Job ID = 1295458 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 22,396,040 reads read : 44,792,080 reads written : 44,792,080 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: 01:00:32 22396040 reads; of these: 22396040 (100.00%) were paired; of these: 2572769 (11.49%) aligned concordantly 0 times 13030731 (58.18%) aligned concordantly exactly 1 time 6792540 (30.33%) aligned concordantly >1 times ---- 2572769 pairs aligned concordantly 0 times; of these: 137469 (5.34%) aligned discordantly 1 time ---- 2435300 pairs aligned 0 times concordantly or discordantly; of these: 4870600 mates make up the pairs; of these: 3715510 (76.28%) aligned 0 times 584331 (12.00%) aligned exactly 1 time 570759 (11.72%) aligned >1 times 91.70% overall alignment rate Time searching: 01:00:32 Overall time: 01:00:32 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] 1236771 / 19890498 = 0.0622 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 15:11:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.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 15:11:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:11:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:11:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.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 15:11:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:11:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:11:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.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 15:11:25: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:11:25: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:11:31: 1000000 INFO @ Mon, 03 Jun 2019 15:11:32: 1000000 INFO @ Mon, 03 Jun 2019 15:11:32: 1000000 INFO @ Mon, 03 Jun 2019 15:11:37: 2000000 INFO @ Mon, 03 Jun 2019 15:11:39: 2000000 INFO @ Mon, 03 Jun 2019 15:11:39: 2000000 INFO @ Mon, 03 Jun 2019 15:11:43: 3000000 INFO @ Mon, 03 Jun 2019 15:11:45: 3000000 INFO @ Mon, 03 Jun 2019 15:11:46: 3000000 INFO @ Mon, 03 Jun 2019 15:11:48: 4000000 INFO @ Mon, 03 Jun 2019 15:11:52: 4000000 INFO @ Mon, 03 Jun 2019 15:11:52: 4000000 INFO @ Mon, 03 Jun 2019 15:11:54: 5000000 INFO @ Mon, 03 Jun 2019 15:11:59: 5000000 INFO @ Mon, 03 Jun 2019 15:11:59: 5000000 INFO @ Mon, 03 Jun 2019 15:12:00: 6000000 INFO @ Mon, 03 Jun 2019 15:12:05: 6000000 INFO @ Mon, 03 Jun 2019 15:12:06: 7000000 INFO @ Mon, 03 Jun 2019 15:12:06: 6000000 INFO @ Mon, 03 Jun 2019 15:12:11: 8000000 INFO @ Mon, 03 Jun 2019 15:12:12: 7000000 INFO @ Mon, 03 Jun 2019 15:12:14: 7000000 INFO @ Mon, 03 Jun 2019 15:12:17: 9000000 INFO @ Mon, 03 Jun 2019 15:12:18: 8000000 INFO @ Mon, 03 Jun 2019 15:12:20: 8000000 INFO @ Mon, 03 Jun 2019 15:12:23: 10000000 INFO @ Mon, 03 Jun 2019 15:12:24: 9000000 INFO @ Mon, 03 Jun 2019 15:12:26: 9000000 INFO @ Mon, 03 Jun 2019 15:12:29: 11000000 INFO @ Mon, 03 Jun 2019 15:12:31: 10000000 INFO @ Mon, 03 Jun 2019 15:12:33: 10000000 INFO @ Mon, 03 Jun 2019 15:12:34: 12000000 INFO @ Mon, 03 Jun 2019 15:12:37: 11000000 INFO @ Mon, 03 Jun 2019 15:12:39: 11000000 INFO @ Mon, 03 Jun 2019 15:12:40: 13000000 INFO @ Mon, 03 Jun 2019 15:12:43: 12000000 INFO @ Mon, 03 Jun 2019 15:12:46: 14000000 INFO @ Mon, 03 Jun 2019 15:12:46: 12000000 INFO @ Mon, 03 Jun 2019 15:12:50: 13000000 INFO @ Mon, 03 Jun 2019 15:12:51: 15000000 INFO @ Mon, 03 Jun 2019 15:12:53: 13000000 INFO @ Mon, 03 Jun 2019 15:12:56: 14000000 INFO @ Mon, 03 Jun 2019 15:12:57: 16000000 INFO @ Mon, 03 Jun 2019 15:12:59: 14000000 INFO @ Mon, 03 Jun 2019 15:13:02: 15000000 INFO @ Mon, 03 Jun 2019 15:13:03: 17000000 INFO @ Mon, 03 Jun 2019 15:13:06: 15000000 INFO @ Mon, 03 Jun 2019 15:13:08: 16000000 INFO @ Mon, 03 Jun 2019 15:13:09: 18000000 INFO @ Mon, 03 Jun 2019 15:13:13: 16000000 INFO @ Mon, 03 Jun 2019 15:13:14: 19000000 INFO @ Mon, 03 Jun 2019 15:13:15: 