Job ID = 1295001 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 30,731,781 reads read : 61,463,562 reads written : 61,463,562 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: 00:45:14 30731781 reads; of these: 30731781 (100.00%) were paired; of these: 20084806 (65.36%) aligned concordantly 0 times 5832091 (18.98%) aligned concordantly exactly 1 time 4814884 (15.67%) aligned concordantly >1 times ---- 20084806 pairs aligned concordantly 0 times; of these: 162776 (0.81%) aligned discordantly 1 time ---- 19922030 pairs aligned 0 times concordantly or discordantly; of these: 39844060 mates make up the pairs; of these: 23026215 (57.79%) aligned 0 times 12042008 (30.22%) aligned exactly 1 time 4775837 (11.99%) aligned >1 times 62.54% overall alignment rate Time searching: 00:45:14 Overall time: 00:45:14 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 4912386 / 10653048 = 0.4611 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 12:17:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.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 12:17:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:17:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:17:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.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 12:17:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:17:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:17:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.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 12:17:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 12:17:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 12:17:25: 1000000 INFO @ Mon, 03 Jun 2019 12:17:26: 1000000 INFO @ Mon, 03 Jun 2019 12:17:26: 1000000 INFO @ Mon, 03 Jun 2019 12:17:31: 2000000 INFO @ Mon, 03 Jun 2019 12:17:32: 2000000 INFO @ Mon, 03 Jun 2019 12:17:32: 2000000 INFO @ Mon, 03 Jun 2019 12:17:38: 3000000 INFO @ Mon, 03 Jun 2019 12:17:38: 3000000 INFO @ Mon, 03 Jun 2019 12:17:39: 3000000 INFO @ Mon, 03 Jun 2019 12:17:44: 4000000 INFO @ Mon, 03 Jun 2019 12:17:45: 4000000 INFO @ Mon, 03 Jun 2019 12:17:45: 4000000 INFO @ Mon, 03 Jun 2019 12:17:49: 5000000 INFO @ Mon, 03 Jun 2019 12:17:51: 5000000 INFO @ Mon, 03 Jun 2019 12:17:52: 5000000 INFO @ Mon, 03 Jun 2019 12:17:54: 6000000 INFO @ Mon, 03 Jun 2019 12:17:58: 6000000 INFO @ Mon, 03 Jun 2019 12:17:58: 6000000 INFO @ Mon, 03 Jun 2019 12:18:00: 7000000 INFO @ Mon, 03 Jun 2019 12:18:05: 7000000 INFO @ Mon, 03 Jun 2019 12:18:05: 7000000 INFO @ Mon, 03 Jun 2019 12:18:05: 8000000 INFO @ Mon, 03 Jun 2019 12:18:11: 9000000 INFO @ Mon, 03 Jun 2019 12:18:11: 8000000 INFO @ Mon, 03 Jun 2019 12:18:11: 8000000 INFO @ Mon, 03 Jun 2019 12:18:16: 10000000 INFO @ Mon, 03 Jun 2019 12:18:17: 9000000 INFO @ Mon, 03 Jun 2019 12:18:18: 9000000 INFO @ Mon, 03 Jun 2019 12:18:22: 11000000 INFO @ Mon, 03 Jun 2019 12:18:24: 10000000 INFO @ Mon, 03 Jun 2019 12:18:24: 10000000 INFO @ Mon, 03 Jun 2019 12:18:27: 12000000 INFO @ Mon, 03 Jun 2019 12:18:30: 11000000 INFO @ Mon, 03 Jun 2019 12:18:31: 11000000 INFO @ Mon, 03 Jun 2019 12:18:32: 13000000 INFO @ Mon, 03 Jun 2019 12:18:37: 12000000 INFO @ Mon, 03 Jun 2019 12:18:38: 12000000 INFO @ Mon, 03 Jun 2019 12:18:38: 14000000 INFO @ Mon, 03 Jun 2019 12:18:43: 13000000 INFO @ Mon, 03 Jun 2019 12:18:43: 15000000 INFO @ Mon, 03 Jun 2019 12:18:44: 13000000 INFO @ Mon, 03 Jun 2019 12:18:49: 14000000 INFO @ Mon, 03 Jun 2019 12:18:49: 16000000 