Job ID = 1307870 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,106,797 reads read : 42,213,594 reads written : 21,106,797 reads 0-length : 21,106,797 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: 00:07:30 21106797 reads; of these: 21106797 (100.00%) were unpaired; of these: 2040259 (9.67%) aligned 0 times 16368158 (77.55%) aligned exactly 1 time 2698380 (12.78%) aligned >1 times 90.33% overall alignment rate Time searching: 00:07:30 Overall time: 00:07:30 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 8 files... [bam_rmdupse_core] 7309135 / 19066538 = 0.3833 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 22:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.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 22:52:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.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 22:52:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.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 22:52:46: #1 read tag files... INFO @ Mon, 03 Jun 2019 22:52:46: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 22:52:54: 1000000 INFO @ Mon, 03 Jun 2019 22:52:56: 1000000 INFO @ Mon, 03 Jun 2019 22:52:57: 1000000 INFO @ Mon, 03 Jun 2019 22:53:01: 2000000 INFO @ Mon, 03 Jun 2019 22:53:05: 2000000 INFO @ Mon, 03 Jun 2019 22:53:06: 2000000 INFO @ Mon, 03 Jun 2019 22:53:09: 3000000 INFO @ Mon, 03 Jun 2019 22:53:14: 3000000 INFO @ Mon, 03 Jun 2019 22:53:16: 3000000 INFO @ Mon, 03 Jun 2019 22:53:18: 4000000 INFO @ Mon, 03 Jun 2019 22:53:23: 4000000 INFO @ Mon, 03 Jun 2019 22:53:25: 5000000 INFO @ Mon, 03 Jun 2019 22:53:26: 4000000 INFO @ Mon, 03 Jun 2019 22:53:31: 5000000 INFO @ Mon, 03 Jun 2019 22:53:33: 6000000 INFO @ Mon, 03 Jun 2019 22:53:36: 5000000 INFO @ Mon, 03 Jun 2019 22:53:40: 6000000 INFO @ Mon, 03 Jun 2019 22:53:40: 7000000 INFO @ Mon, 03 Jun 2019 22:53:45: 6000000 INFO @ Mon, 03 Jun 2019 22:53:47: 8000000 INFO @ Mon, 03 Jun 2019 22:53:48: 7000000 INFO @ Mon, 03 Jun 2019 22:53:55: 9000000 INFO @ Mon, 03 Jun 2019 22:53:55: 7000000 INFO @ Mon, 03 Jun 2019 22:53:56: 8000000 INFO @ Mon, 03 Jun 2019 22:54:02: 10000000 INFO @ Mon, 03 Jun 2019 22:54:04: 8000000 INFO @ Mon, 03 Jun 2019 22:54:04: 9000000 INFO @ Mon, 03 Jun 2019 22:54:10: 11000000 INFO @ Mon, 03 Jun 2019 22:54:14: 9000000 INFO @ Mon, 03 Jun 2019 22:54:15: 10000000 INFO @ Mon, 03 Jun 2019 22:54:17: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:54:17: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:54:17: #1 total tags in treatment: 11757403 INFO @ Mon, 03 Jun 2019 22:54:17: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:54:17: #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 22:54:17: #1 tags after filtering in treatment: 11757403 INFO @ Mon, 03 Jun 2019 22:54:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:54:17: #1 finished! INFO @ Mon, 03 Jun 2019 22:54:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:54:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:54:19: #2 number of paired peaks: 8055 INFO @ Mon, 03 Jun 2019 22:54:19: start model_add_line... INFO @ Mon, 03 Jun 2019 22:54:19: start X-correlation... INFO @ Mon, 03 Jun 2019 22:54:19: end of X-cor INFO @ Mon, 03 Jun 2019 22:54:19: #2 finished! INFO @ Mon, 03 Jun 2019 22:54:19: #2 predicted fragment length is 153 bps INFO @ Mon, 03 Jun 2019 22:54:19: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 03 Jun 2019 22:54:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.20_model.r INFO @ Mon, 03 Jun 2019 22:54:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:54:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:54:24: 11000000 INFO @ Mon, 03 Jun 2019 22:54:25: 10000000 INFO @ Mon, 03 Jun 2019 22:54:30: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:54:30: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:54:30: #1 total tags in treatment: 11757403 INFO @ Mon, 03 Jun 2019 22:54:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:54:30: #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 22:54:31: #1 tags after filtering in treatment: 11757403 INFO @ Mon, 03 Jun 2019 22:54:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:54:31: #1 finished! INFO @ Mon, 03 Jun 2019 22:54:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:54:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:54:32: #2 number of paired peaks: 8055 INFO @ Mon, 03 Jun 2019 22:54:32: start model_add_line... INFO @ Mon, 03 Jun 2019 22:54:33: start X-correlation... INFO @ Mon, 03 Jun 2019 22:54:33: end of X-cor INFO @ Mon, 03 Jun 2019 22:54:33: #2 finished! INFO @ Mon, 03 Jun 2019 22:54:33: #2 predicted fragment length is 153 bps INFO @ Mon, 03 Jun 2019 22:54:33: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 03 Jun 2019 22:54:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.10_model.r INFO @ Mon, 03 Jun 2019 22:54:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:54:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:54:34: 11000000 INFO @ Mon, 03 Jun 2019 22:54:41: #1 tag size is determined as 65 bps INFO @ Mon, 03 Jun 2019 22:54:41: #1 tag size = 65 INFO @ Mon, 03 Jun 2019 22:54:41: #1 total tags in treatment: 11757403 INFO @ Mon, 03 Jun 2019 22:54:41: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 22:54:41: #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 22:54:41: #1 tags after filtering in treatment: 11757403 INFO @ Mon, 03 Jun 2019 22:54:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 22:54:41: #1 finished! INFO @ Mon, 03 Jun 2019 22:54:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 22:54:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 22:54:43: #2 number of paired peaks: 8055 INFO @ Mon, 03 Jun 2019 22:54:43: start model_add_line... INFO @ Mon, 03 Jun 2019 22:54:43: start X-correlation... INFO @ Mon, 03 Jun 2019 22:54:43: end of X-cor INFO @ Mon, 03 Jun 2019 22:54:43: #2 finished! INFO @ Mon, 03 Jun 2019 22:54:43: #2 predicted fragment length is 153 bps INFO @ Mon, 03 Jun 2019 22:54:43: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 03 Jun 2019 22:54:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.05_model.r INFO @ Mon, 03 Jun 2019 22:54:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 22:54:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 22:54:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:55:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:55:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.20_peaks.xls INFO @ Mon, 03 Jun 2019 22:55:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:55:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.20_summits.bed INFO @ Mon, 03 Jun 2019 22:55:13: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6536 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:55:22: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 22:55:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.10_peaks.xls INFO @ Mon, 03 Jun 2019 22:55:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:55:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.10_summits.bed INFO @ Mon, 03 Jun 2019 22:55:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7730 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 22:55:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.05_peaks.xls INFO @ Mon, 03 Jun 2019 22:55:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 22:55:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5343121/SRX5343121.05_summits.bed INFO @ Mon, 03 Jun 2019 22:55:42: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8622 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。