17000000 INFO @ Mon, 03 Jun 2019 15:13:20: 17000000 INFO @ Mon, 03 Jun 2019 15:13:20: 20000000 INFO @ Mon, 03 Jun 2019 15:13:22: 18000000 INFO @ Mon, 03 Jun 2019 15:13:26: 21000000 INFO @ Mon, 03 Jun 2019 15:13:26: 18000000 INFO @ Mon, 03 Jun 2019 15:13:29: 19000000 INFO @ Mon, 03 Jun 2019 15:13:31: 22000000 INFO @ Mon, 03 Jun 2019 15:13:33: 19000000 INFO @ Mon, 03 Jun 2019 15:13:35: 20000000 INFO @ Mon, 03 Jun 2019 15:13:37: 23000000 INFO @ Mon, 03 Jun 2019 15:13:40: 20000000 INFO @ Mon, 03 Jun 2019 15:13:42: 21000000 INFO @ Mon, 03 Jun 2019 15:13:43: 24000000 INFO @ Mon, 03 Jun 2019 15:13:47: 21000000 INFO @ Mon, 03 Jun 2019 15:13:49: 25000000 INFO @ Mon, 03 Jun 2019 15:13:49: 22000000 INFO @ Mon, 03 Jun 2019 15:13:54: 22000000 INFO @ Mon, 03 Jun 2019 15:13:54: 26000000 INFO @ Mon, 03 Jun 2019 15:13:56: 23000000 INFO @ Mon, 03 Jun 2019 15:14:00: 27000000 INFO @ Mon, 03 Jun 2019 15:14:00: 23000000 INFO @ Mon, 03 Jun 2019 15:14:02: 24000000 INFO @ Mon, 03 Jun 2019 15:14:06: 28000000 INFO @ Mon, 03 Jun 2019 15:14:07: 24000000 INFO @ Mon, 03 Jun 2019 15:14:09: 25000000 INFO @ Mon, 03 Jun 2019 15:14:12: 29000000 INFO @ Mon, 03 Jun 2019 15:14:14: 25000000 INFO @ Mon, 03 Jun 2019 15:14:17: 26000000 INFO @ Mon, 03 Jun 2019 15:14:17: 30000000 INFO @ Mon, 03 Jun 2019 15:14:21: 26000000 INFO @ Mon, 03 Jun 2019 15:14:23: 31000000 INFO @ Mon, 03 Jun 2019 15:14:24: 27000000 INFO @ Mon, 03 Jun 2019 15:14:28: 27000000 INFO @ Mon, 03 Jun 2019 15:14:29: 32000000 INFO @ Mon, 03 Jun 2019 15:14:30: 28000000 INFO @ Mon, 03 Jun 2019 15:14:35: 33000000 INFO @ Mon, 03 Jun 2019 15:14:35: 28000000 INFO @ Mon, 03 Jun 2019 15:14:37: 29000000 INFO @ Mon, 03 Jun 2019 15:14:40: 34000000 INFO @ Mon, 03 Jun 2019 15:14:42: 29000000 INFO @ Mon, 03 Jun 2019 15:14:44: 30000000 INFO @ Mon, 03 Jun 2019 15:14:46: 35000000 INFO @ Mon, 03 Jun 2019 15:14:49: 30000000 INFO @ Mon, 03 Jun 2019 15:14:51: 31000000 INFO @ Mon, 03 Jun 2019 15:14:52: 36000000 INFO @ Mon, 03 Jun 2019 15:14:56: 31000000 INFO @ Mon, 03 Jun 2019 15:14:58: 37000000 INFO @ Mon, 03 Jun 2019 15:14:58: 32000000 INFO @ Mon, 03 Jun 2019 15:15:03: 32000000 INFO @ Mon, 03 Jun 2019 15:15:04: 38000000 INFO @ Mon, 03 Jun 2019 15:15:05: 33000000 INFO @ Mon, 03 Jun 2019 15:15:08: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:15:08: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:15:08: #1 total tags in treatment: 18587564 INFO @ Mon, 03 Jun 2019 15:15:08: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:15:08: #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 15:15:08: #1 tags after filtering in treatment: 16840209 INFO @ Mon, 03 Jun 2019 15:15:08: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 15:15:08: #1 finished! INFO @ Mon, 03 Jun 2019 15:15:08: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:15:09: 33000000 INFO @ Mon, 03 Jun 2019 15:15:10: #2 number of paired peaks: 1317 INFO @ Mon, 03 Jun 2019 15:15:10: start model_add_line... INFO @ Mon, 03 Jun 2019 15:15:10: start X-correlation... INFO @ Mon, 03 Jun 2019 15:15:10: end of X-cor INFO @ Mon, 03 Jun 2019 15:15:10: #2 finished! INFO @ Mon, 03 Jun 2019 15:15:10: #2 predicted fragment length is 163 bps INFO @ Mon, 03 Jun 2019 15:15:10: #2 alternative fragment length(s) may be 4,163 bps INFO @ Mon, 03 Jun 2019 15:15:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.05_model.r INFO @ Mon, 03 Jun 2019 15:15:10: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:15:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:15:12: 34000000 INFO @ Mon, 03 Jun 2019 15:15:16: 34000000 INFO @ Mon, 03 Jun 2019 15:15:18: 35000000 INFO @ Mon, 03 Jun 2019 15:15:23: 35000000 INFO @ Mon, 03 Jun 2019 15:15:25: 36000000 INFO @ Mon, 03 Jun 2019 15:15:30: 36000000 INFO @ Mon, 03 Jun 2019 15:15:32: 37000000 INFO @ Mon, 03 Jun 2019 15:15:37: 37000000 INFO @ Mon, 03 Jun 