INFO @ Mon, 03 Jun 2019 12:18:50: 14000000 INFO @ Mon, 03 Jun 2019 12:18:55: 17000000 INFO @ Mon, 03 Jun 2019 12:18:55: 15000000 INFO @ Mon, 03 Jun 2019 12:18:57: 15000000 INFO @ Mon, 03 Jun 2019 12:19:01: 18000000 INFO @ Mon, 03 Jun 2019 12:19:02: 16000000 INFO @ Mon, 03 Jun 2019 12:19:04: 16000000 INFO @ Mon, 03 Jun 2019 12:19:07: 19000000 INFO @ Mon, 03 Jun 2019 12:19:08: 17000000 INFO @ Mon, 03 Jun 2019 12:19:11: 17000000 INFO @ Mon, 03 Jun 2019 12:19:13: 20000000 INFO @ Mon, 03 Jun 2019 12:19:15: 18000000 INFO @ Mon, 03 Jun 2019 12:19:18: 18000000 INFO @ Mon, 03 Jun 2019 12:19:19: 21000000 INFO @ Mon, 03 Jun 2019 12:19:21: 19000000 INFO @ Mon, 03 Jun 2019 12:19:25: 19000000 INFO @ Mon, 03 Jun 2019 12:19:25: 22000000 INFO @ Mon, 03 Jun 2019 12:19:28: 20000000 INFO @ Mon, 03 Jun 2019 12:19:31: 23000000 INFO @ Mon, 03 Jun 2019 12:19:32: 20000000 INFO @ Mon, 03 Jun 2019 12:19:35: 21000000 INFO @ Mon, 03 Jun 2019 12:19:38: 24000000 INFO @ Mon, 03 Jun 2019 12:19:39: 21000000 INFO @ Mon, 03 Jun 2019 12:19:42: 22000000 INFO @ Mon, 03 Jun 2019 12:19:44: 25000000 INFO @ Mon, 03 Jun 2019 12:19:46: 22000000 INFO @ Mon, 03 Jun 2019 12:19:49: 23000000 INFO @ Mon, 03 Jun 2019 12:19:50: 26000000 INFO @ Mon, 03 Jun 2019 12:19:53: 23000000 INFO @ Mon, 03 Jun 2019 12:19:55: 24000000 INFO @ Mon, 03 Jun 2019 12:19:56: 27000000 INFO @ Mon, 03 Jun 2019 12:20:00: 24000000 INFO @ Mon, 03 Jun 2019 12:20:02: 28000000 INFO @ Mon, 03 Jun 2019 12:20:02: 25000000 INFO @ Mon, 03 Jun 2019 12:20:06: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:20:06: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:20:06: #1 total tags in treatment: 5744211 INFO @ Mon, 03 Jun 2019 12:20:06: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:20:06: #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 12:20:06: #1 tags after filtering in treatment: 4489275 INFO @ Mon, 03 Jun 2019 12:20:06: #1 Redundant rate of treatment: 0.22 INFO @ Mon, 03 Jun 2019 12:20:06: #1 finished! INFO @ Mon, 03 Jun 2019 12:20:06: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:20:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:20:06: #2 number of paired peaks: 1084 INFO @ Mon, 03 Jun 2019 12:20:06: start model_add_line... INFO @ Mon, 03 Jun 2019 12:20:06: start X-correlation... INFO @ Mon, 03 Jun 2019 12:20:07: end of X-cor INFO @ Mon, 03 Jun 2019 12:20:07: #2 finished! INFO @ Mon, 03 Jun 2019 12:20:07: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 12:20:07: #2 alternative fragment length(s) may be 79 bps INFO @ Mon, 03 Jun 2019 12:20:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.05_model.r INFO @ Mon, 03 Jun 2019 12:20:07: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:20:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:20:07: 25000000 INFO @ Mon, 03 Jun 2019 12:20:09: 26000000 INFO @ Mon, 03 Jun 2019 12:20:15: 26000000 INFO @ Mon, 03 Jun 2019 12:20:15: 27000000 INFO @ Mon, 03 Jun 2019 12:20:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:20:21: 27000000 INFO @ Mon, 03 Jun 2019 12:20:22: 28000000 INFO @ Mon, 03 Jun 2019 12:20:26: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:20:26: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:20:26: #1 total tags in treatment: 5744211 INFO @ Mon, 03 Jun 2019 12:20:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:20:26: #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 12:20:26: #1 tags after filtering in treatment: 4489275 INFO @ Mon, 