Job ID = 1295444 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 27,051,198 reads read : 54,102,396 reads written : 54,102,396 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: 01:03:58 27051198 reads; of these: 27051198 (100.00%) were paired; of these: 4130140 (15.27%) aligned concordantly 0 times 16948762 (62.65%) aligned concordantly exactly 1 time 5972296 (22.08%) aligned concordantly >1 times ---- 4130140 pairs aligned concordantly 0 times; of these: 172753 (4.18%) aligned discordantly 1 time ---- 3957387 pairs aligned 0 times concordantly or discordantly; of these: 7914774 mates make up the pairs; of these: 6256554 (79.05%) aligned 0 times 755320 (9.54%) aligned exactly 1 time 902900 (11.41%) aligned >1 times 88.44% overall alignment rate Time searching: 01:03:58 Overall time: 01:03:58 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] 2162029 / 23062236 = 0.0937 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 15:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.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 15:17:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:17:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.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 15:17:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:17:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:17:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.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 15:17:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:17:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:17:16: 1000000 INFO @ Mon, 03 Jun 2019 15:17:16: 1000000 INFO @ Mon, 03 Jun 2019 15:17:16: 1000000 INFO @ Mon, 03 Jun 2019 15:17:23: 2000000 INFO @ Mon, 03 Jun 2019 15:17:23: 2000000 INFO @ Mon, 03 Jun 2019 15:17:24: 2000000 INFO @ Mon, 03 Jun 2019 15:17:30: 3000000 INFO @ Mon, 03 Jun 2019 15:17:30: 3000000 INFO @ Mon, 03 Jun 2019 15:17:32: 3000000 INFO @ Mon, 03 Jun 2019 15:17:36: 4000000 INFO @ Mon, 03 Jun 2019 15:17:36: 4000000 INFO @ Mon, 03 Jun 2019 15:17:39: 4000000 INFO @ Mon, 03 Jun 2019 15:17:42: 5000000 INFO @ Mon, 03 Jun 2019 15:17:42: 5000000 INFO @ Mon, 03 Jun 2019 15:17:47: 5000000 INFO @ Mon, 03 Jun 2019 15:17:48: 6000000 INFO @ Mon, 03 Jun 2019 15:17:48: 6000000 INFO @ Mon, 03 Jun 2019 15:17:54: 7000000 INFO @ Mon, 03 Jun 2019 15:17:54: 6000000 INFO @ Mon, 03 Jun 2019 15:17:54: 7000000 INFO @ Mon, 03 Jun 2019 15:18:00: 8000000 INFO @ Mon, 03 Jun 2019 15:18:00: 8000000 INFO @ Mon, 03 Jun 2019 15:18:02: 7000000 INFO @ Mon, 03 Jun 2019 15:18:06: 9000000 INFO @ Mon, 03 Jun 2019 15:18:06: 9000000 INFO @ Mon, 03 Jun 2019 15:18:09: 8000000 INFO @ Mon, 03 Jun 2019 15:18:12: 10000000 INFO @ Mon, 03 Jun 2019 15:18:12: 10000000 INFO @ Mon, 03 Jun 2019 15:18:16: 9000000 INFO @ Mon, 03 Jun 2019 15:18:18: 11000000 INFO @ Mon, 03 Jun 2019 15:18:18: 11000000 INFO @ Mon, 03 Jun 2019 15:18:24: 12000000 INFO @ Mon, 03 Jun 2019 15:18:24: 12000000 INFO @ Mon, 03 Jun 2019 15:18:24: 10000000 INFO @ Mon, 03 Jun 2019 15:18:30: 13000000 INFO @ Mon, 03 Jun 2019 15:18:30: 13000000 INFO @ Mon, 03 Jun 2019 15:18:31: 11000000 INFO @ Mon, 03 Jun 2019 15:18:35: 14000000 INFO @ Mon, 03 Jun 2019 15:18:35: 14000000 INFO @ Mon, 03 Jun 2019 15:18:38: 12000000 INFO @ Mon, 03 Jun 2019 15:18:41: 15000000 INFO @ Mon, 03 Jun 2019 15:18:41: 15000000 INFO @ Mon, 03 Jun 2019 15:18:46: 13000000 INFO @ Mon, 03 Jun 2019 15:18:47: 16000000 INFO @ Mon, 03 Jun 2019 15:18:47: 16000000 INFO @ Mon, 03 Jun 2019 15:18:53: 14000000 INFO @ Mon, 03 Jun 2019 15:18:53: 17000000 INFO @ Mon, 03 Jun 2019 15:18:53: 17000000 INFO @ Mon, 03 Jun 2019 15:18:59: 18000000 INFO @ Mon, 03 Jun 2019 15:19:00: 18000000 INFO @ Mon, 03 Jun 2019 15:19:00: 15000000 INFO @ Mon, 03 Jun 2019 15:19:05: 19000000 INFO @ Mon, 03 Jun 2019 15:19:06: 19000000 INFO @ Mon, 03 Jun 2019 15:19:08: 16000000 INFO @ Mon, 03 Jun 2019 15:19:11: 20000000 INFO @ Mon, 03 Jun 2019 15:19:12: 20000000 INFO @ Mon, 03 Jun 2019 15:19:15: 17000000 INFO @ Mon, 03 Jun 2019 15:19:17: 