Job ID = 1293999 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 37,850,575 reads read : 37,850,575 reads written : 37,850,575 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: 00:10:37 37850575 reads; of these: 37850575 (100.00%) were unpaired; of these: 12399588 (32.76%) aligned 0 times 18855631 (49.82%) aligned exactly 1 time 6595356 (17.42%) aligned >1 times 67.24% overall alignment rate Time searching: 00:10:37 Overall time: 00:10:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 5053526 / 25450987 = 0.1986 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, 03 Jun 2019 04:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 04:12:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:12:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 04:12:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:12:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:12:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2019 04:12:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:12:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:12:09: 1000000 INFO @ Mon, 03 Jun 2019 04:12:10: 1000000 INFO @ Mon, 03 Jun 2019 04:12:10: 1000000 INFO @ Mon, 03 Jun 2019 04:12:17: 2000000 INFO @ Mon, 03 Jun 2019 04:12:17: 2000000 INFO @ Mon, 03 Jun 2019 04:12:17: 2000000 INFO @ Mon, 03 Jun 2019 04:12:24: 3000000 INFO @ Mon, 03 Jun 2019 04:12:25: 3000000 INFO @ Mon, 03 Jun 2019 04:12:25: 3000000 INFO @ Mon, 03 Jun 2019 04:12:32: 4000000 INFO @ Mon, 03 Jun 2019 04:12:32: 4000000 INFO @ Mon, 03 Jun 2019 04:12:33: 4000000 INFO @ Mon, 03 Jun 2019 04:12:40: 5000000 INFO @ Mon, 03 Jun 2019 04:12:40: 5000000 INFO @ Mon, 03 Jun 2019 04:12:40: 5000000 INFO @ Mon, 03 Jun 2019 04:12:47: 6000000 INFO @ Mon, 03 Jun 2019 04:12:47: 6000000 INFO @ Mon, 03 Jun 2019 04:12:48: 6000000 INFO @ Mon, 03 Jun 2019 04:12:54: 7000000 INFO @ Mon, 03 Jun 2019 04:12:55: 7000000 INFO @ Mon, 03 Jun 2019 04:12:56: 7000000 INFO @ Mon, 03 Jun 2019 04:13:02: 8000000 INFO @ Mon, 03 Jun 2019 04:13:03: 8000000 INFO @ Mon, 03 Jun 2019 04:13:03: 8000000 INFO @ Mon, 03 Jun 2019 04:13:10: 9000000 INFO @ Mon, 03 Jun 2019 04:13:10: 9000000 INFO @ Mon, 03 Jun 2019 04:13:11: 9000000 INFO @ Mon, 03 Jun 2019 04:13:17: 10000000 INFO @ Mon, 03 Jun 2019 04:13:18: 10000000 INFO @ Mon, 03 Jun 2019 04:13:19: 10000000 INFO @ Mon, 03 Jun 2019 04:13:25: 11000000 INFO @ Mon, 03 Jun 2019 04:13:25: 11000000 INFO @ Mon, 03 Jun 2019 04:13:26: 11000000 INFO @ Mon, 03 Jun 2019 04:13:33: 12000000 INFO @ Mon, 03 Jun 2019 04:13:33: 12000000 INFO @ Mon, 03 Jun 2019 04:13:34: 12000000 INFO @ Mon, 03 Jun 2019 04:13:40: 13000000 INFO @ Mon, 03 Jun 2019 04:13:40: 13000000 INFO @ Mon, 03 Jun 2019 04:13:42: 13000000 INFO @ Mon, 03 Jun 2019 04:13:48: 14000000 INFO @ Mon, 03 Jun 2019 04:13:48: 14000000 INFO @ Mon, 03 Jun 2019 04:13:49: 14000000 INFO @ Mon, 03 Jun 2019 04:13:55: 15000000 INFO @ Mon, 03 Jun 2019 04:13:56: 15000000 INFO @ Mon, 03 Jun 2019 04:13:57: 15000000 INFO @ Mon, 03 Jun 2019 04:14:03: 16000000 INFO @ Mon, 03 Jun 2019 04:14:04: 16000000 INFO @ Mon, 03 Jun 2019 04:14:05: 16000000 INFO @ Mon, 03 Jun 2019 04:14:10: 17000000 INFO @ Mon, 03 Jun 2019 04:14:12: 17000000 INFO @ Mon, 03 Jun 2019 04:14:12: 17000000 INFO @ Mon, 03 Jun 2019 04:14:18: 18000000 INFO @ Mon, 03 Jun 2019 04:14:20: 18000000 INFO @ Mon, 03 Jun 2019 04:14:20: 18000000 INFO @ Mon, 03 Jun 2019 04:14:25: 19000000 INFO @ Mon, 03 Jun 2019 04:14:28: 19000000 INFO @ Mon, 03 Jun 2019 04:14:28: 19000000 INFO @ Mon, 03 Jun 2019 04:14:33: 20000000 INFO @ Mon, 03 Jun 2019 04:14:36: 20000000 INFO @ Mon, 03 Jun 2019 04:14:36: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:14:36: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:14:36: #1 total tags in treatment: 20397461 INFO @ Mon, 03 Jun 2019 04:14:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:14:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:14:36: 20000000 INFO @ Mon, 03 Jun 2019 04:14:36: #1 tags after filtering in treatment: 20397461 INFO @ Mon, 03 Jun 2019 04:14:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:14:36: #1 finished! INFO @ Mon, 03 Jun 2019 