Job ID = 1293371 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 20,316,195 reads read : 40,632,390 reads written : 40,632,390 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: 00:45:09 20316195 reads; of these: 20316195 (100.00%) were paired; of these: 2738851 (13.48%) aligned concordantly 0 times 14271433 (70.25%) aligned concordantly exactly 1 time 3305911 (16.27%) aligned concordantly >1 times ---- 2738851 pairs aligned concordantly 0 times; of these: 230424 (8.41%) aligned discordantly 1 time ---- 2508427 pairs aligned 0 times concordantly or discordantly; of these: 5016854 mates make up the pairs; of these: 4226190 (84.24%) aligned 0 times 473685 (9.44%) aligned exactly 1 time 316979 (6.32%) aligned >1 times 89.60% overall alignment rate Time searching: 00:45:09 Overall time: 00:45:09 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 16 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] 2593990 / 17771851 = 0.1460 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 00:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.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 00:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.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 00:25:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:25:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:25:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:25:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:25:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.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 00:25:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 00:25:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 00:25:15: 1000000 INFO @ Mon, 03 Jun 2019 00:25:17: 1000000 INFO @ Mon, 03 Jun 2019 00:25:18: 1000000 INFO @ Mon, 03 Jun 2019 00:25:22: 2000000 INFO @ Mon, 03 Jun 2019 00:25:27: 2000000 INFO @ Mon, 03 Jun 2019 00:25:28: 2000000 INFO @ Mon, 03 Jun 2019 00:25:29: 3000000 INFO @ Mon, 03 Jun 2019 00:25:36: 4000000 INFO @ Mon, 03 Jun 2019 00:25:37: 3000000 INFO @ Mon, 03 Jun 2019 00:25:38: 3000000 INFO @ Mon, 03 Jun 2019 00:25:44: 5000000 INFO @ Mon, 03 Jun 2019 00:25:48: 4000000 INFO @ Mon, 03 Jun 2019 00:25:48: 4000000 INFO @ Mon, 03 Jun 2019 00:25:51: 6000000 INFO @ Mon, 03 Jun 2019 00:25:58: 7000000 INFO @ Mon, 03 Jun 2019 00:25:58: 5000000 INFO @ Mon, 03 Jun 2019 00:25:59: 5000000 INFO @ Mon, 03 Jun 2019 00:26:05: 8000000 INFO @ Mon, 03 Jun 2019 00:26:08: 6000000 INFO @ Mon, 03 Jun 2019 00:26:10: 6000000 INFO @ Mon, 03 Jun 2019 00:26:12: 9000000 INFO @ Mon, 03 Jun 2019 00:26:17: 7000000 INFO @ Mon, 03 Jun 2019 00:26:19: 10000000 INFO @ Mon, 03 Jun 2019 00:26:21: 7000000 INFO @ Mon, 03 Jun 2019 00:26:26: 11000000 INFO @ Mon, 03 Jun 2019 00:26:27: 8000000 INFO @ Mon, 03 Jun 2019 00:26:31: 8000000 INFO @ Mon, 03 Jun 2019 00:26:33: 12000000 INFO @ Mon, 03 Jun 2019 00:26:37: 9000000 INFO @ Mon, 03 Jun 2019 00:26:41: 13000000 INFO @ Mon, 03 Jun 2019 00:26:41: 9000000 INFO @ Mon, 03 Jun 2019 00:26:46: 10000000 INFO @ Mon, 03 Jun 2019 00:26:48: 14000000 INFO @ Mon, 03 Jun 2019 00:26:53: 10000000 INFO @ Mon, 03 Jun 2019 00:26:55: 15000000 INFO @ Mon, 03 Jun 2019 00:26:56: 11000000 INFO @ Mon, 03 Jun 2019 00:27:02: 16000000 INFO @ Mon, 03 Jun 2019 00:27:04: 11000000 INFO @ Mon, 03 Jun 2019 00:27:05: 12000000 INFO @ Mon, 03 Jun 2019 00:27:09: 17000000 INFO @ Mon, 03 Jun 2019 00:27:14: 12000000 INFO @ Mon, 03 Jun 2019 00:27:15: 13000000 INFO @ Mon, 03 Jun 2019 00:27:16: 18000000 INFO @ Mon, 03 Jun 2019 00:27:23: 19000000 INFO @ Mon, 03 Jun 2019 