Job ID = 1295470 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 26,520,385 reads read : 53,040,770 reads written : 53,040,770 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: 01:01:10 26520385 reads; of these: 26520385 (100.00%) were paired; of these: 6382166 (24.07%) aligned concordantly 0 times 14590411 (55.02%) aligned concordantly exactly 1 time 5547808 (20.92%) aligned concordantly >1 times ---- 6382166 pairs aligned concordantly 0 times; of these: 200227 (3.14%) aligned discordantly 1 time ---- 6181939 pairs aligned 0 times concordantly or discordantly; of these: 12363878 mates make up the pairs; of these: 10408234 (84.18%) aligned 0 times 826486 (6.68%) aligned exactly 1 time 1129158 (9.13%) aligned >1 times 80.38% overall alignment rate Time searching: 01:01:10 Overall time: 01:01:10 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] 1935383 / 20319759 = 0.0952 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 15:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.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 15:20:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:20:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.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 15:20:37: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:20:37: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:20:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.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 15:20:38: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:20:38: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:20:46: 1000000 INFO @ Mon, 03 Jun 2019 15:20:46: 1000000 INFO @ Mon, 03 Jun 2019 15:20:47: 1000000 INFO @ Mon, 03 Jun 2019 15:20:55: 2000000 INFO @ Mon, 03 Jun 2019 15:20:55: 2000000 INFO @ Mon, 03 Jun 2019 15:20:57: 2000000 INFO @ Mon, 03 Jun 2019 15:21:03: 3000000 INFO @ Mon, 03 Jun 2019 15:21:04: 3000000 INFO @ Mon, 03 Jun 2019 15:21:06: 3000000 INFO @ Mon, 03 Jun 2019 15:21:12: 4000000 INFO @ Mon, 03 Jun 2019 15:21:12: 4000000 INFO @ Mon, 03 Jun 2019 15:21:16: 4000000 INFO @ Mon, 03 Jun 2019 15:21:21: 5000000 INFO @ Mon, 03 Jun 2019 15:21:21: 5000000 INFO @ Mon, 03 Jun 2019 15:21:24: 5000000 INFO @ Mon, 03 Jun 2019 15:21:30: 6000000 INFO @ Mon, 03 Jun 2019 15:21:30: 6000000 INFO @ Mon, 03 Jun 2019 15:21:33: 6000000 INFO @ Mon, 03 Jun 2019 15:21:38: 7000000 INFO @ Mon, 03 Jun 2019 15:21:38: 7000000 INFO @ Mon, 03 Jun 2019 15:21:41: 7000000 INFO @ Mon, 03 Jun 2019 15:21:47: 8000000 INFO @ Mon, 03 Jun 2019 15:21:47: 8000000 INFO @ Mon, 03 Jun 2019 15:21:49: 8000000 INFO @ Mon, 03 Jun 2019 15:21:55: 9000000 INFO @ Mon, 03 Jun 2019 15:21:56: 9000000 INFO @ Mon, 03 Jun 2019 15:21:58: 9000000 INFO @ Mon, 03 Jun 2019 15:22:04: 10000000 INFO @ Mon, 03 Jun 2019 15:22:04: 10000000 INFO @ Mon, 03 Jun 2019 15:22:06: 10000000 INFO @ Mon, 03 Jun 2019 15:22:13: 11000000 INFO @ Mon, 03 Jun 2019 15:22:13: 11000000 INFO @ Mon, 03 Jun 2019 15:22:15: 11000000 INFO @ Mon, 03 Jun 2019 15:22:21: 12000000 INFO @ Mon, 03 Jun 2019 15:22:21: 12000000 INFO @ Mon, 03 Jun 2019 15:22:23: 12000000 INFO @ Mon, 03 Jun 2019 15:22:30: 13000000 INFO @ Mon, 03 Jun 2019 15:22:30: 13000000 INFO @ Mon, 03 Jun 2019 15:22:32: 13000000 INFO @ Mon, 03 Jun 2019 15:22:38: 14000000 INFO @ Mon, 03 Jun 2019 15:22:38: 14000000 INFO @ Mon, 03 Jun 2019 15:22:40: 14000000 INFO @ Mon, 03 Jun 2019 15:22:46: 15000000 INFO @ Mon, 03 Jun 2019 15:22:46: 15000000 INFO @ Mon, 03 Jun 2019 15:22:49: 15000000 INFO @ Mon, 03 Jun 2019 15:22:54: 16000000 INFO @ Mon, 03 Jun 2019 15:22:55: 16000000 INFO @ Mon, 03 Jun 2019 15:22:57: 16000000 INFO @ Mon, 03 Jun 2019 15:23:03: 17000000 INFO @ Mon, 03 Jun 2019 15:23:03: 17000000 INFO @ Mon, 03 Jun 2019 15:23:05: 17000000 INFO @ Mon, 03 Jun 2019 15:23:11: 18000000 INFO @ Mon, 03 Jun 2019 15:23:11: 18000000 INFO @ Mon, 03 