Job ID = 1295468 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,163,555 reads read : 50,327,110 reads written : 50,327,110 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: 00:59:17 25163555 reads; of these: 25163555 (100.00%) were paired; of these: 3335308 (13.25%) aligned concordantly 0 times 16137854 (64.13%) aligned concordantly exactly 1 time 5690393 (22.61%) aligned concordantly >1 times ---- 3335308 pairs aligned concordantly 0 times; of these: 109435 (3.28%) aligned discordantly 1 time ---- 3225873 pairs aligned 0 times concordantly or discordantly; of these: 6451746 mates make up the pairs; of these: 4849708 (75.17%) aligned 0 times 731008 (11.33%) aligned exactly 1 time 871030 (13.50%) aligned >1 times 90.36% overall alignment rate Time searching: 00:59:17 Overall time: 00:59:17 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] 1700180 / 21909388 = 0.0776 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 15:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.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 15:16:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:16:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.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 15:16:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:16:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:16:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.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 15:16:23: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:16:23: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:16:31: 1000000 INFO @ Mon, 03 Jun 2019 15:16:31: 1000000 INFO @ Mon, 03 Jun 2019 15:16:32: 1000000 INFO @ Mon, 03 Jun 2019 15:16:40: 2000000 INFO @ Mon, 03 Jun 2019 15:16:40: 2000000 INFO @ Mon, 03 Jun 2019 15:16:40: 2000000 INFO @ Mon, 03 Jun 2019 15:16:48: 3000000 INFO @ Mon, 03 Jun 2019 15:16:48: 3000000 INFO @ Mon, 03 Jun 2019 15:16:48: 3000000 INFO @ Mon, 03 Jun 2019 15:16:55: 4000000 INFO @ Mon, 03 Jun 2019 15:16:57: 4000000 INFO @ Mon, 03 Jun 2019 15:16:57: 4000000 INFO @ Mon, 03 Jun 2019 15:17:03: 5000000 INFO @ Mon, 03 Jun 2019 15:17:05: 5000000 INFO @ Mon, 03 Jun 2019 15:17:05: 5000000 INFO @ Mon, 03 Jun 2019 15:17:10: 6000000 INFO @ Mon, 03 Jun 2019 15:17:14: 6000000 INFO @ Mon, 03 Jun 2019 15:17:14: 6000000 INFO @ Mon, 03 Jun 2019 15:17:18: 7000000 INFO @ Mon, 03 Jun 2019 15:17:22: 7000000 INFO @ Mon, 03 Jun 2019 15:17:22: 7000000 INFO @ Mon, 03 Jun 2019 15:17:25: 8000000 INFO @ Mon, 03 Jun 2019 15:17:31: 8000000 INFO @ Mon, 03 Jun 2019 15:17:31: 8000000 INFO @ Mon, 03 Jun 2019 15:17:33: 9000000 INFO @ Mon, 03 Jun 2019 15:17:39: 9000000 INFO @ Mon, 03 Jun 2019 15:17:39: 9000000 INFO @ Mon, 03 Jun 2019 15:17:40: 10000000 INFO @ Mon, 03 Jun 2019 15:17:47: 10000000 INFO @ Mon, 03 Jun 2019 15:17:47: 10000000 INFO @ Mon, 03 Jun 2019 15:17:48: 11000000 INFO @ Mon, 03 Jun 2019 15:17:55: 12000000 INFO @ Mon, 03 Jun 2019 15:17:56: 11000000 INFO @ Mon, 03 Jun 2019 15:17:56: 11000000 INFO @ Mon, 03 Jun 2019 15:18:03: 13000000 INFO @ Mon, 03 Jun 2019 15:18:04: 12000000 INFO @ Mon, 03 Jun 2019 15:18:04: 12000000 INFO @ Mon, 03 Jun 2019 15:18:10: 14000000 INFO @ Mon, 03 Jun 2019 15:18:12: 13000000 INFO @ Mon, 03 Jun 2019 15:18:13: 13000000 INFO @ Mon, 03 Jun 2019 15:18:18: 15000000 INFO @ Mon, 03 Jun 2019 15:18:21: 14000000 INFO @ Mon, 03 Jun 2019 15:18:21: 14000000 INFO @ Mon, 03 Jun 2019 15:18:25: 16000000 INFO @ Mon, 03 Jun 2019 15:18:29: 15000000 INFO @ Mon, 03 Jun 2019 15:18:29: 15000000 INFO @ Mon, 03 Jun 2019 15:18:32: 17000000 INFO @ Mon, 03 Jun 2019 15:18:37: 16000000 INFO @ Mon, 03 Jun 2019 15:18:38: 16000000 INFO @ Mon, 03 Jun 2019 15:18:40: 18000000 INFO @ Mon, 03 Jun 2019 15:18:46: 17000000 INFO @ Mon, 03 Jun 2019 15:18:46: 17000000 INFO @ Mon, 03 Jun 2019 15:18:48: 19000000 INFO @ Mon, 03 Jun 2019 15:18:54: 18000000 INFO @ Mon, 03 Jun 2019 15:18:54: 18000000 INFO @ Mon, 03 Jun 2019 