04:14:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:14:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:14:38: #2 number of paired peaks: 1251 INFO @ Mon, 03 Jun 2019 04:14:38: start model_add_line... INFO @ Mon, 03 Jun 2019 04:14:39: start X-correlation... INFO @ Mon, 03 Jun 2019 04:14:39: end of X-cor INFO @ Mon, 03 Jun 2019 04:14:39: #2 finished! INFO @ Mon, 03 Jun 2019 04:14:39: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 04:14:39: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 04:14:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.05_model.r INFO @ Mon, 03 Jun 2019 04:14:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:14:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:14:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:14:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:14:39: #1 total tags in treatment: 20397461 INFO @ Mon, 03 Jun 2019 04:14:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:14:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:14:39: #1 tags after filtering in treatment: 20397461 INFO @ Mon, 03 Jun 2019 04:14:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:14:39: #1 finished! INFO @ Mon, 03 Jun 2019 04:14:39: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:14:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:14:39: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 04:14:39: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 04:14:39: #1 total tags in treatment: 20397461 INFO @ Mon, 03 Jun 2019 04:14:39: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:14:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 04:14:40: #1 tags after filtering in treatment: 20397461 INFO @ Mon, 03 Jun 2019 04:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 04:14:40: #1 finished! INFO @ Mon, 03 Jun 2019 04:14:40: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:14:41: #2 number of paired peaks: 1251 INFO @ Mon, 03 Jun 2019 04:14:41: start model_add_line... INFO @ Mon, 03 Jun 2019 04:14:41: start X-correlation... INFO @ Mon, 03 Jun 2019 04:14:41: end of X-cor INFO @ Mon, 03 Jun 2019 04:14:41: #2 finished! INFO @ Mon, 03 Jun 2019 04:14:41: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 04:14:41: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 04:14:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.20_model.r INFO @ Mon, 03 Jun 2019 04:14:41: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:14:42: #2 number of paired peaks: 1251 INFO @ Mon, 03 Jun 2019 04:14:42: start model_add_line... INFO @ Mon, 03 Jun 2019 04:14:42: start X-correlation... INFO @ Mon, 03 Jun 2019 04:14:42: end of X-cor INFO @ Mon, 03 Jun 2019 04:14:42: #2 finished! INFO @ Mon, 03 Jun 2019 04:14:42: #2 predicted fragment length is 138 bps INFO @ Mon, 03 Jun 2019 04:14:42: #2 alternative fragment length(s) may be 138 bps INFO @ Mon, 03 Jun 2019 04:14:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.10_model.r INFO @ Mon, 03 Jun 2019 04:14:42: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:14:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:15:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:15:42: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:15:43: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:16:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:16:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:16:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.05_summits.bed INFO @ Mon, 03 Jun 2019 04:16:05: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9661 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:16:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.20_summits.bed INFO @ Mon, 03 Jun 2019 04:16:13: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4632 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:16:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:16:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:16:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX159170/SRX159170.10_summits.bed INFO @ Mon, 03 Jun 2019 04:16:13: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (6980 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。