Job ID = 1295450 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 29,311,857 reads read : 58,623,714 reads written : 58,623,714 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: 01:08:33 29311857 reads; of these: 29311857 (100.00%) were paired; of these: 4419635 (15.08%) aligned concordantly 0 times 18513753 (63.16%) aligned concordantly exactly 1 time 6378469 (21.76%) aligned concordantly >1 times ---- 4419635 pairs aligned concordantly 0 times; of these: 181650 (4.11%) aligned discordantly 1 time ---- 4237985 pairs aligned 0 times concordantly or discordantly; of these: 8475970 mates make up the pairs; of these: 6724825 (79.34%) aligned 0 times 800999 (9.45%) aligned exactly 1 time 950146 (11.21%) aligned >1 times 88.53% overall alignment rate Time searching: 01:08:33 Overall time: 01:08:33 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] 2429895 / 25041374 = 0.0970 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 15:23:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.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 15:23:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:23:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:23:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.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 15:23:27: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:23:27: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:23:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.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 15:23:28: #1 read tag files... INFO @ Mon, 03 Jun 2019 15:23:28: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 15:23:36: 1000000 INFO @ Mon, 03 Jun 2019 15:23:36: 1000000 INFO @ Mon, 03 Jun 2019 15:23:37: 1000000 INFO @ Mon, 03 Jun 2019 15:23:44: 2000000 INFO @ Mon, 03 Jun 2019 15:23:45: 2000000 INFO @ Mon, 03 Jun 2019 15:23:46: 2000000 INFO @ Mon, 03 Jun 2019 15:23:53: 3000000 INFO @ Mon, 03 Jun 2019 15:23:54: 3000000 INFO @ Mon, 03 Jun 2019 15:23:56: 3000000 INFO @ Mon, 03 Jun 2019 15:24:01: 4000000 INFO @ Mon, 03 Jun 2019 15:24:02: 4000000 INFO @ Mon, 03 Jun 2019 15:24:05: 4000000 INFO @ Mon, 03 Jun 2019 15:24:10: 5000000 INFO @ Mon, 03 Jun 2019 15:24:11: 5000000 INFO @ Mon, 03 Jun 2019 15:24:15: 5000000 INFO @ Mon, 03 Jun 2019 15:24:18: 6000000 INFO @ Mon, 03 Jun 2019 15:24:19: 6000000 INFO @ Mon, 03 Jun 2019 15:24:25: 6000000 INFO @ Mon, 03 Jun 2019 15:24:26: 7000000 INFO @ Mon, 03 Jun 2019 15:24:28: 7000000 INFO @ Mon, 03 Jun 2019 15:24:34: 7000000 INFO @ Mon, 03 Jun 2019 15:24:35: 8000000 INFO @ Mon, 03 Jun 2019 15:24:36: 8000000 INFO @ Mon, 03 Jun 2019 15:24:43: 9000000 INFO @ Mon, 03 Jun 2019 15:24:43: 8000000 INFO @ Mon, 03 Jun 2019 15:24:45: 9000000 INFO @ Mon, 03 Jun 2019 15:24:52: 10000000 INFO @ Mon, 03 Jun 2019 15:24:53: 9000000 INFO @ Mon, 03 Jun 2019 15:24:53: 10000000 INFO @ Mon, 03 Jun 2019 15:25:00: 11000000 INFO @ Mon, 03 Jun 2019 15:25:01: 11000000 INFO @ Mon, 03 Jun 2019 15:25:02: 10000000 INFO @ Mon, 03 Jun 2019 15:25:08: 12000000 INFO @ Mon, 03 Jun 2019 15:25:10: 12000000 INFO @ Mon, 03 Jun 2019 15:25:11: 11000000 INFO @ Mon, 03 Jun 2019 15:25:17: 13000000 INFO @ Mon, 03 Jun 2019 15:25:18: 13000000 