15:18:56: 20000000 INFO @ Mon, 03 Jun 2019 15:19:02: 19000000 INFO @ Mon, 03 Jun 2019 15:19:02: 19000000 INFO @ Mon, 03 Jun 2019 15:19:03: 21000000 INFO @ Mon, 03 Jun 2019 15:19:10: 20000000 INFO @ Mon, 03 Jun 2019 15:19:10: 22000000 INFO @ Mon, 03 Jun 2019 15:19:10: 20000000 INFO @ Mon, 03 Jun 2019 15:19:18: 23000000 INFO @ Mon, 03 Jun 2019 15:19:18: 21000000 INFO @ Mon, 03 Jun 2019 15:19:19: 21000000 INFO @ Mon, 03 Jun 2019 15:19:25: 24000000 INFO @ Mon, 03 Jun 2019 15:19:26: 22000000 INFO @ Mon, 03 Jun 2019 15:19:27: 22000000 INFO @ Mon, 03 Jun 2019 15:19:32: 25000000 INFO @ Mon, 03 Jun 2019 15:19:35: 23000000 INFO @ Mon, 03 Jun 2019 15:19:35: 23000000 INFO @ Mon, 03 Jun 2019 15:19:40: 26000000 INFO @ Mon, 03 Jun 2019 15:19:43: 24000000 INFO @ Mon, 03 Jun 2019 15:19:43: 24000000 INFO @ Mon, 03 Jun 2019 15:19:47: 27000000 INFO @ Mon, 03 Jun 2019 15:19:51: 25000000 INFO @ Mon, 03 Jun 2019 15:19:51: 25000000 INFO @ Mon, 03 Jun 2019 15:19:54: 28000000 INFO @ Mon, 03 Jun 2019 15:19:59: 26000000 INFO @ Mon, 03 Jun 2019 15:19:59: 26000000 INFO @ Mon, 03 Jun 2019 15:20:01: 29000000 INFO @ Mon, 03 Jun 2019 15:20:07: 27000000 INFO @ Mon, 03 Jun 2019 15:20:07: 27000000 INFO @ Mon, 03 Jun 2019 15:20:08: 30000000 INFO @ Mon, 03 Jun 2019 15:20:15: 28000000 INFO @ Mon, 03 Jun 2019 15:20:16: 28000000 INFO @ Mon, 03 Jun 2019 15:20:16: 31000000 INFO @ Mon, 03 Jun 2019 15:20:23: 32000000 INFO @ Mon, 03 Jun 2019 15:20:23: 29000000 INFO @ Mon, 03 Jun 2019 15:20:24: 29000000 INFO @ Mon, 03 Jun 2019 15:20:30: 33000000 INFO @ Mon, 03 Jun 2019 15:20:31: 30000000 INFO @ Mon, 03 Jun 2019 15:20:31: 30000000 INFO @ Mon, 03 Jun 2019 15:20:39: 34000000 INFO @ Mon, 03 Jun 2019 15:20:39: 31000000 INFO @ Mon, 03 Jun 2019 15:20:40: 31000000 INFO @ Mon, 03 Jun 2019 15:20:47: 35000000 INFO @ Mon, 03 Jun 2019 15:20:48: 32000000 INFO @ Mon, 03 Jun 2019 15:20:48: 32000000 INFO @ Mon, 03 Jun 2019 15:20:55: 36000000 INFO @ Mon, 03 Jun 2019 15:20:57: 33000000 INFO @ Mon, 03 Jun 2019 15:20:57: 33000000 INFO @ Mon, 03 Jun 2019 15:21:03: 37000000 INFO @ Mon, 03 Jun 2019 15:21:05: 34000000 INFO @ Mon, 03 Jun 2019 15:21:05: 34000000 INFO @ Mon, 03 Jun 2019 15:21:11: 38000000 INFO @ Mon, 03 Jun 2019 15:21:14: 35000000 INFO @ Mon, 03 Jun 2019 15:21:14: 35000000 INFO @ Mon, 03 Jun 2019 15:21:18: 39000000 INFO @ Mon, 03 Jun 2019 15:21:22: 36000000 INFO @ Mon, 03 Jun 2019 15:21:22: 36000000 INFO @ Mon, 03 Jun 2019 15:21:25: 40000000 INFO @ Mon, 03 Jun 2019 15:21:30: 37000000 INFO @ Mon, 03 Jun 2019 15:21:30: 37000000 INFO @ Mon, 03 Jun 2019 15:21:32: 41000000 INFO @ Mon, 03 Jun 2019 15:21:38: 38000000 INFO @ Mon, 03 Jun 2019 15:21:38: 38000000 INFO @ Mon, 03 Jun 2019 15:21:39: 42000000 INFO @ Mon, 03 Jun 2019 15:21:40: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:21:40: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:21:40: #1 total tags in treatment: 20130068 INFO @ Mon, 03 Jun 2019 15:21:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:21:40: #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 15:21:41: #1 tags after filtering in treatment: 11417907 INFO @ Mon, 03 Jun 2019 15:21:41: #1 Redundant rate of treatment: 0.43 INFO @ Mon, 03 Jun 2019 15:21:41: #1 finished! INFO @ Mon, 03 Jun 2019 15:21:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:21:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:21:43: #2 number of paired peaks: 8996 INFO @ Mon, 03 Jun 2019 15:21:43: start model_add_line... INFO @ Mon, 03 Jun 2019 15:21:43: start X-correlation... INFO @ Mon, 03 Jun 2019 15:21:43: end of X-cor INFO @ Mon, 03 Jun 2019 15:21:43: #2 finished! INFO @ Mon, 03 Jun 2019 15:21:43: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 15:21:43: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 15:21:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.10_model.r INFO @ Mon, 03 Jun 2019 15:21:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:21:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:21:47: 