00:27:24: 14000000 INFO @ Mon, 03 Jun 2019 00:27:25: 13000000 INFO @ Mon, 03 Jun 2019 00:27:30: 20000000 INFO @ Mon, 03 Jun 2019 00:27:33: 15000000 INFO @ Mon, 03 Jun 2019 00:27:36: 14000000 INFO @ Mon, 03 Jun 2019 00:27:37: 21000000 INFO @ Mon, 03 Jun 2019 00:27:43: 16000000 INFO @ Mon, 03 Jun 2019 00:27:44: 22000000 INFO @ Mon, 03 Jun 2019 00:27:46: 15000000 INFO @ Mon, 03 Jun 2019 00:27:51: 23000000 INFO @ Mon, 03 Jun 2019 00:27:52: 17000000 INFO @ Mon, 03 Jun 2019 00:27:56: 16000000 INFO @ Mon, 03 Jun 2019 00:27:58: 24000000 INFO @ Mon, 03 Jun 2019 00:28:02: 18000000 INFO @ Mon, 03 Jun 2019 00:28:06: 25000000 INFO @ Mon, 03 Jun 2019 00:28:07: 17000000 INFO @ Mon, 03 Jun 2019 00:28:11: 19000000 INFO @ Mon, 03 Jun 2019 00:28:13: 26000000 INFO @ Mon, 03 Jun 2019 00:28:18: 18000000 INFO @ Mon, 03 Jun 2019 00:28:20: 27000000 INFO @ Mon, 03 Jun 2019 00:28:20: 20000000 INFO @ Mon, 03 Jun 2019 00:28:27: 28000000 INFO @ Mon, 03 Jun 2019 00:28:28: 19000000 INFO @ Mon, 03 Jun 2019 00:28:30: 21000000 INFO @ Mon, 03 Jun 2019 00:28:34: 29000000 INFO @ Mon, 03 Jun 2019 00:28:39: 20000000 INFO @ Mon, 03 Jun 2019 00:28:39: 22000000 INFO @ Mon, 03 Jun 2019 00:28:41: 30000000 INFO @ Mon, 03 Jun 2019 00:28:48: 31000000 INFO @ Mon, 03 Jun 2019 00:28:49: 23000000 INFO @ Mon, 03 Jun 2019 00:28:50: 21000000 INFO @ Mon, 03 Jun 2019 00:28:50: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:28:50: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:28:50: #1 total tags in treatment: 14994146 INFO @ Mon, 03 Jun 2019 00:28:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:28:50: #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 00:28:50: #1 tags after filtering in treatment: 13845033 INFO @ Mon, 03 Jun 2019 00:28:50: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 00:28:50: #1 finished! INFO @ Mon, 03 Jun 2019 00:28:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:28:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:28:51: #2 number of paired peaks: 1608 INFO @ Mon, 03 Jun 2019 00:28:51: start model_add_line... INFO @ Mon, 03 Jun 2019 00:28:51: start X-correlation... INFO @ Mon, 03 Jun 2019 00:28:51: end of X-cor INFO @ Mon, 03 Jun 2019 00:28:51: #2 finished! INFO @ Mon, 03 Jun 2019 00:28:51: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 00:28:51: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 00:28:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.05_model.r INFO @ Mon, 03 Jun 2019 00:28:51: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:28:51: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:28:58: 24000000 INFO @ Mon, 03 Jun 2019 00:29:00: 22000000 INFO @ Mon, 03 Jun 2019 00:29:08: 25000000 INFO @ Mon, 03 Jun 2019 00:29:10: 23000000 INFO @ Mon, 03 Jun 2019 00:29:17: 26000000 INFO @ Mon, 03 Jun 2019 00:29:20: 24000000 INFO @ Mon, 03 Jun 2019 00:29:27: 27000000 INFO @ Mon, 03 Jun 2019 00:29:32: 25000000 INFO @ Mon, 03 Jun 2019 00:29:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:29:37: 28000000 INFO @ Mon, 03 Jun 2019 00:29:42: 26000000 INFO @ Mon, 03 Jun 2019 00:29:46: 29000000 INFO @ Mon, 03 Jun 2019 00:29:53: 27000000 INFO @ Mon, 03 Jun 2019 00:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.05_peaks.xls INFO @ Mon, 03 Jun 2019 00:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.05_summits.bed INFO @ Mon, 03 Jun 2019 00:29:54: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (6288 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:29:55: 30000000 INFO @ Mon, 03 Jun 2019 00:30:04: 28000000 INFO @ Mon, 03 Jun 2019 00:30:05: 31000000 