Job ID = 1295473 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 27,746,898 reads read : 55,493,796 reads written : 55,493,796 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: 01:07:52 27746898 reads; of these: 27746898 (100.00%) were paired; of these: 5740553 (20.69%) aligned concordantly 0 times 16027022 (57.76%) aligned concordantly exactly 1 time 5979323 (21.55%) aligned concordantly >1 times ---- 5740553 pairs aligned concordantly 0 times; of these: 272123 (4.74%) aligned discordantly 1 time ---- 5468430 pairs aligned 0 times concordantly or discordantly; of these: 10936860 mates make up the pairs; of these: 9049059 (82.74%) aligned 0 times 822168 (7.52%) aligned exactly 1 time 1065633 (9.74%) aligned >1 times 83.69% overall alignment rate Time searching: 01:07:52 Overall time: 01:07:52 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] 1570451 / 22255058 = 0.0706 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 15:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.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 15:31:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:31:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.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 15:31:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:31:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:31:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.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 15:31:20: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:31:20: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:31:28: 1000000 INFO @ Mon, 03 Jun 2019 15:31:29: 1000000 INFO @ Mon, 03 Jun 2019 15:31:29: 1000000 INFO @ Mon, 03 Jun 2019 15:31:35: 2000000 INFO @ Mon, 03 Jun 2019 15:31:38: 2000000 INFO @ Mon, 03 Jun 2019 15:31:38: 2000000 INFO @ Mon, 03 Jun 2019 15:31:42: 3000000 INFO @ Mon, 03 Jun 2019 15:31:47: 3000000 INFO @ Mon, 03 Jun 2019 15:31:47: 3000000 INFO @ Mon, 03 Jun 2019 15:31:50: 4000000 INFO @ Mon, 03 Jun 2019 15:31:56: 4000000 INFO @ Mon, 03 Jun 2019 15:31:56: 4000000 INFO @ Mon, 03 Jun 2019 15:31:57: 5000000 INFO @ Mon, 03 Jun 2019 15:32:04: 5000000 INFO @ Mon, 03 Jun 2019 15:32:05: 6000000 INFO @ Mon, 03 Jun 2019 15:32:05: 5000000 INFO @ Mon, 03 Jun 2019 15:32:12: 6000000 INFO @ Mon, 03 Jun 2019 15:32:13: 7000000 INFO @ Mon, 03 Jun 2019 15:32:14: 6000000 INFO @ Mon, 03 Jun 2019 15:32:20: 8000000 INFO @ Mon, 03 Jun 2019 15:32:21: 7000000 INFO @ Mon, 03 Jun 2019 15:32:23: 7000000 INFO @ Mon, 03 Jun 2019 15:32:27: 9000000 INFO @ Mon, 03 Jun 2019 15:32:30: 8000000 INFO @ Mon, 03 Jun 2019 15:32:32: 8000000 INFO @ Mon, 03 Jun 2019 15:32:35: 10000000 INFO @ Mon, 03 Jun 2019 15:32:39: 9000000 INFO @ Mon, 03 Jun 2019 15:32:40: 9000000 INFO @ Mon, 03 Jun 2019 15:32:42: 11000000 INFO @ Mon, 03 Jun 2019 15:32:48: 10000000 INFO @ Mon, 03 Jun 2019 15:32:49: 10000000 INFO @ Mon, 03 Jun 2019 15:32:50: 12000000 INFO @ Mon, 03 Jun 2019 15:32:57: 11000000 INFO @ Mon, 03 Jun 2019 15:32:57: 13000000 INFO @ Mon, 03 Jun 2019 15:32:59: 11000000 INFO @ Mon, 03 Jun 2019 15:33:04: 14000000 INFO @ Mon, 03 Jun 2019 15:33:06: 12000000 INFO @ Mon, 03 Jun 2019 15:33:08: 12000000 INFO @ Mon, 03 Jun 2019 15:33:11: 15000000 INFO @ Mon, 03 Jun 2019 15:33:14: 13000000 INFO @ Mon, 03 Jun 2019 15:33:16: 13000000 INFO @ Mon, 03 Jun 2019 15:33:18: 16000000 INFO @ Mon, 03 Jun 2019 15:33:23: 14000000 INFO @ Mon, 03 Jun 2019 15:33:25: 14000000 INFO @ Mon, 03 Jun 2019 15:33:25: 17000000 INFO @ Mon, 03 Jun 2019 15:33:32: 15000000 INFO @ Mon, 03 Jun 2019 15:33:33: 18000000 INFO @ Mon, 03 Jun 2019 15:33:34: 15000000 INFO @ Mon, 03 Jun 2019 15:33:40: 19000000 INFO @ Mon, 03 Jun 2019 15:33:40: 16000000 INFO @ Mon, 03 Jun 2019 15:33:42: 16000000 INFO @ Mon, 03 Jun 2019 15:33:47: 20000000 INFO @ Mon, 03 Jun 2019 15:33:48: 17000000 INFO @ Mon, 03 Jun 2019 15:33:50: 17000000 INFO @ Mon, 03 Jun 2019 15:33:54: 21000000 INFO @ Mon, 03 Jun 2019 15:33:56: 18000000 INFO @ Mon, 03 Jun 2019 15:33:58: 18000000 INFO @ Mon, 03 Jun 2019 15:34:02: 22000000 INFO @ Mon, 03 Jun 2019 15:34:04: 19000000 INFO @ Mon, 03 Jun 2019 15:34:06: 19000000 INFO @ Mon, 03 Jun 2019 15:34:09: 23000000 INFO @ Mon, 03 Jun 2019 15:34:12: 20000000 INFO @ Mon, 03 Jun 2019 15:34:14: 20000000 INFO @ Mon, 03 Jun 2019 15:34:16: 24000000 INFO @ Mon, 03 Jun 2019 15:34:21: 21000000 INFO @ Mon, 03 Jun 2019 15:34:23: 21000000 INFO @ Mon, 03 Jun 2019 15:34:24: 25000000 INFO @ Mon, 03 Jun 2019 15:34:29: 22000000 INFO @ Mon, 03 Jun 2019 15:34:31: 26000000 INFO @ Mon, 03 Jun 2019 15:34:31: 22000000 INFO @ Mon, 03 Jun 2019 15:34:37: 23000000 INFO @ Mon, 03 Jun 2019 15:34:38: 27000000 INFO @ Mon, 03 Jun 2019 15:34:40: 23000000 INFO @ Mon, 03 Jun 2019 15:34:45: 28000000 INFO @ Mon, 03 Jun 2019 15:34:45: 24000000 INFO @ Mon, 03 Jun 2019 15:34:49: 24000000 INFO @ Mon, 03 Jun 2019 15:34:52: 29000000 INFO @ Mon, 03 Jun 2019 15:34:53: 25000000 INFO @ Mon, 03 Jun 2019 15:34:59: 25000000 INFO @ Mon, 03 Jun 2019 15:34:59: 30000000 INFO @ Mon, 03 Jun 2019 15:35:01: 26000000 INFO @ Mon, 03 Jun 2019 15:35:07: 31000000 INFO @ Mon, 03 Jun 2019 15:35:07: 26000000 INFO @ Mon, 03 Jun 2019 15:35:10: 27000000 INFO @ Mon, 03 Jun 2019 15:35:14: 32000000 INFO @ Mon, 03 Jun 2019 15:35:15: 27000000 INFO @ Mon, 03 Jun 2019 15:35:18: 28000000 INFO @ Mon, 03 Jun 2019 15:35:21: 33000000 INFO @ Mon, 03 Jun 2019 15:35:23: 28000000 INFO @ Mon, 03 Jun 2019 15:35:26: 29000000 INFO @ Mon, 03 Jun 2019 15:35:28: 34000000 INFO @ Mon, 03 Jun 2019 15:35:32: 29000000 INFO @ Mon, 03 Jun 2019 15:35:34: 30000000 INFO @ Mon, 03 Jun 2019 15:35:35: 35000000 INFO @ Mon, 03 Jun 2019 15:35:40: 30000000 INFO @ Mon, 03 Jun 2019 15:35:42: 31000000 INFO @ Mon, 03 Jun 2019 15:35:43: 36000000 INFO @ Mon, 03 Jun 2019 15:35:49: 31000000 INFO @ Mon, 03 Jun 2019 15:35:50: 37000000 INFO @ Mon, 03 Jun 2019 15:35:51: 32000000 INFO @ Mon, 03 Jun 2019 15:35:57: 32000000 INFO @ Mon, 03 Jun 2019 15:35:57: 38000000 INFO @ Mon, 03 Jun 2019 15:35:59: 33000000 INFO @ Mon, 03 Jun 2019 15:36:05: 39000000 INFO @ Mon, 03 Jun 2019 15:36:05: 33000000 INFO @ Mon, 03 Jun 2019 15:36:07: 34000000 INFO @ Mon, 03 Jun 2019 15:36:13: 40000000 INFO @ Mon, 03 Jun 2019 15:36:14: 34000000 INFO @ Mon, 03 Jun 2019 15:36:16: 35000000 INFO @ Mon, 03 Jun 2019 15:36:21: 41000000 INFO @ Mon, 03 Jun 2019 15:36:23: 35000000 INFO @ Mon, 03 Jun 2019 15:36:25: 36000000 INFO @ Mon, 03 Jun 2019 15:36:29: 42000000 INFO @ Mon, 03 Jun 2019 15:36:31: 36000000 INFO @ Mon, 03 Jun 2019 15:36:34: 37000000 INFO @ Mon, 03 Jun 2019 15:36:37: 43000000 INFO @ Mon, 03 Jun 2019 15:36:40: 37000000 INFO @ Mon, 03 Jun 2019 15:36:40: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:36:40: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:36:40: #1 total tags in treatment: 20441606 INFO @ Mon, 03 Jun 2019 15:36:40: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:36:40: #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 15:36:41: #1 tags after filtering in treatment: 12050399 INFO @ Mon, 03 Jun 2019 15:36:41: #1 Redundant rate of treatment: 0.41 INFO @ Mon, 03 Jun 2019 15:36:41: #1 finished! INFO @ Mon, 03 Jun 2019 15:36:41: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:36:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:36:43: #2 number of paired peaks: 7914 INFO @ Mon, 03 Jun 2019 15:36:43: start model_add_line... INFO @ Mon, 03 Jun 2019 15:36:43: start X-correlation... INFO @ Mon, 03 Jun 2019 15:36:43: end of X-cor INFO @ Mon, 03 Jun 2019 15:36:43: #2 finished! INFO @ Mon, 03 Jun 2019 15:36:43: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 15:36:43: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 15:36:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.20_model.r INFO @ Mon, 03 Jun 2019 15:36:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:36:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:36:43: 38000000 INFO @ Mon, 03 Jun 2019 15:36:50: 38000000 INFO @ Mon, 03 Jun 2019 15:36:53: 39000000 INFO @ Mon, 03 Jun 2019 15:37:00: 39000000 INFO @ Mon, 03 Jun 2019 15:37:02: 40000000 INFO @ Mon, 03 Jun 2019 15:37:08: 40000000 