21000000 INFO @ Mon, 03 Jun 2019 15:19:17: 21000000 INFO @ Mon, 03 Jun 2019 15:19:21: 18000000 INFO @ Mon, 03 Jun 2019 15:19:23: 22000000 INFO @ Mon, 03 Jun 2019 15:19:23: 22000000 INFO @ Mon, 03 Jun 2019 15:19:28: 19000000 INFO @ Mon, 03 Jun 2019 15:19:29: 23000000 INFO @ Mon, 03 Jun 2019 15:19:29: 23000000 INFO @ Mon, 03 Jun 2019 15:19:35: 24000000 INFO @ Mon, 03 Jun 2019 15:19:35: 24000000 INFO @ Mon, 03 Jun 2019 15:19:35: 20000000 INFO @ Mon, 03 Jun 2019 15:19:41: 25000000 INFO @ Mon, 03 Jun 2019 15:19:41: 25000000 INFO @ Mon, 03 Jun 2019 15:19:42: 21000000 INFO @ Mon, 03 Jun 2019 15:19:47: 26000000 INFO @ Mon, 03 Jun 2019 15:19:47: 26000000 INFO @ Mon, 03 Jun 2019 15:19:49: 22000000 INFO @ Mon, 03 Jun 2019 15:19:53: 27000000 INFO @ Mon, 03 Jun 2019 15:19:53: 27000000 INFO @ Mon, 03 Jun 2019 15:19:57: 23000000 INFO @ Mon, 03 Jun 2019 15:19:59: 28000000 INFO @ Mon, 03 Jun 2019 15:19:59: 28000000 INFO @ Mon, 03 Jun 2019 15:20:04: 24000000 INFO @ Mon, 03 Jun 2019 15:20:05: 29000000 INFO @ Mon, 03 Jun 2019 15:20:05: 29000000 INFO @ Mon, 03 Jun 2019 15:20:11: 25000000 INFO @ Mon, 03 Jun 2019 15:20:12: 30000000 INFO @ Mon, 03 Jun 2019 15:20:12: 30000000 INFO @ Mon, 03 Jun 2019 15:20:18: 31000000 INFO @ Mon, 03 Jun 2019 15:20:18: 31000000 INFO @ Mon, 03 Jun 2019 15:20:19: 26000000 INFO @ Mon, 03 Jun 2019 15:20:25: 32000000 INFO @ Mon, 03 Jun 2019 15:20:25: 32000000 INFO @ Mon, 03 Jun 2019 15:20:26: 27000000 INFO @ Mon, 03 Jun 2019 15:20:31: 33000000 INFO @ Mon, 03 Jun 2019 15:20:31: 33000000 INFO @ Mon, 03 Jun 2019 15:20:33: 28000000 INFO @ Mon, 03 Jun 2019 15:20:37: 34000000 INFO @ Mon, 03 Jun 2019 15:20:37: 34000000 INFO @ Mon, 03 Jun 2019 15:20:41: 29000000 INFO @ Mon, 03 Jun 2019 15:20:43: 35000000 INFO @ Mon, 03 Jun 2019 15:20:43: 35000000 INFO @ Mon, 03 Jun 2019 15:20:48: 30000000 INFO @ Mon, 03 Jun 2019 15:20:49: 36000000 INFO @ Mon, 03 Jun 2019 15:20:49: 36000000 INFO @ Mon, 03 Jun 2019 15:20:55: 37000000 INFO @ Mon, 03 Jun 2019 15:20:55: 37000000 INFO @ Mon, 03 Jun 2019 15:20:55: 31000000 INFO @ Mon, 03 Jun 2019 15:21:01: 38000000 INFO @ Mon, 03 Jun 2019 15:21:02: 38000000 INFO @ Mon, 03 Jun 2019 15:21:03: 32000000 INFO @ Mon, 03 Jun 2019 15:21:08: 39000000 INFO @ Mon, 03 Jun 2019 15:21:08: 39000000 INFO @ Mon, 03 Jun 2019 15:21:10: 33000000 INFO @ Mon, 03 Jun 2019 15:21:14: 40000000 INFO @ Mon, 03 Jun 2019 15:21:14: 40000000 INFO @ Mon, 03 Jun 2019 15:21:17: 34000000 INFO @ Mon, 03 Jun 2019 15:21:20: 41000000 INFO @ Mon, 03 Jun 2019 15:21:21: 41000000 INFO @ Mon, 03 Jun 2019 15:21:24: 35000000 INFO @ Mon, 03 Jun 2019 15:21:26: 42000000 INFO @ Mon, 03 Jun 2019 15:21:26: 42000000 INFO @ Mon, 03 Jun 2019 15:21:31: 36000000 INFO @ Mon, 03 Jun 2019 15:21:32: 43000000 INFO @ Mon, 03 Jun 2019 15:21:32: 43000000 INFO @ Mon, 03 Jun 2019 15:21:36: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:21:36: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:21:36: #1 total tags in treatment: 20763817 INFO @ Mon, 03 Jun 2019 15:21:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:21:36: #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 15:21:36: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:21:36: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:21:36: #1 total tags in treatment: 20763817 INFO @ Mon, 03 Jun 2019 15:21:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:21:36: #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 15:21:36: #1 tags after filtering in treatment: 11696134 INFO @ Mon, 03 Jun 2019 15:21:36: #1 Redundant rate of treatment: 0.44 INFO @ Mon, 03 Jun 2019 15:21:36: #1 finished! INFO @ Mon, 03 Jun 2019 15:21:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:21:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:21:36: #1 tags after filtering in treatment: 11696134 INFO @ Mon, 03 Jun 2019 15:21:36: #1 Redundant rate of treatment: 0.44 INFO @ Mon, 03 Jun 2019 15:21:36: #1 finished! INFO @ Mon, 03 Jun 2019 15:21:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:21:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:21:38: #2 number of paired peaks: 8429 INFO @ Mon, 03 Jun 2019 15:21:38: start model_add_line... INFO @ Mon, 03 Jun 2019 15:21:38: start X-correlation... INFO @ Mon, 03 Jun 2019 15:21:38: end of X-cor INFO @ Mon, 03 Jun 2019 15:21:38: #2 finished! INFO @ Mon, 03 Jun 2019 15:21:38: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 15:21:38: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 15:21:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.20_model.r INFO @ Mon, 03 Jun 2019 15:21:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:21:38: #2 number of paired peaks: 8429 INFO @ Mon, 03 Jun 2019 15:21:38: start model_add_line... INFO @ Mon, 03 Jun 2019 15:21:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:21:38: 37000000 INFO @ Mon, 03 Jun 2019 15:21:39: start X-correlation... INFO @ Mon, 03 Jun 2019 15:21:39: end of X-cor INFO @ Mon, 03 Jun 2019 15:21:39: #2 finished! INFO @ Mon, 03 Jun 2019 15:21:39: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 15:21:39: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 15:21:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.05_model.r INFO @ Mon, 03 Jun 2019 15:21:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:21:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:21:46: 38000000 INFO @ Mon, 03 Jun 2019 15:21:54: 39000000 INFO @ Mon, 03 Jun 2019 15:22:01: 40000000 INFO @ Mon, 03 Jun 2019 15:22:09: 41000000 INFO @ Mon, 03 Jun 2019 15:22:16: 42000000 INFO @ Mon, 03 Jun 2019 15:22:24: 43000000 INFO @ Mon, 03 Jun 2019 15:22:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:22:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:22:28: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:22:28: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:22:28: #1 total tags in treatment: 20763817 INFO @ Mon, 03 Jun 2019 15:22:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:22:28: #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 15:22:29: #1 tags after filtering in treatment: 11696134 INFO @ Mon, 03 Jun 2019 15:22:29: #1 Redundant rate of treatment: 0.44 INFO @ Mon, 03 Jun 2019 15:22:29: #1 finished! INFO @ Mon, 03 Jun 2019 15:22:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:22:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:22:31: #2 number of paired peaks: 8429 INFO @ Mon, 03 Jun 2019 15:22:31: start model_add_line... INFO @ Mon, 03 Jun 2019 15:22:31: start X-correlation... INFO @ Mon, 03 Jun 2019 15:22:31: end of X-cor INFO @ Mon, 03 Jun 2019 15:22:31: #2 finished! INFO @ Mon, 03 Jun 2019 15:22:31: #2 predicted fragment length is 204 bps INFO @ Mon, 03 Jun 2019 15:22:31: #2 alternative fragment length(s) may be 204 bps INFO @ Mon, 03 Jun 2019 15:22:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.10_model.r INFO @ Mon, 03 Jun 2019 15:22:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:22:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:22:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:22:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:22:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.20_summits.bed INFO @ Mon, 03 Jun 2019 15:22:43: Done! INFO @ Mon, 03 Jun 2019 15:22:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:22:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.05_summits.bed INFO @ Mon, 03 Jun 2019 15:22:43: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7869 records, 4 fields): 18 millis CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10407 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:23:17: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:23:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:23:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:23:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393659/SRX3393659.10_summits.bed INFO @ Mon, 03 Jun 2019 15:23:37: Done! pass1 - making usageList (15 chroms): 5 millis pass2 - checking and writing primary data (9232 records, 4 fields): 18 millis CompletedMACS2peakCalling BigWig に変換しました。