Job ID = 1291882 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 34,691,176 reads read : 69,382,352 reads written : 34,691,176 reads 0-length : 34,691,176 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:08:37 34691176 reads; of these: 34691176 (100.00%) were unpaired; of these: 2309681 (6.66%) aligned 0 times 28204103 (81.30%) aligned exactly 1 time 4177392 (12.04%) aligned >1 times 93.34% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 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] 10043978 / 32381495 = 0.3102 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 @ Sun, 02 Jun 2019 17:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.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 @ Sun, 02 Jun 2019 17:16:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:16:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.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 @ Sun, 02 Jun 2019 17:16:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:16:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:16:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.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 @ Sun, 02 Jun 2019 17:16:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:16:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:16:10: 1000000 INFO @ Sun, 02 Jun 2019 17:16:10: 1000000 INFO @ Sun, 02 Jun 2019 17:16:10: 1000000 INFO @ Sun, 02 Jun 2019 17:16:20: 2000000 INFO @ Sun, 02 Jun 2019 17:16:20: 2000000 INFO @ Sun, 02 Jun 2019 17:16:20: 2000000 INFO @ Sun, 02 Jun 2019 17:16:30: 3000000 INFO @ Sun, 02 Jun 2019 17:16:30: 3000000 INFO @ Sun, 02 Jun 2019 17:16:31: 3000000 INFO @ Sun, 02 Jun 2019 17:16:39: 4000000 INFO @ Sun, 02 Jun 2019 17:16:40: 4000000 INFO @ Sun, 02 Jun 2019 17:16:40: 4000000 INFO @ Sun, 02 Jun 2019 17:16:48: 5000000 INFO @ Sun, 02 Jun 2019 17:16:48: 5000000 INFO @ Sun, 02 Jun 2019 17:16:49: 5000000 INFO @ Sun, 02 Jun 2019 17:16:58: 6000000 INFO @ Sun, 02 Jun 2019 17:16:59: 6000000 INFO @ Sun, 02 Jun 2019 17:17:00: 6000000 INFO @ Sun, 02 Jun 2019 17:17:08: 7000000 INFO @ Sun, 02 Jun 2019 17:17:09: 7000000 INFO @ Sun, 02 Jun 2019 17:17:10: 7000000 INFO @ Sun, 02 Jun 2019 17:17:18: 8000000 INFO @ Sun, 02 Jun 2019 17:17:19: 8000000 INFO @ Sun, 02 Jun 2019 17:17:19: 8000000 INFO @ Sun, 02 Jun 2019 17:17:28: 9000000 INFO @ Sun, 02 Jun 2019 17:17:29: 9000000 INFO @ Sun, 02 Jun 2019 17:17:30: 9000000 INFO @ Sun, 02 Jun 2019 17:17:37: 10000000 INFO @ Sun, 02 Jun 2019 17:17:39: 10000000 INFO @ Sun, 02 Jun 2019 17:17:39: 10000000 INFO @ Sun, 02 Jun 2019 17:17:45: 11000000 INFO @ Sun, 02 Jun 2019 17:17:48: 11000000 INFO @ Sun, 02 Jun 2019 17:17:50: 11000000 INFO @ Sun, 02 Jun 2019 17:17:53: 12000000 INFO @ Sun, 02 Jun 2019 17:17:56: 12000000 INFO @ Sun, 02 Jun 2019 17:18:00: 12000000 INFO @ Sun, 02 Jun 2019 17:18:01: 13000000 INFO @ Sun, 02 Jun 2019 17:18:04: 13000000 INFO @ Sun, 02 Jun 2019 17:18:09: 14000000 INFO @ Sun, 02 Jun 2019 17:18:10: 13000000 INFO @ Sun, 02 Jun 2019 17:18:13: 14000000 INFO @ Sun, 02 Jun 2019 17:18:18: 15000000 INFO @ Sun, 02 Jun 2019 17:18:20: 14000000 INFO @ Sun, 02 Jun 2019 17:18:21: 15000000 INFO @ Sun, 02 Jun 2019 17:18:26: 16000000 INFO @ Sun, 02 Jun 2019 17:18:30: 16000000 INFO @ Sun, 02 Jun 2019 17:18:30: 15000000 INFO @ Sun, 02 Jun 2019 17:18:36: 17000000 INFO @ Sun, 02 Jun 2019 17:18:40: 17000000 INFO @ Sun, 02 Jun 2019 17:18:41: 16000000 INFO @ Sun, 02 Jun 2019 17:18:44: 18000000 INFO @ Sun, 02 Jun 2019 17:18:49: 18000000 INFO @ Sun, 02 Jun 2019 17:18:51: 17000000 INFO @ Sun, 02 Jun 2019 17:18:53: 19000000 INFO @ Sun, 02 Jun 2019 17:18:58: 19000000 INFO @ Sun, 02 Jun 2019 17:19:00: 18000000 INFO @ Sun, 02 Jun 2019 17:19:01: 20000000 INFO @ Sun, 02 Jun 2019 17:19:07: 20000000 INFO @ Sun, 02 Jun 2019 17:19:09: 21000000 INFO @ Sun, 02 Jun 2019 17:19:10: 19000000 INFO @ Sun, 02 Jun 2019 17:19:15: 21000000 INFO @ Sun, 02 Jun 2019 17:19:17: 22000000 INFO @ Sun, 02 Jun 2019 17:19:20: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:19:20: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:19:20: #1 total tags in treatment: 22337517 INFO @ Sun, 02 Jun 2019 17:19:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:19:20: 20000000 INFO @ Sun, 02 Jun 2019 17:19:21: #1 tags after filtering in treatment: 22337517 INFO @ Sun, 02 Jun 2019 