03 Jun 2019 12:20:26: #1 Redundant rate of treatment: 0.22 INFO @ Mon, 03 Jun 2019 12:20:26: #1 finished! INFO @ Mon, 03 Jun 2019 12:20:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:20:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:20:27: #2 number of paired peaks: 1084 INFO @ Mon, 03 Jun 2019 12:20:27: start model_add_line... INFO @ Mon, 03 Jun 2019 12:20:27: start X-correlation... INFO @ Mon, 03 Jun 2019 12:20:27: end of X-cor INFO @ Mon, 03 Jun 2019 12:20:27: #2 finished! INFO @ Mon, 03 Jun 2019 12:20:27: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 12:20:27: #2 alternative fragment length(s) may be 79 bps INFO @ Mon, 03 Jun 2019 12:20:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.10_model.r INFO @ Mon, 03 Jun 2019 12:20:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:20:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:20:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.05_peaks.xls INFO @ Mon, 03 Jun 2019 12:20:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:20:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.05_summits.bed INFO @ Mon, 03 Jun 2019 12:20:27: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3714 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:20:28: 28000000 INFO @ Mon, 03 Jun 2019 12:20:32: #1 tag size is determined as 24 bps INFO @ Mon, 03 Jun 2019 12:20:32: #1 tag size = 24 INFO @ Mon, 03 Jun 2019 12:20:32: #1 total tags in treatment: 5744211 INFO @ Mon, 03 Jun 2019 12:20:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 12:20:32: #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 12:20:32: #1 tags after filtering in treatment: 4489275 INFO @ Mon, 03 Jun 2019 12:20:32: #1 Redundant rate of treatment: 0.22 INFO @ Mon, 03 Jun 2019 12:20:32: #1 finished! INFO @ Mon, 03 Jun 2019 12:20:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 12:20:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 12:20:33: #2 number of paired peaks: 1084 INFO @ Mon, 03 Jun 2019 12:20:33: start model_add_line... INFO @ Mon, 03 Jun 2019 12:20:33: start X-correlation... INFO @ Mon, 03 Jun 2019 12:20:33: end of X-cor INFO @ Mon, 03 Jun 2019 12:20:33: #2 finished! INFO @ Mon, 03 Jun 2019 12:20:33: #2 predicted fragment length is 79 bps INFO @ Mon, 03 Jun 2019 12:20:33: #2 alternative fragment length(s) may be 79 bps INFO @ Mon, 03 Jun 2019 12:20:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.20_model.r INFO @ Mon, 03 Jun 2019 12:20:33: #3 Call peaks... INFO @ Mon, 03 Jun 2019 12:20:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 12:20:41: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:20:47: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 12:20:48: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.10_peaks.xls INFO @ Mon, 03 Jun 2019 12:20:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:20:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.10_summits.bed INFO @ Mon, 03 Jun 2019 12:20:48: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1329 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 12:20:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.20_peaks.xls INFO @ Mon, 03 Jun 2019 12:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 12:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX300935/SRX300935.20_summits.bed INFO @ Mon, 03 Jun 2019 12:20:54: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (830 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。