39000000 INFO @ Mon, 03 Jun 2019 15:21:47: 39000000 INFO @ Mon, 03 Jun 2019 15:21:55: 40000000 INFO @ Mon, 03 Jun 2019 15:21:55: 40000000 INFO @ Mon, 03 Jun 2019 15:22:03: 41000000 INFO @ Mon, 03 Jun 2019 15:22:03: 41000000 INFO @ Mon, 03 Jun 2019 15:22:11: 42000000 INFO @ Mon, 03 Jun 2019 15:22:11: 42000000 INFO @ Mon, 03 Jun 2019 15:22:12: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:22:12: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:22:12: #1 total tags in treatment: 20130068 INFO @ Mon, 03 Jun 2019 15:22:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:22:12: #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 15:22:12: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:22:12: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:22:12: #1 total tags in treatment: 20130068 INFO @ Mon, 03 Jun 2019 15:22:12: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:22:12: #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 15:22:12: #1 tags after filtering in treatment: 11417907 INFO @ Mon, 03 Jun 2019 15:22:12: #1 Redundant rate of treatment: 0.43 INFO @ Mon, 03 Jun 2019 15:22:12: #1 finished! INFO @ Mon, 03 Jun 2019 15:22:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:22:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:22:12: #1 tags after filtering in treatment: 11417907 INFO @ Mon, 03 Jun 2019 15:22:12: #1 Redundant rate of treatment: 0.43 INFO @ Mon, 03 Jun 2019 15:22:12: #1 finished! INFO @ Mon, 03 Jun 2019 15:22:12: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:22:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:22:14: #2 number of paired peaks: 8996 INFO @ Mon, 03 Jun 2019 15:22:14: start model_add_line... INFO @ Mon, 03 Jun 2019 15:22:14: #2 number of paired peaks: 8996 INFO @ Mon, 03 Jun 2019 15:22:14: start model_add_line... INFO @ Mon, 03 Jun 2019 15:22:14: start X-correlation... INFO @ Mon, 03 Jun 2019 15:22:14: end of X-cor INFO @ Mon, 03 Jun 2019 15:22:14: #2 finished! INFO @ Mon, 03 Jun 2019 15:22:14: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 15:22:14: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 15:22:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.05_model.r INFO @ Mon, 03 Jun 2019 15:22:14: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:22:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:22:14: start X-correlation... INFO @ Mon, 03 Jun 2019 15:22:14: end of X-cor INFO @ Mon, 03 Jun 2019 15:22:14: #2 finished! INFO @ Mon, 03 Jun 2019 15:22:14: #2 predicted fragment length is 199 bps INFO @ Mon, 03 Jun 2019 15:22:14: #2 alternative fragment length(s) may be 199 bps INFO @ Mon, 03 Jun 2019 15:22:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.20_model.r INFO @ Mon, 03 Jun 2019 15:22:15: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:22:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:22:28: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:22:45: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:22:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:22:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.10_summits.bed INFO @ Mon, 03 Jun 2019 15:22:45: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9267 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:22:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:23:00: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:23:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.05_summits.bed INFO @ Mon, 03 Jun 2019 15:23:16: Done! INFO @ Mon, 03 Jun 2019 15:23:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:23:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393673/SRX3393673.20_summits.bed INFO @ Mon, 03 Jun 2019 15:23:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10445 records, 4 fields): 15 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8014 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。