Jun 2019 15:23:13: 18000000 INFO @ Mon, 03 Jun 2019 15:23:19: 19000000 INFO @ Mon, 03 Jun 2019 15:23:19: 19000000 INFO @ Mon, 03 Jun 2019 15:23:21: 19000000 INFO @ Mon, 03 Jun 2019 15:23:28: 20000000 INFO @ Mon, 03 Jun 2019 15:23:28: 20000000 INFO @ Mon, 03 Jun 2019 15:23:29: 20000000 INFO @ Mon, 03 Jun 2019 15:23:36: 21000000 INFO @ Mon, 03 Jun 2019 15:23:36: 21000000 INFO @ Mon, 03 Jun 2019 15:23:37: 21000000 INFO @ Mon, 03 Jun 2019 15:23:45: 22000000 INFO @ Mon, 03 Jun 2019 15:23:45: 22000000 INFO @ Mon, 03 Jun 2019 15:23:46: 22000000 INFO @ Mon, 03 Jun 2019 15:23:53: 23000000 INFO @ Mon, 03 Jun 2019 15:23:53: 23000000 INFO @ Mon, 03 Jun 2019 15:23:54: 23000000 INFO @ Mon, 03 Jun 2019 15:24:02: 24000000 INFO @ Mon, 03 Jun 2019 15:24:02: 24000000 INFO @ Mon, 03 Jun 2019 15:24:03: 24000000 INFO @ Mon, 03 Jun 2019 15:24:11: 25000000 INFO @ Mon, 03 Jun 2019 15:24:11: 25000000 INFO @ Mon, 03 Jun 2019 15:24:12: 25000000 INFO @ Mon, 03 Jun 2019 15:24:20: 26000000 INFO @ Mon, 03 Jun 2019 15:24:20: 26000000 INFO @ Mon, 03 Jun 2019 15:24:22: 26000000 INFO @ Mon, 03 Jun 2019 15:24:28: 27000000 INFO @ Mon, 03 Jun 2019 15:24:29: 27000000 INFO @ Mon, 03 Jun 2019 15:24:30: 27000000 INFO @ Mon, 03 Jun 2019 15:24:37: 28000000 INFO @ Mon, 03 Jun 2019 15:24:38: 28000000 INFO @ Mon, 03 Jun 2019 15:24:39: 28000000 INFO @ Mon, 03 Jun 2019 15:24:45: 29000000 INFO @ Mon, 03 Jun 2019 15:24:47: 29000000 INFO @ Mon, 03 Jun 2019 15:24:48: 29000000 INFO @ Mon, 03 Jun 2019 15:24:54: 30000000 INFO @ Mon, 03 Jun 2019 15:24:56: 30000000 INFO @ Mon, 03 Jun 2019 15:24:56: 30000000 INFO @ Mon, 03 Jun 2019 15:25:02: 31000000 INFO @ Mon, 03 Jun 2019 15:25:04: 31000000 INFO @ Mon, 03 Jun 2019 15:25:05: 31000000 INFO @ Mon, 03 Jun 2019 15:25:10: 32000000 INFO @ Mon, 03 Jun 2019 15:25:13: 32000000 INFO @ Mon, 03 Jun 2019 15:25:14: 32000000 INFO @ Mon, 03 Jun 2019 15:25:19: 33000000 INFO @ Mon, 03 Jun 2019 15:25:22: 33000000 INFO @ Mon, 03 Jun 2019 15:25:23: 33000000 INFO @ Mon, 03 Jun 2019 15:25:28: 34000000 INFO @ Mon, 03 Jun 2019 15:25:31: 34000000 INFO @ Mon, 03 Jun 2019 15:25:32: 34000000 INFO @ Mon, 03 Jun 2019 15:25:36: 35000000 BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:25:40: 35000000 INFO @ Mon, 03 Jun 2019 15:25:41: 35000000 INFO @ Mon, 03 Jun 2019 15:25:44: 36000000 INFO @ Mon, 03 Jun 2019 15:25:49: 36000000 INFO @ Mon, 03 Jun 2019 15:25:49: 36000000 INFO @ Mon, 03 Jun 2019 15:25:53: 37000000 INFO @ Mon, 03 Jun 2019 15:25:58: 37000000 INFO @ Mon, 03 Jun 2019 15:25:58: 37000000 INFO @ Mon, 03 Jun 2019 15:26:01: 38000000 INFO @ Mon, 03 Jun 2019 15:26:07: 38000000 INFO @ Mon, 03 Jun 2019 15:26:07: 38000000 INFO @ Mon, 03 Jun 2019 15:26:08: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:26:08: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:26:08: #1 total tags in treatment: 18211446 INFO @ Mon, 03 Jun 2019 15:26:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:26:08: #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 15:26:08: #1 tags after filtering in treatment: 9395675 INFO @ Mon, 03 Jun 2019 15:26:08: #1 Redundant rate of treatment: 0.48 INFO @ Mon, 03 Jun 2019 15:26:08: #1 finished! INFO @ Mon, 03 Jun 2019 15:26:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:26:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:26:10: #2 number of paired peaks: 10337 INFO @ Mon, 03 Jun 2019 15:26:10: start model_add_line... INFO @ Mon, 03 Jun 2019 15:26:10: start X-correlation... INFO @ Mon, 03 Jun 2019 15:26:10: end of X-cor INFO @ Mon, 03 Jun 2019 15:26:10: #2 finished! INFO @ Mon, 03 Jun 2019 15:26:10: #2 predicted fragment length is 217 bps INFO @ Mon, 03 Jun 2019 15:26:10: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 03 Jun 2019 15:26:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.10_model.r INFO @ Mon, 03 Jun 2019 