INFO @ Mon, 03 Jun 2019 15:25:20: 12000000 INFO @ Mon, 03 Jun 2019 15:25:25: 14000000 INFO @ Mon, 03 Jun 2019 15:25:27: 14000000 INFO @ Mon, 03 Jun 2019 15:25:30: 13000000 INFO @ Mon, 03 Jun 2019 15:25:34: 15000000 INFO @ Mon, 03 Jun 2019 15:25:35: 15000000 INFO @ Mon, 03 Jun 2019 15:25:39: 14000000 INFO @ Mon, 03 Jun 2019 15:25:42: 16000000 INFO @ Mon, 03 Jun 2019 15:25:44: 16000000 INFO @ Mon, 03 Jun 2019 15:25:49: 15000000 INFO @ Mon, 03 Jun 2019 15:25:51: 17000000 INFO @ Mon, 03 Jun 2019 15:25:52: 17000000 INFO @ Mon, 03 Jun 2019 15:25:58: 16000000 INFO @ Mon, 03 Jun 2019 15:25:59: 18000000 INFO @ Mon, 03 Jun 2019 15:26:01: 18000000 INFO @ Mon, 03 Jun 2019 15:26:07: 19000000 INFO @ Mon, 03 Jun 2019 15:26:08: 17000000 INFO @ Mon, 03 Jun 2019 15:26:09: 19000000 INFO @ Mon, 03 Jun 2019 15:26:15: 20000000 INFO @ Mon, 03 Jun 2019 15:26:17: 18000000 INFO @ Mon, 03 Jun 2019 15:26:17: 20000000 INFO @ Mon, 03 Jun 2019 15:26:24: 21000000 INFO @ Mon, 03 Jun 2019 15:26:26: 21000000 INFO @ Mon, 03 Jun 2019 15:26:27: 19000000 INFO @ Mon, 03 Jun 2019 15:26:32: 22000000 INFO @ Mon, 03 Jun 2019 15:26:34: 22000000 INFO @ Mon, 03 Jun 2019 15:26:36: 20000000 INFO @ Mon, 03 Jun 2019 15:26:40: 23000000 INFO @ Mon, 03 Jun 2019 15:26:42: 23000000 INFO @ Mon, 03 Jun 2019 15:26:45: 21000000 INFO @ Mon, 03 Jun 2019 15:26:47: 24000000 INFO @ Mon, 03 Jun 2019 15:26:50: 24000000 INFO @ Mon, 03 Jun 2019 15:26:54: 22000000 INFO @ Mon, 03 Jun 2019 15:26:56: 25000000 INFO @ Mon, 03 Jun 2019 15:26:59: 25000000 INFO @ Mon, 03 Jun 2019 15:27:03: 23000000 INFO @ Mon, 03 Jun 2019 15:27:04: 26000000 INFO @ Mon, 03 Jun 2019 15:27:07: 26000000 INFO @ Mon, 03 Jun 2019 15:27:12: 27000000 INFO @ Mon, 03 Jun 2019 15:27:12: 24000000 INFO @ Mon, 03 Jun 2019 15:27:16: 27000000 INFO @ Mon, 03 Jun 2019 15:27:20: 28000000 INFO @ Mon, 03 Jun 2019 15:27:21: 25000000 INFO @ Mon, 03 Jun 2019 15:27:24: 28000000 INFO @ Mon, 03 Jun 2019 15:27:28: 29000000 INFO @ Mon, 03 Jun 2019 15:27:31: 26000000 INFO @ Mon, 03 Jun 2019 15:27:32: 29000000 INFO @ Mon, 03 Jun 2019 15:27:36: 30000000 INFO @ Mon, 03 Jun 2019 15:27:40: 27000000 INFO @ Mon, 03 Jun 2019 15:27:41: 30000000 INFO @ Mon, 03 Jun 2019 15:27:44: 31000000 INFO @ Mon, 03 Jun 2019 15:27:49: 28000000 INFO @ Mon, 03 Jun 2019 15:27:49: 31000000 INFO @ Mon, 03 Jun 2019 15:27:53: 32000000 INFO @ Mon, 03 Jun 2019 15:27:58: 32000000 INFO @ Mon, 03 Jun 2019 15:27:58: 29000000 INFO @ Mon, 03 Jun 2019 15:28:01: 33000000 INFO @ Mon, 03 Jun 2019 15:28:06: 33000000 INFO @ Mon, 03 Jun 2019 15:28:07: 30000000 INFO @ Mon, 03 Jun 2019 15:28:09: 34000000 INFO @ Mon, 03 Jun 2019 15:28:15: 34000000 INFO @ Mon, 03 Jun 2019 15:28:17: 31000000 INFO @ Mon, 03 Jun 2019 15:28:17: 35000000 INFO @ Mon, 03 Jun 2019 15:28:23: 35000000 INFO @ Mon, 03 Jun 2019 15:28:26: 36000000 INFO @ Mon, 03 Jun 2019 15:28:26: 32000000 INFO @ Mon, 03 Jun 2019 15:28:32: 36000000 INFO @ Mon, 03 Jun 2019 15:28:34: 37000000 INFO @ Mon, 03 Jun 2019 15:28:34: 33000000 INFO @ Mon, 03 Jun 2019 15:28:42: 37000000 INFO @ Mon, 03 Jun 2019 15:28:42: 38000000 INFO @ Mon, 03 Jun 2019 15:28:43: 34000000 INFO @ Mon, 03 Jun 2019 15:28:50: 39000000 INFO @ Mon, 03 Jun 2019 15:28:51: 38000000 INFO @ Mon, 03 Jun 2019 15:28:52: 35000000 INFO @ Mon, 03 Jun 2019 15:28:59: 40000000 INFO @ Mon, 03 Jun 2019 15:29:00: 36000000 INFO @ Mon, 03 Jun 2019 15:29:01: 39000000 INFO @ Mon, 03 Jun 2019 15:29:07: 41000000 INFO @ Mon, 03 Jun 2019 15:29:09: 37000000 INFO @ Mon, 03 Jun 2019 15:29:11: 40000000 INFO @ Mon, 03 Jun 2019 15:29:15: 42000000 INFO @ Mon, 03 Jun 2019 15:29:17: 38000000 INFO @ Mon, 03 Jun 2019 15:29:20: 41000000 INFO @ Mon, 03 Jun 2019 15:29:23: 43000000 INFO @ Mon, 03 Jun 2019 15:29:26: 39000000 INFO @ Mon, 03 Jun 2019 15:29:29: 42000000 INFO @ Mon, 03 Jun 2019 15:29:32: 44000000 INFO @ Mon, 03 Jun 2019 15:29:34: 40000000 INFO @ Mon, 03 Jun 2019 15:29:39: 43000000 INFO @ Mon, 03 Jun 2019 15:29:40: 45000000 INFO @ Mon, 03 Jun 2019 15:29:43: 41000000 INFO @ Mon, 03 Jun 2019 15:29:48: 46000000 INFO @ Mon, 03 Jun 2019 15:29:48: 44000000 INFO @ Mon, 03 Jun 2019 15:29:52: 42000000 INFO @ Mon, 03 Jun 2019 15:29:56: 47000000 INFO @ Mon, 03 Jun 2019 15:29:56: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:29:56: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:29:56: #1 total tags in treatment: 22467572 INFO @ Mon, 03 Jun 2019 15:29:56: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:29:56: #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 15:29:57: #1 tags after filtering in treatment: 12446560 INFO @ Mon, 03 Jun 2019 15:29:57: #1 Redundant rate of treatment: 0.45 INFO @ Mon, 03 Jun 2019 15:29:57: #1 finished! INFO @ Mon, 03 Jun 2019 15:29:57: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:29:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:29:58: 45000000 INFO @ Mon, 03 Jun 2019 15:29:59: #2 number of paired peaks: 8312 INFO @ Mon, 03 Jun 2019 15:29:59: start model_add_line... INFO @ Mon, 03 Jun 2019 15:29:59: start X-correlation... INFO @ Mon, 03 Jun 2019 15:29:59: end of X-cor INFO @ Mon, 03 Jun 2019 15:29:59: #2 finished! INFO @ Mon, 03 Jun 2019 15:29:59: #2 predicted fragment length is 205 bps INFO @ Mon, 03 Jun 2019 15:29:59: #2 alternative fragment length(s) may be 205 bps INFO @ Mon, 03 Jun 2019 15:29:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.05_model.r INFO @ Mon, 03 Jun 2019 15:29:59: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:29:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:30:00: 43000000 INFO @ Mon, 03 Jun 2019 15:30:07: 46000000 INFO @ Mon, 03 Jun 2019 15:30:08: 44000000 INFO @ Mon, 03 Jun 2019 15:30:16: 47000000 INFO @ Mon, 03 Jun 2019 15:30:16: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:30:16: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:30:16: #1 total tags in treatment: 22467572 INFO @ Mon, 03 Jun 2019 15:30:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:30:16: #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 15:30:17: 45000000 INFO @ Mon, 03 Jun 2019 15:30:17: #1 tags after filtering in treatment: 12446560 INFO @ Mon, 03 Jun 2019 15:30:17: #1 Redundant rate of treatment: 0.45 INFO @ Mon, 03 Jun 2019 15:30:17: #1 finished! INFO @ Mon, 03 Jun 2019 15:30:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:30:19: #2 number of paired peaks: 8312 INFO @ Mon, 03 Jun 2019 15:30:19: start model_add_line... INFO @ Mon, 03 Jun 