Job ID = 2590969 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 24,827,331 reads read : 49,654,662 reads written : 49,654,662 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: 01:01:45 24827331 reads; of these: 24827331 (100.00%) were paired; of these: 6720405 (27.07%) aligned concordantly 0 times 11699618 (47.12%) aligned concordantly exactly 1 time 6407308 (25.81%) aligned concordantly >1 times ---- 6720405 pairs aligned concordantly 0 times; of these: 879737 (13.09%) aligned discordantly 1 time ---- 5840668 pairs aligned 0 times concordantly or discordantly; of these: 11681336 mates make up the pairs; of these: 9720752 (83.22%) aligned 0 times 691478 (5.92%) aligned exactly 1 time 1269106 (10.86%) aligned >1 times 80.42% overall alignment rate Time searching: 01:01:45 Overall time: 01:01:45 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 20 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] 2816410 / 18820187 = 0.1496 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 @ Tue, 13 Aug 2019 01:44:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.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 @ Tue, 13 Aug 2019 01:44:50: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:44:50: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:44:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.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 @ Tue, 13 Aug 2019 01:44:51: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:44:51: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:44:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.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 @ Tue, 13 Aug 2019 01:44:52: #1 read tag files... INFO @ Tue, 13 Aug 2019 01:44:52: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 01:44:58: 1000000 INFO @ Tue, 13 Aug 2019 01:44:59: 1000000 INFO @ Tue, 13 Aug 2019 01:45:01: 1000000 INFO @ Tue, 13 Aug 2019 01:45:07: 2000000 INFO @ Tue, 13 Aug 2019 01:45:08: 2000000 INFO @ Tue, 13 Aug 2019 01:45:09: 2000000 INFO @ Tue, 13 Aug 2019 01:45:15: 3000000 INFO @ Tue, 13 Aug 2019 01:45:16: 3000000 INFO @ Tue, 13 Aug 2019 01:45:17: 3000000 INFO @ Tue, 13 Aug 2019 01:45:23: 4000000 INFO @ Tue, 13 Aug 2019 01:45:24: 4000000 INFO @ Tue, 13 Aug 2019 01:45:25: 4000000 INFO @ Tue, 13 Aug 2019 01:45:31: 5000000 INFO @ Tue, 13 Aug 2019 01:45:32: 5000000 INFO @ Tue, 13 Aug 2019 01:45:33: 5000000 INFO @ Tue, 13 Aug 2019 01:45:39: 6000000 INFO @ Tue, 13 Aug 2019 01:45:40: 6000000 INFO @ Tue, 13 Aug 2019 01:45:42: 6000000 INFO @ Tue, 13 Aug 2019 01:45:47: 7000000 INFO @ Tue, 13 Aug 2019 01:45:48: 7000000 INFO @ Tue, 13 Aug 2019 01:45:50: 7000000 INFO @ Tue, 13 Aug 2019 01:45:55: 8000000 INFO @ Tue, 13 Aug 2019 01:45:57: 8000000 INFO @ Tue, 13 Aug 2019 01:45:58: 8000000 INFO @ Tue, 13 Aug 2019 01:46:03: 9000000 INFO @ Tue, 13 Aug 2019 01:46:05: 9000000 INFO @ Tue, 13 Aug 2019 01:46:06: 9000000 INFO @ Tue, 13 Aug 2019 01:46:12: 10000000 INFO @ Tue, 13 Aug 2019 01:46:13: 10000000 INFO @ Tue, 13 Aug 2019 01:46:15: 10000000 INFO @ Tue, 13 Aug 2019 01:46:20: 11000000 INFO @ Tue, 13 Aug 2019 01:46:21: 11000000 INFO @ Tue, 13 Aug 2019 01:46:23: 11000000 INFO @ Tue, 13 Aug 2019 01:46:28: 12000000 INFO @ Tue, 13 Aug 2019 01:46:29: 12000000 INFO @ Tue, 13 Aug 2019 01:46:31: 12000000 INFO @ Tue, 13 Aug 2019 01:46:36: 13000000 INFO @ Tue, 13 Aug 2019 01:46:38: 13000000 INFO @ Tue, 13 Aug 2019 01:46:39: 13000000 INFO @ Tue, 13 Aug 2019 01:46:44: 14000000 INFO @ Tue, 13 Aug 2019 01:46:46: 14000000 INFO @ Tue, 13 Aug 2019 01:46:48: 14000000 INFO @ Tue, 13 Aug 2019 01:46:52: 15000000 INFO @ Tue, 13 Aug 2019 01:46:54: 15000000 INFO @ Tue, 13 Aug 2019 01:46:56: 15000000 INFO @ Tue, 13 Aug 2019 01:47:01: 16000000 INFO @ Tue, 13 Aug 2019 01:47:02: 16000000 INFO @ Tue, 13 Aug 2019 01:47:04: 16000000 INFO @ Tue, 13 Aug 2019 01:47:09: 17000000 INFO @ Tue, 13 