15:26:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:26:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:26:13: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:26:13: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:26:13: #1 total tags in treatment: 18211446 INFO @ Mon, 03 Jun 2019 15:26:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:26:13: #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 15:26:13: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:26:13: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:26:13: #1 total tags in treatment: 18211446 INFO @ Mon, 03 Jun 2019 15:26:13: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:26:13: #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 15:26:14: #1 tags after filtering in treatment: 9395675 INFO @ Mon, 03 Jun 2019 15:26:14: #1 Redundant rate of treatment: 0.48 INFO @ Mon, 03 Jun 2019 15:26:14: #1 finished! INFO @ Mon, 03 Jun 2019 15:26:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:26:14: #1 tags after filtering in treatment: 9395675 INFO @ Mon, 03 Jun 2019 15:26:14: #1 Redundant rate of treatment: 0.48 INFO @ Mon, 03 Jun 2019 15:26:14: #1 finished! INFO @ Mon, 03 Jun 2019 15:26:14: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:26:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:26:15: #2 number of paired peaks: 10337 INFO @ Mon, 03 Jun 2019 15:26:15: start model_add_line... INFO @ Mon, 03 Jun 2019 15:26:16: #2 number of paired peaks: 10337 INFO @ Mon, 03 Jun 2019 15:26:16: start model_add_line... INFO @ Mon, 03 Jun 2019 15:26:16: start X-correlation... INFO @ Mon, 03 Jun 2019 15:26:16: end of X-cor INFO @ Mon, 03 Jun 2019 15:26:16: #2 finished! INFO @ Mon, 03 Jun 2019 15:26:16: #2 predicted fragment length is 217 bps INFO @ Mon, 03 Jun 2019 15:26:16: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 03 Jun 2019 15:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.05_model.r INFO @ Mon, 03 Jun 2019 15:26:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:26:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:26:16: start X-correlation... INFO @ Mon, 03 Jun 2019 15:26:16: end of X-cor INFO @ Mon, 03 Jun 2019 15:26:16: #2 finished! INFO @ Mon, 03 Jun 2019 15:26:16: #2 predicted fragment length is 217 bps INFO @ Mon, 03 Jun 2019 15:26:16: #2 alternative fragment length(s) may be 217 bps INFO @ Mon, 03 Jun 2019 15:26:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.20_model.r INFO @ Mon, 03 Jun 2019 15:26:16: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:26:16: #3 Pre-compute pvalue-qvalue table... BigWig に変換しました。 INFO @ Mon, 03 Jun 2019 15:26:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:26:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:26:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:27:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:27:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:27:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.10_summits.bed INFO @ Mon, 03 Jun 2019 15:27:04: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9226 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:27:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:27:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:27:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.20_summits.bed INFO @ Mon, 03 Jun 2019 15:27:09: Done! INFO @ Mon, 03 Jun 2019 15:27:10: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.05_peaks.xls pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8103 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:27:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:27:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393675/SRX3393675.05_summits.bed INFO @ Mon, 03 Jun 2019 15:27:10: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (10244 records, 4 fields): 18 millis CompletedMACS2peakCalling