Job ID = 2590819 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,352,596 reads read : 36,705,192 reads written : 18,352,596 reads 0-length : 18,352,596 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:58 18352596 reads; of these: 18352596 (100.00%) were unpaired; of these: 2537110 (13.82%) aligned 0 times 12621586 (68.77%) aligned exactly 1 time 3193900 (17.40%) aligned >1 times 86.18% overall alignment rate Time searching: 00:05:58 Overall time: 00:05:58 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] 8132407 / 15815486 = 0.5142 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, 12 Aug 2019 23:33:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.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, 12 Aug 2019 23:33:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:33:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:33:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.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, 12 Aug 2019 23:33:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:33:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:33:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.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, 12 Aug 2019 23:33:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:33:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:33:32: 1000000 INFO @ Mon, 12 Aug 2019 23:33:33: 1000000 INFO @ Mon, 12 Aug 2019 23:33:33: 1000000 INFO @ Mon, 12 Aug 2019 23:33:40: 2000000 INFO @ Mon, 12 Aug 2019 23:33:41: 2000000 INFO @ Mon, 12 Aug 2019 23:33:41: 2000000 INFO @ Mon, 12 Aug 2019 23:33:48: 3000000 INFO @ Mon, 12 Aug 2019 23:33:48: 3000000 INFO @ Mon, 12 Aug 2019 23:33:49: 3000000 INFO @ Mon, 12 Aug 2019 23:33:55: 4000000 INFO @ Mon, 12 Aug 2019 23:33:56: 4000000 INFO @ Mon, 12 Aug 2019 23:33:57: 4000000 INFO @ Mon, 12 Aug 2019 23:34:03: 5000000 INFO @ Mon, 12 Aug 2019 23:34:04: 5000000 INFO @ Mon, 12 Aug 2019 23:34:05: 5000000 INFO @ Mon, 12 Aug 2019 23:34:10: 6000000 INFO @ Mon, 12 Aug 2019 23:34:12: 6000000 INFO @ Mon, 12 Aug 2019 23:34:13: 6000000 INFO @ Mon, 12 Aug 2019 23:34:17: 7000000 INFO @ Mon, 12 Aug 2019 23:34:20: 7000000 INFO @ Mon, 12 Aug 2019 23:34:21: 7000000 INFO @ Mon, 12 Aug 2019 23:34:22: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:34:22: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:34:22: #1 total tags in treatment: 7683079 INFO @ Mon, 12 Aug 2019 23:34:22: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:34:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:34:22: #1 tags after filtering in treatment: 7683079 INFO @ Mon, 12 Aug 2019 23:34:22: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:34:22: #1 finished! INFO @ Mon, 12 Aug 2019 23:34:22: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:34:22: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:34:23: #2 number of paired peaks: 2999 INFO @ Mon, 12 Aug 2019 23:34:23: start model_add_line... INFO @ Mon, 12 Aug 2019 23:34:23: start X-correlation... INFO @ Mon, 12 Aug 2019 23:34:23: end of X-cor INFO @ Mon, 12 Aug 2019 23:34:23: #2 finished! INFO @ Mon, 12 Aug 2019 23:34:23: #2 predicted fragment length is 229 bps INFO @ Mon, 12 Aug 2019 23:34:23: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 12 Aug 2019 23:34:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.20_model.r INFO @ Mon, 12 Aug 2019 23:34:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:34:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:34:25: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:34:25: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:34:25: #1 total tags in treatment: 7683079 INFO @ Mon, 12 Aug 2019 23:34:25: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:34:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:34:25: #1 tags after filtering in treatment: 7683079 INFO @ Mon, 12 Aug 2019 23:34:25: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:34:25: #1 finished! INFO @ Mon, 12 Aug 2019 23:34:25: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:34:25: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:34:26: #2 number of paired peaks: 2999 INFO @ Mon, 12 Aug 2019 23:34:26: start model_add_line... INFO @ Mon, 12 Aug 2019 23:34:26: start X-correlation... INFO @ Mon, 12 Aug 2019 23:34:26: end of X-cor INFO @ Mon, 12 Aug 2019 23:34:26: #2 finished! INFO @ Mon, 12 Aug 2019 23:34:26: #2 predicted fragment length is 229 bps INFO @ Mon, 12 Aug 2019 23:34:26: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 12 Aug 2019 23:34:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.05_model.r INFO @ Mon, 12 Aug 2019 23:34:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:34:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:34:27: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:34:27: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:34:27: #1 total tags in treatment: 7683079 INFO @ Mon, 12 Aug 2019 23:34:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:34:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 23:34:27: #1 tags after filtering in treatment: 7683079 INFO @ Mon, 12 Aug 2019 23:34:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:34:27: #1 finished! INFO @ Mon, 12 Aug 2019 23:34:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:34:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:34:28: #2 number of paired peaks: 2999 INFO @ Mon, 12 Aug 2019 23:34:28: start model_add_line... INFO @ Mon, 12 Aug 2019 23:34:28: start X-correlation... INFO @ Mon, 12 Aug 2019 23:34:28: end of X-cor INFO @ Mon, 12 Aug 2019 23:34:28: #2 finished! INFO @ Mon, 12 Aug 2019 23:34:28: #2 predicted fragment length is 229 bps INFO @ Mon, 12 Aug 2019 23:34:28: #2 alternative fragment length(s) may be 229 bps INFO @ Mon, 12 Aug 2019 23:34:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.10_model.r INFO @ Mon, 12 Aug 2019 23:34:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:34:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:34:49: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:34:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:34:54: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:35:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:35:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:35:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.20_summits.bed INFO @ Mon, 12 Aug 2019 23:35:01: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3472 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:35:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:35:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:35:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.05_summits.bed INFO @ Mon, 12 Aug 2019 23:35:04: Done! pass1 - making usageList (14 chroms): 5 millis pass2 - checking and writing primary data (8843 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:35:05: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:35:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:35:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011058/SRX5011058.10_summits.bed INFO @ Mon, 12 Aug 2019 23:35:06: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5972 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。