2019 15:15:39: 38000000 INFO @ Mon, 03 Jun 2019 15:15:44: 38000000 INFO @ Mon, 03 Jun 2019 15:15:44: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:15:44: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:15:44: #1 total tags in treatment: 18587564 INFO @ Mon, 03 Jun 2019 15:15:44: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:15:44: #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 15:15:44: #1 tags after filtering in treatment: 16840209 INFO @ Mon, 03 Jun 2019 15:15:44: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 15:15:44: #1 finished! INFO @ Mon, 03 Jun 2019 15:15:44: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:15:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:15:46: #2 number of paired peaks: 1317 INFO @ Mon, 03 Jun 2019 15:15:46: start model_add_line... INFO @ Mon, 03 Jun 2019 15:15:46: start X-correlation... INFO @ Mon, 03 Jun 2019 15:15:46: end of X-cor INFO @ Mon, 03 Jun 2019 15:15:46: #2 finished! INFO @ Mon, 03 Jun 2019 15:15:46: #2 predicted fragment length is 163 bps INFO @ Mon, 03 Jun 2019 15:15:46: #2 alternative fragment length(s) may be 4,163 bps INFO @ Mon, 03 Jun 2019 15:15:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.20_model.r INFO @ Mon, 03 Jun 2019 15:15:46: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:15:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:15:48: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:15:48: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:15:48: #1 total tags in treatment: 18587564 INFO @ Mon, 03 Jun 2019 15:15:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:15:48: #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 15:15:48: #1 tags after filtering in treatment: 16840209 INFO @ Mon, 03 Jun 2019 15:15:48: #1 Redundant rate of treatment: 0.09 INFO @ Mon, 03 Jun 2019 15:15:48: #1 finished! INFO @ Mon, 03 Jun 2019 15:15:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:15:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:15:50: #2 number of paired peaks: 1317 INFO @ Mon, 03 Jun 2019 15:15:50: start model_add_line... INFO @ Mon, 03 Jun 2019 15:15:50: start X-correlation... INFO @ Mon, 03 Jun 2019 15:15:50: end of X-cor INFO @ Mon, 03 Jun 2019 15:15:50: #2 finished! INFO @ Mon, 03 Jun 2019 15:15:50: #2 predicted fragment length is 163 bps INFO @ Mon, 03 Jun 2019 15:15:50: #2 alternative fragment length(s) may be 4,163 bps INFO @ Mon, 03 Jun 2019 15:15:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.10_model.r INFO @ Mon, 03 Jun 2019 15:15:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:15:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:15:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:16:21: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:16:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:16:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.05_summits.bed INFO @ Mon, 03 Jun 2019 15:16:21: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3022 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:16:35: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:16:39: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:16:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:16:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:16:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.20_summits.bed INFO @ Mon, 03 Jun 2019 15:16:58: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1053 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:17:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:17:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:17:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393662/SRX3393662.10_summits.bed INFO @ Mon, 03 Jun 2019 15:17:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1910 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。