INFO @ Mon, 03 Jun 2019 00:30:07: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:30:07: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:30:07: #1 total tags in treatment: 14994146 INFO @ Mon, 03 Jun 2019 00:30:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:30:07: #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 00:30:07: #1 tags after filtering in treatment: 13845033 INFO @ Mon, 03 Jun 2019 00:30:07: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 00:30:07: #1 finished! INFO @ Mon, 03 Jun 2019 00:30:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:30:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:30:09: #2 number of paired peaks: 1608 INFO @ Mon, 03 Jun 2019 00:30:09: start model_add_line... INFO @ Mon, 03 Jun 2019 00:30:09: start X-correlation... INFO @ Mon, 03 Jun 2019 00:30:09: end of X-cor INFO @ Mon, 03 Jun 2019 00:30:09: #2 finished! INFO @ Mon, 03 Jun 2019 00:30:09: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 00:30:09: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 00:30:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.10_model.r INFO @ Mon, 03 Jun 2019 00:30:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:30:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:30:14: 29000000 INFO @ Mon, 03 Jun 2019 00:30:23: 30000000 INFO @ Mon, 03 Jun 2019 00:30:33: 31000000 INFO @ Mon, 03 Jun 2019 00:30:35: #1 tag size is determined as 75 bps INFO @ Mon, 03 Jun 2019 00:30:35: #1 tag size = 75 INFO @ Mon, 03 Jun 2019 00:30:35: #1 total tags in treatment: 14994146 INFO @ Mon, 03 Jun 2019 00:30:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 00:30:35: #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 00:30:35: #1 tags after filtering in treatment: 13845033 INFO @ Mon, 03 Jun 2019 00:30:35: #1 Redundant rate of treatment: 0.08 INFO @ Mon, 03 Jun 2019 00:30:35: #1 finished! INFO @ Mon, 03 Jun 2019 00:30:35: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 00:30:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 00:30:36: #2 number of paired peaks: 1608 INFO @ Mon, 03 Jun 2019 00:30:36: start model_add_line... INFO @ Mon, 03 Jun 2019 00:30:37: start X-correlation... INFO @ Mon, 03 Jun 2019 00:30:37: end of X-cor INFO @ Mon, 03 Jun 2019 00:30:37: #2 finished! INFO @ Mon, 03 Jun 2019 00:30:37: #2 predicted fragment length is 208 bps INFO @ Mon, 03 Jun 2019 00:30:37: #2 alternative fragment length(s) may be 208 bps INFO @ Mon, 03 Jun 2019 00:30:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.20_model.r INFO @ Mon, 03 Jun 2019 00:30:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 00:30:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 00:30:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:31:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.10_peaks.xls INFO @ Mon, 03 Jun 2019 00:31:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:31:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.10_summits.bed INFO @ Mon, 03 Jun 2019 00:31:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (4700 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 00:31:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 00:31:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.20_peaks.xls INFO @ Mon, 03 Jun 2019 00:31:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 00:31:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX1818289/ERX1818289.20_summits.bed INFO @ Mon, 03 Jun 2019 00:31:41: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3039 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。