INFO @ Mon, 03 Jun 2019 15:37:11: 41000000 INFO @ Mon, 03 Jun 2019 15:37:16: 41000000 INFO @ Mon, 03 Jun 2019 15:37:20: 42000000 INFO @ Mon, 03 Jun 2019 15:37:25: 42000000 INFO @ Mon, 03 Jun 2019 15:37:28: 43000000 INFO @ Mon, 03 Jun 2019 15:37:31: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:37:31: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:37:31: #1 total tags in treatment: 20441606 INFO @ Mon, 03 Jun 2019 15:37:31: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:37:31: #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 15:37:32: #1 tags after filtering in treatment: 12050399 INFO @ Mon, 03 Jun 2019 15:37:32: #1 Redundant rate of treatment: 0.41 INFO @ Mon, 03 Jun 2019 15:37:32: #1 finished! INFO @ Mon, 03 Jun 2019 15:37:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:37:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:37:32: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:37:33: 43000000 INFO @ Mon, 03 Jun 2019 15:37:34: #2 number of paired peaks: 7914 INFO @ Mon, 03 Jun 2019 15:37:34: start model_add_line... INFO @ Mon, 03 Jun 2019 15:37:34: start X-correlation... INFO @ Mon, 03 Jun 2019 15:37:34: end of X-cor INFO @ Mon, 03 Jun 2019 15:37:34: #2 finished! INFO @ Mon, 03 Jun 2019 15:37:34: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 15:37:34: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 15:37:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.05_model.r INFO @ Mon, 03 Jun 2019 15:37:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:37:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:37:35: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:37:35: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:37:35: #1 total tags in treatment: 20441606 INFO @ Mon, 03 Jun 2019 15:37:35: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:37:35: #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 15:37:36: #1 tags after filtering in treatment: 12050399 INFO @ Mon, 03 Jun 2019 15:37:36: #1 Redundant rate of treatment: 0.41 INFO @ Mon, 03 Jun 2019 15:37:36: #1 finished! INFO @ Mon, 03 Jun 2019 15:37:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:37:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:37:38: #2 number of paired peaks: 7914 INFO @ Mon, 03 Jun 2019 15:37:38: start model_add_line... INFO @ Mon, 03 Jun 2019 15:37:38: start X-correlation... INFO @ Mon, 03 Jun 2019 15:37:38: end of X-cor INFO @ Mon, 03 Jun 2019 15:37:38: #2 finished! INFO @ Mon, 03 Jun 2019 15:37:38: #2 predicted fragment length is 215 bps INFO @ Mon, 03 Jun 2019 15:37:38: #2 alternative fragment length(s) may be 215 bps INFO @ Mon, 03 Jun 2019 15:37:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.10_model.r INFO @ Mon, 03 Jun 2019 15:37:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:37:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:37:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:37:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:37:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.20_summits.bed INFO @ Mon, 03 Jun 2019 15:37:50: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7345 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:38:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:38:26: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:38:46: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:38:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:38:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.10_summits.bed INFO @ Mon, 03 Jun 2019 15:38:46: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (8713 records, 4 fields): 17 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:38:47: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:38:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:38:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393677/SRX3393677.05_summits.bed INFO @ Mon, 03 Jun 2019 15:38:47: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9882 records, 4 fields): 15 millis CompletedMACS2peakCalling BigWig に変換しました。