17:19:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:21: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:23: #2 number of paired peaks: 1422 INFO @ Sun, 02 Jun 2019 17:19:23: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:23: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:23: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:23: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:23: #2 predicted fragment length is 156 bps INFO @ Sun, 02 Jun 2019 17:19:23: #2 alternative fragment length(s) may be 3,156,164 bps INFO @ Sun, 02 Jun 2019 17:19:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.10_model.r INFO @ Sun, 02 Jun 2019 17:19:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:24: 22000000 INFO @ Sun, 02 Jun 2019 17:19:27: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:19:27: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:19:27: #1 total tags in treatment: 22337517 INFO @ Sun, 02 Jun 2019 17:19:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:19:27: #1 tags after filtering in treatment: 22337517 INFO @ Sun, 02 Jun 2019 17:19:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:27: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:29: #2 number of paired peaks: 1422 INFO @ Sun, 02 Jun 2019 17:19:29: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:30: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:30: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:30: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:30: #2 predicted fragment length is 156 bps INFO @ Sun, 02 Jun 2019 17:19:30: #2 alternative fragment length(s) may be 3,156,164 bps INFO @ Sun, 02 Jun 2019 17:19:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.20_model.r INFO @ Sun, 02 Jun 2019 17:19:30: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:19:30: 21000000 INFO @ Sun, 02 Jun 2019 17:19:40: 22000000 INFO @ Sun, 02 Jun 2019 17:19:44: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 17:19:44: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 17:19:44: #1 total tags in treatment: 22337517 INFO @ Sun, 02 Jun 2019 17:19:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:19:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:19:44: #1 tags after filtering in treatment: 22337517 INFO @ Sun, 02 Jun 2019 17:19:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:19:44: #1 finished! INFO @ Sun, 02 Jun 2019 17:19:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:19:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:19:46: #2 number of paired peaks: 1422 INFO @ Sun, 02 Jun 2019 17:19:46: start model_add_line... INFO @ Sun, 02 Jun 2019 17:19:47: start X-correlation... INFO @ Sun, 02 Jun 2019 17:19:47: end of X-cor INFO @ Sun, 02 Jun 2019 17:19:47: #2 finished! INFO @ Sun, 02 Jun 2019 17:19:47: #2 predicted fragment length is 156 bps INFO @ Sun, 02 Jun 2019 17:19:47: #2 alternative fragment length(s) may be 3,156,164 bps INFO @ Sun, 02 Jun 2019 17:19:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.05_model.r INFO @ Sun, 02 Jun 2019 17:19:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:19:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:20:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:20:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:20:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:20:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:20:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.10_summits.bed INFO @ Sun, 02 Jun 2019 17:20:55: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (5229 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:20:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:21:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:21:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:21:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.20_summits.bed INFO @ Sun, 02 Jun 2019 17:21:01: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2387 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 17:21:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:21:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:21:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2737093/SRX2737093.05_summits.bed INFO @ Sun, 02 Jun 2019 17:21:24: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (8296 records, 4 fields): 19 millis CompletedMACS2peakCalling BigWig に変換しました。