Job ID = 1294392 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,337,759 reads read : 21,337,759 reads written : 21,337,759 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: 00:07:48 21337759 reads; of these: 21337759 (100.00%) were unpaired; of these: 1342686 (6.29%) aligned 0 times 15642312 (73.31%) aligned exactly 1 time 4352761 (20.40%) aligned >1 times 93.71% overall alignment rate Time searching: 00:07:48 Overall time: 00:07:48 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] 2862347 / 19995073 = 0.1432 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 07:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.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 07:31:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:31:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.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 07:31:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:31:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:31:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.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 07:31:39: #1 read tag files... INFO @ Mon, 03 Jun 2019 07:31:39: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 07:31:48: 1000000 INFO @ Mon, 03 Jun 2019 07:31:49: 1000000 INFO @ Mon, 03 Jun 2019 07:31:50: 1000000 INFO @ Mon, 03 Jun 2019 07:31:56: 2000000 INFO @ Mon, 03 Jun 2019 07:31:58: 2000000 INFO @ Mon, 03 Jun 2019 07:31:59: 2000000 INFO @ Mon, 03 Jun 2019 07:32:04: 3000000 INFO @ Mon, 03 Jun 2019 07:32:07: 3000000 INFO @ Mon, 03 Jun 2019 07:32:09: 3000000 INFO @ Mon, 03 Jun 2019 07:32:12: 4000000 INFO @ Mon, 03 Jun 2019 07:32:16: 4000000 INFO @ Mon, 03 Jun 2019 07:32:19: 4000000 INFO @ Mon, 03 Jun 2019 07:32:21: 5000000 INFO @ Mon, 03 Jun 2019 07:32:26: 5000000 INFO @ Mon, 03 Jun 2019 07:32:29: 6000000 INFO @ Mon, 03 Jun 2019 07:32:29: 5000000 INFO @ Mon, 03 Jun 2019 07:32:35: 6000000 INFO @ Mon, 03 Jun 2019 07:32:37: 7000000 INFO @ Mon, 03 Jun 2019 07:32:39: 6000000 INFO @ Mon, 03 Jun 2019 07:32:44: 7000000 INFO @ Mon, 03 Jun 2019 07:32:46: 8000000 INFO @ Mon, 03 Jun 2019 07:32:49: 7000000 INFO @ Mon, 03 Jun 2019 07:32:54: 9000000 INFO @ Mon, 03 Jun 2019 07:32:54: 8000000 INFO @ Mon, 03 Jun 2019 07:32:59: 8000000 INFO @ Mon, 03 Jun 2019 07:33:01: 10000000 INFO @ Mon, 03 Jun 2019 07:33:03: 9000000 INFO @ Mon, 03 Jun 2019 07:33:08: 9000000 INFO @ Mon, 03 Jun 2019 07:33:09: 11000000 INFO @ Mon, 03 Jun 2019 07:33:12: 10000000 INFO @ Mon, 03 Jun 2019 07:33:17: 12000000 INFO @ Mon, 03 Jun 2019 07:33:18: 10000000 INFO @ Mon, 03 Jun 2019 07:33:20: 11000000 INFO @ Mon, 03 Jun 2019 07:33:25: 13000000 INFO @ Mon, 03 Jun 2019 07:33:28: 11000000 INFO @ Mon, 03 Jun 2019 07:33:29: 12000000 INFO @ Mon, 03 Jun 2019 07:33:33: 14000000 INFO @ Mon, 03 Jun 2019 07:33:37: 12000000 INFO @ Mon, 03 Jun 2019 07:33:38: 13000000 INFO @ Mon, 03 Jun 2019 07:33:42: 15000000 INFO @ Mon, 03 Jun 2019 07:33:47: 14000000 INFO @ Mon, 03 Jun 2019 07:33:47: 13000000 INFO @ Mon, 03 Jun 2019 07:33:50: 16000000 INFO @ Mon, 03 Jun 2019 07:33:56: 15000000 INFO @ Mon, 03 Jun 2019 07:33:57: 14000000 INFO @ Mon, 03 Jun 2019 07:33:57: 17000000 INFO @ Mon, 03 Jun 2019 07:33:59: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:33:59: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:33:59: #1 total tags in treatment: 17132726 INFO @ Mon, 03 Jun 2019 07:33:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:33:59: #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 07:33:59: #1 tags after filtering in treatment: 17132726 INFO @ Mon, 03 Jun 2019 07:33:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:33:59: #1 finished! INFO @ Mon, 03 Jun 2019 07:33:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:33:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:34:01: #2 number of paired peaks: 1467 INFO @ Mon, 03 Jun 2019 07:34:01: start model_add_line... INFO @ Mon, 03 Jun 2019 07:34:01: start X-correlation... INFO @ Mon, 03 Jun 2019 07:34:01: end of X-cor INFO @ Mon, 03 Jun 2019 07:34:01: #2 finished! INFO @ Mon, 03 Jun 2019 07:34:01: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 07:34:01: #2 alternative fragment length(s) may be 4,221 bps INFO @ Mon, 03 Jun 2019 07:34:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.20_model.r