon, 12 Aug 2019 20:03:25: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:03:25: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:04:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:04:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:04:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.05_summits.bed INFO @ Mon, 12 Aug 2019 20:04:38: Done! pass1 - making usageList (6 chroms): 4 millis pass2 - checking and writing primary data (6456 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:04:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:04:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:04:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.10_summits.bed INFO @ Mon, 12 Aug 2019 20:04:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3646 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:04:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:04:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494920/SRX494920.20_summits.bed INFO @ Mon, 12 Aug 2019 20:04:45: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1401 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。