Aug 2019 01:47:10: 17000000 INFO @ Tue, 13 Aug 2019 01:47:12: 17000000 INFO @ Tue, 13 Aug 2019 01:47:17: 18000000 INFO @ Tue, 13 Aug 2019 01:47:18: 18000000 INFO @ Tue, 13 Aug 2019 01:47:21: 18000000 INFO @ Tue, 13 Aug 2019 01:47:25: 19000000 INFO @ Tue, 13 Aug 2019 01:47:27: 19000000 INFO @ Tue, 13 Aug 2019 01:47:29: 19000000 INFO @ Tue, 13 Aug 2019 01:47:33: 20000000 INFO @ Tue, 13 Aug 2019 01:47:35: 20000000 INFO @ Tue, 13 Aug 2019 01:47:37: 20000000 INFO @ Tue, 13 Aug 2019 01:47:41: 21000000 INFO @ Tue, 13 Aug 2019 01:47:43: 21000000 INFO @ Tue, 13 Aug 2019 01:47:45: 21000000 INFO @ Tue, 13 Aug 2019 01:47:49: 22000000 INFO @ Tue, 13 Aug 2019 01:47:51: 22000000 INFO @ Tue, 13 Aug 2019 01:47:53: 22000000 INFO @ Tue, 13 Aug 2019 01:47:57: 23000000 INFO @ Tue, 13 Aug 2019 01:47:59: 23000000 INFO @ Tue, 13 Aug 2019 01:48:02: 23000000 INFO @ Tue, 13 Aug 2019 01:48:05: 24000000 INFO @ Tue, 13 Aug 2019 01:48:07: 24000000 INFO @ Tue, 13 Aug 2019 01:48:10: 24000000 INFO @ Tue, 13 Aug 2019 01:48:13: 25000000 INFO @ Tue, 13 Aug 2019 01:48:15: 25000000 INFO @ Tue, 13 Aug 2019 01:48:18: 25000000 INFO @ Tue, 13 Aug 2019 01:48:21: 26000000 INFO @ Tue, 13 Aug 2019 01:48:23: 26000000 INFO @ Tue, 13 Aug 2019 01:48:26: 26000000 INFO @ Tue, 13 Aug 2019 01:48:29: 27000000 INFO @ Tue, 13 Aug 2019 01:48:31: 27000000 INFO @ Tue, 13 Aug 2019 01:48:34: 27000000 INFO @ Tue, 13 Aug 2019 01:48:37: 28000000 INFO @ Tue, 13 Aug 2019 01:48:39: 28000000 INFO @ Tue, 13 Aug 2019 01:48:42: 28000000 INFO @ Tue, 13 Aug 2019 01:48:45: 29000000 INFO @ Tue, 13 Aug 2019 01:48:47: 29000000 INFO @ Tue, 13 Aug 2019 01:48:50: 29000000 INFO @ Tue, 13 Aug 2019 01:48:53: 30000000 INFO @ Tue, 13 Aug 2019 01:48:55: 30000000 INFO @ Tue, 13 Aug 2019 01:48:57: 30000000 INFO @ Tue, 13 Aug 2019 01:49:00: 31000000 INFO @ Tue, 13 Aug 2019 01:49:03: 31000000 INFO @ Tue, 13 Aug 2019 01:49:05: 31000000 INFO @ Tue, 13 Aug 2019 01:49:08: 32000000 INFO @ Tue, 13 Aug 2019 01:49:10: 32000000 INFO @ Tue, 13 Aug 2019 01:49:13: 32000000 INFO @ Tue, 13 Aug 2019 01:49:16: 33000000 INFO @ Tue, 13 Aug 2019 01:49:18: 33000000 INFO @ Tue, 13 Aug 2019 01:49:21: 33000000 INFO @ Tue, 13 Aug 2019 01:49:23: 34000000 INFO @ Tue, 13 Aug 2019 01:49:26: 34000000 INFO @ Tue, 13 Aug 2019 01:49:26: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:49:26: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:49:26: #1 total tags in treatment: 15363172 INFO @ Tue, 13 Aug 2019 01:49:26: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:49:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:49:26: #1 tags after filtering in treatment: 12980150 INFO @ Tue, 13 Aug 2019 01:49:26: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 13 Aug 2019 01:49:26: #1 finished! INFO @ Tue, 13 Aug 2019 01:49:26: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:49:26: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:49:27: #2 number of paired peaks: 138 WARNING @ Tue, 13 Aug 2019 01:49:27: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 13 Aug 2019 01:49:27: start model_add_line... INFO @ Tue, 13 Aug 2019 01:49:27: start X-correlation... INFO @ Tue, 13 Aug 2019 01:49:27: end of X-cor INFO @ Tue, 13 Aug 2019 01:49:27: #2 finished! INFO @ Tue, 13 Aug 2019 01:49:27: #2 predicted fragment length is 103 bps INFO @ Tue, 13 Aug 2019 01:49:27: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 13 Aug 2019 01:49:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.05_model.r INFO @ Tue, 13 Aug 2019 01:49:27: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:49:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:49:28: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:49:28: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:49:28: #1 total tags in treatment: 15363172 INFO @ Tue, 13 Aug 2019 01:49:28: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:49:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:49:29: #1 tags after filtering in treatment: 12980150 INFO @ Tue, 13 Aug 2019 01:49:29: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 13 Aug 2019 01:49:29: #1 finished! INFO @ Tue, 13 Aug 2019 01:49:29: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:49:29: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:49:29: 34000000 INFO @ Tue, 13 Aug 2019 01:49:30: #2 number of paired peaks: 138 WARNING @ Tue, 13 Aug 2019 01:49:30: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 13 Aug 2019 01:49:30: start model_add_line... INFO @ Tue, 13 Aug 2019 01:49:30: start X-correlation... INFO @ Tue, 13 Aug 2019 01:49:30: end of X-cor INFO @ Tue, 13 Aug 2019 01:49:30: #2 finished! INFO @ Tue, 13 Aug 2019 01:49:30: #2 predicted fragment length is 103 bps INFO @ Tue, 13 Aug 2019 01:49:30: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 13 Aug 2019 01:49:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.10_model.r INFO @ Tue, 13 Aug 2019 01:49:30: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:49:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:49:31: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 01:49:31: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 01:49:31: #1 total tags in treatment: 15363172 INFO @ Tue, 13 Aug 2019 01:49:31: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 01:49:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 01:49:31: #1 tags after filtering in treatment: 12980150 INFO @ Tue, 13 Aug 2019 01:49:31: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 13 Aug 2019 01:49:31: #1 finished! INFO @ Tue, 13 Aug 2019 01:49:31: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 01:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 01:49:32: #2 number of paired peaks: 138 WARNING @ Tue, 13 Aug 2019 01:49:32: Fewer paired peaks (138) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 138 pairs to build model! INFO @ Tue, 13 Aug 2019 01:49:32: start model_add_line... INFO @ Tue, 13 Aug 2019 01:49:33: start X-correlation... INFO @ Tue, 13 Aug 2019 01:49:33: end of X-cor INFO @ Tue, 13 Aug 2019 01:49:33: #2 finished! INFO @ Tue, 13 Aug 2019 01:49:33: #2 predicted fragment length is 103 bps INFO @ Tue, 13 Aug 2019 01:49:33: #2 alternative fragment length(s) may be 103 bps INFO @ Tue, 13 Aug 2019 01:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.20_model.r INFO @ Tue, 13 Aug 2019 01:49:33: #3 Call peaks... INFO @ Tue, 13 Aug 2019 01:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 01:50:02: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:50:04: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:50:06: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 01:50:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.05_peaks.xls INFO @ Tue, 13 Aug 2019 01:50:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:50:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.05_summits.bed INFO @ Tue, 13 Aug 2019 01:50:19: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2411 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:50:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.10_peaks.xls INFO @ Tue, 13 Aug 2019 01:50:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:50:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.10_summits.bed INFO @ Tue, 13 Aug 2019 01:50:22: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1042 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 01:50:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.20_peaks.xls INFO @ Tue, 13 Aug 2019 01:50:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 01:50:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865784/SRX5865784.20_summits.bed INFO @ Tue, 13 Aug 2019 01:50:25: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (286 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。