INFO @ Mon, 03 Jun 2019 07:34:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:34:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:34:04: 16000000 INFO @ Mon, 03 Jun 2019 07:34:06: 15000000 INFO @ Mon, 03 Jun 2019 07:34:13: 17000000 INFO @ Mon, 03 Jun 2019 07:34:14: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:34:14: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:34:14: #1 total tags in treatment: 17132726 INFO @ Mon, 03 Jun 2019 07:34:14: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:34:14: #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 07:34:14: #1 tags after filtering in treatment: 17132726 INFO @ Mon, 03 Jun 2019 07:34:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:34:14: #1 finished! INFO @ Mon, 03 Jun 2019 07:34:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:34:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:34:15: 16000000 INFO @ Mon, 03 Jun 2019 07:34:16: #2 number of paired peaks: 1467 INFO @ Mon, 03 Jun 2019 07:34:16: start model_add_line... INFO @ Mon, 03 Jun 2019 07:34:16: start X-correlation... INFO @ Mon, 03 Jun 2019 07:34:16: end of X-cor INFO @ Mon, 03 Jun 2019 07:34:16: #2 finished! INFO @ Mon, 03 Jun 2019 07:34:16: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 07:34:16: #2 alternative fragment length(s) may be 4,221 bps INFO @ Mon, 03 Jun 2019 07:34:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.10_model.r INFO @ Mon, 03 Jun 2019 07:34:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:34:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:34:24: 17000000 INFO @ Mon, 03 Jun 2019 07:34:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 07:34:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 07:34:26: #1 total tags in treatment: 17132726 INFO @ Mon, 03 Jun 2019 07:34:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 07:34:26: #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 07:34:26: #1 tags after filtering in treatment: 17132726 INFO @ Mon, 03 Jun 2019 07:34:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 07:34:26: #1 finished! INFO @ Mon, 03 Jun 2019 07:34:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 07:34:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 07:34:28: #2 number of paired peaks: 1467 INFO @ Mon, 03 Jun 2019 07:34:28: start model_add_line... INFO @ Mon, 03 Jun 2019 07:34:28: start X-correlation... INFO @ Mon, 03 Jun 2019 07:34:28: end of X-cor INFO @ Mon, 03 Jun 2019 07:34:28: #2 finished! INFO @ Mon, 03 Jun 2019 07:34:28: #2 predicted fragment length is 221 bps INFO @ Mon, 03 Jun 2019 07:34:28: #2 alternative fragment length(s) may be 4,221 bps INFO @ Mon, 03 Jun 2019 07:34:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.05_model.r INFO @ Mon, 03 Jun 2019 07:34:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 07:34:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 07:34:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:35:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:35:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.20_peaks.xls INFO @ Mon, 03 Jun 2019 07:35:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:35:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.20_summits.bed INFO @ Mon, 03 Jun 2019 07:35:20: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (540 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:35:23: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 07:35:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.10_peaks.xls INFO @ Mon, 03 Jun 2019 07:35:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:35:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.10_summits.bed INFO @ Mon, 03 Jun 2019 07:35:33: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (952 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 07:35:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.05_peaks.xls INFO @ Mon, 03 Jun 2019 07:35:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 07:35:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287569/SRX287569.05_summits.bed INFO @ Mon, 03 Jun 2019 07:35:48: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1774 records, 4 fields): 158 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。