2019 15:30:19: start X-correlation... INFO @ Mon, 03 Jun 2019 15:30:19: end of X-cor INFO @ Mon, 03 Jun 2019 15:30:19: #2 finished! INFO @ Mon, 03 Jun 2019 15:30:19: #2 predicted fragment length is 205 bps INFO @ Mon, 03 Jun 2019 15:30:19: #2 alternative fragment length(s) may be 205 bps INFO @ Mon, 03 Jun 2019 15:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.20_model.r INFO @ Mon, 03 Jun 2019 15:30:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:30:24: 46000000 INFO @ Mon, 03 Jun 2019 15:30:32: 47000000 INFO @ Mon, 03 Jun 2019 15:30:33: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 15:30:33: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 15:30:33: #1 total tags in treatment: 22467572 INFO @ Mon, 03 Jun 2019 15:30:33: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 15:30:33: #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 15:30:33: #1 tags after filtering in treatment: 12446560 INFO @ Mon, 03 Jun 2019 15:30:33: #1 Redundant rate of treatment: 0.45 INFO @ Mon, 03 Jun 2019 15:30:33: #1 finished! INFO @ Mon, 03 Jun 2019 15:30:33: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 15:30:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 15:30:35: #2 number of paired peaks: 8312 INFO @ Mon, 03 Jun 2019 15:30:35: start model_add_line... INFO @ Mon, 03 Jun 2019 15:30:36: start X-correlation... INFO @ Mon, 03 Jun 2019 15:30:36: end of X-cor INFO @ Mon, 03 Jun 2019 15:30:36: #2 finished! INFO @ Mon, 03 Jun 2019 15:30:36: #2 predicted fragment length is 205 bps INFO @ Mon, 03 Jun 2019 15:30:36: #2 alternative fragment length(s) may be 205 bps INFO @ Mon, 03 Jun 2019 15:30:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.10_model.r INFO @ Mon, 03 Jun 2019 15:30:36: #3 Call peaks... INFO @ Mon, 03 Jun 2019 15:30:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 15:30:48: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 15:31:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.05_peaks.xls INFO @ Mon, 03 Jun 2019 15:31:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:31:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.05_summits.bed INFO @ Mon, 03 Jun 2019 15:31:07: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (10554 records, 4 fields): 27 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:31:12: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:31:25: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 15:31:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.20_peaks.xls INFO @ Mon, 03 Jun 2019 15:31:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:31:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.20_summits.bed INFO @ Mon, 03 Jun 2019 15:31:32: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (7974 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 15:31:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.10_peaks.xls INFO @ Mon, 03 Jun 2019 15:31:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 15:31:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393660/SRX3393660.10_summits.bed INFO @ Mon, 03 Jun 2019 15:31:44: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (9363 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。