Job ID = 1294223 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,507,533 reads read : 28,507,533 reads written : 28,507,533 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: 00:07:23 28507533 reads; of these: 28507533 (100.00%) were unpaired; of these: 1508235 (5.29%) aligned 0 times 24664801 (86.52%) aligned exactly 1 time 2334497 (8.19%) aligned >1 times 94.71% overall alignment rate Time searching: 00:07:23 Overall time: 00:07:23 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] 15912409 / 26999298 = 0.5894 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 05:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.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 05:50:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:50:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.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 05:50:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:50:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:50:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.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 05:50:49: #1 read tag files... INFO @ Mon, 03 Jun 2019 05:50:49: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 05:50:58: 1000000 INFO @ Mon, 03 Jun 2019 05:50:59: 1000000 INFO @ Mon, 03 Jun 2019 05:50:59: 1000000 INFO @ Mon, 03 Jun 2019 05:51:06: 2000000 INFO @ Mon, 03 Jun 2019 05:51:09: 2000000 INFO @ Mon, 03 Jun 2019 05:51:09: 2000000 INFO @ Mon, 03 Jun 2019 05:51:15: 3000000 INFO @ Mon, 03 Jun 2019 05:51:18: 3000000 INFO @ Mon, 03 Jun 2019 05:51:19: 3000000 INFO @ Mon, 03 Jun 2019 05:51:23: 4000000 INFO @ Mon, 03 Jun 2019 05:51:28: 4000000 INFO @ Mon, 03 Jun 2019 05:51:28: 4000000 INFO @ Mon, 03 Jun 2019 05:51:31: 5000000 INFO @ Mon, 03 Jun 2019 05:51:37: 5000000 INFO @ Mon, 03 Jun 2019 05:51:38: 5000000 INFO @ Mon, 03 Jun 2019 05:51:40: 6000000 INFO @ Mon, 03 Jun 2019 05:51:46: 6000000 INFO @ Mon, 03 Jun 2019 05:51:47: 6000000 INFO @ Mon, 03 Jun 2019 05:51:48: 7000000 INFO @ Mon, 03 Jun 2019 05:51:55: 7000000 INFO @ Mon, 03 Jun 2019 05:51:56: 8000000 INFO @ Mon, 03 Jun 2019 05:51:56: 7000000 INFO @ Mon, 03 Jun 2019 05:52:04: 8000000 INFO @ Mon, 03 Jun 2019 05:52:05: 9000000 INFO @ Mon, 03 Jun 2019 05:52:06: 8000000 INFO @ Mon, 03 Jun 2019 05:52:13: 10000000 INFO @ Mon, 03 Jun 2019 05:52:14: 9000000 INFO @ Mon, 03 Jun 2019 05:52:15: 9000000 INFO @ Mon, 03 Jun 2019 05:52:21: 11000000 INFO @ Mon, 03 Jun 2019 05:52:22: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:52:22: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:52:22: #1 total tags in treatment: 11086889 INFO @ Mon, 03 Jun 2019 05:52:22: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:52:22: #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 05:52:22: #1 tags after filtering in treatment: 11086889 INFO @ Mon, 03 Jun 2019 05:52:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:52:22: #1 finished! INFO @ Mon, 03 Jun 2019 05:52:22: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:52:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:52:23: 10000000 INFO @ Mon, 03 Jun 2019 05:52:24: #2 number of paired peaks: 8444 INFO @ Mon, 03 Jun 2019 05:52:24: start model_add_line... INFO @ Mon, 03 Jun 2019 05:52:24: start X-correlation... INFO @ Mon, 03 Jun 2019 05:52:24: end of X-cor INFO @ Mon, 03 Jun 2019 05:52:24: #2 finished! INFO @ Mon, 03 Jun 2019 05:52:24: #2 predicted fragment length is 176 bps INFO @ Mon, 03 Jun 2019 05:52:24: #2 alternative fragment length(s) may be 176 bps INFO @ Mon, 03 Jun 2019 05:52:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.20_model.r INFO @ Mon, 03 Jun 2019 05:52:24: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:52:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:52:25: 10000000 INFO @ Mon, 03 Jun 2019 05:52:33: 11000000 INFO @ Mon, 03 Jun 2019 05:52:33: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:52:33: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:52:33: #1 total tags in treatment: 11086889 INFO @ Mon, 03 Jun 2019 05:52:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:52:33: #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 05:52:34: #1 tags after filtering in treatment: 11086889 INFO @ Mon, 03 Jun 2019 05:52:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:52:34: #1 finished! INFO @ Mon, 03 Jun 2019 05:52:34: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:52:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:52:34: 11000000 INFO @ Mon, 03 Jun 2019 05:52:35: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 05:52:35: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 05:52:35: #1 total tags in treatment: 11086889 INFO @ Mon, 03 Jun 2019 05:52:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 05:52:35: #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 05:52:35: #1 tags after filtering in treatment: 11086889 INFO @ Mon, 03 Jun 2019 05:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 05:52:35: #1 finished! INFO @ Mon, 03 Jun 2019 05:52:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 05:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 05:52:35: #2 number of paired peaks: 8444 INFO @ Mon, 03 Jun 2019 05:52:35: start model_add_line... INFO @ Mon, 03 Jun 2019 05:52:36: start X-correlation... INFO @ Mon, 03 Jun 2019 05:52:36: end of X-cor INFO @ Mon, 03 Jun 2019 05:52:36: #2 finished! INFO @ Mon, 03 Jun 2019 05:52:36: #2 predicted fragment length is 176 bps INFO @ Mon, 03 Jun 2019 05:52:36: #2 alternative fragment length(s) may be 176 bps INFO @ Mon, 03 Jun 2019 05:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.05_model.r INFO @ Mon, 03 Jun 2019 05:52:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:52:37: #2 number of paired peaks: 8444 INFO @ Mon, 03 Jun 2019 05:52:37: start model_add_line... INFO @ Mon, 03 Jun 2019 05:52:37: start X-correlation... INFO @ Mon, 03 Jun 2019 05:52:37: end of X-cor INFO @ Mon, 03 Jun 2019 05:52:37: #2 finished! INFO @ Mon, 03 Jun 2019 05:52:37: #2 predicted fragment length is 176 bps INFO @ Mon, 03 Jun 2019 05:52:37: #2 alternative fragment length(s) may be 176 bps INFO @ Mon, 03 Jun 2019 05:52:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.10_model.r INFO @ Mon, 03 Jun 2019 05:52:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 05:52:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 05:53:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:53:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:53:19: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 05:53:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.20_peaks.xls INFO @ Mon, 03 Jun 2019 05:53:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:53:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.20_summits.bed INFO @ Mon, 03 Jun 2019 05:53:24: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6409 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 05:53:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.05_peaks.xls INFO @ Mon, 03 Jun 2019 05:53:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:53:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.05_summits.bed INFO @ Mon, 03 Jun 2019 05:53:35: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (10670 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 05:53:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.10_peaks.xls INFO @ Mon, 03 Jun 2019 05:53:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 05:53:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX201900/SRX201900.10_summits.bed INFO @ Mon, 03 Jun 2019 05:53:36: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8427 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。