Job ID = 1295847 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 10,543,043 reads read : 21,086,086 reads written : 21,086,086 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: 00:00:01 Multiseed full-index search: 00:25:09 10543043 reads; of these: 10543043 (100.00%) were paired; of these: 1120848 (10.63%) aligned concordantly 0 times 7064946 (67.01%) aligned concordantly exactly 1 time 2357249 (22.36%) aligned concordantly >1 times ---- 1120848 pairs aligned concordantly 0 times; of these: 392047 (34.98%) aligned discordantly 1 time ---- 728801 pairs aligned 0 times concordantly or discordantly; of these: 1457602 mates make up the pairs; of these: 750642 (51.50%) aligned 0 times 351117 (24.09%) aligned exactly 1 time 355843 (24.41%) aligned >1 times 96.44% overall alignment rate Time searching: 00:25:10 Overall time: 00:25:10 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 12 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] 1151480 / 9802763 = 0.1175 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 16:21:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.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 16:21:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:21:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:21:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.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 16:21:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:21:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:21:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.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 16:21:17: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:21:17: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:21:24: 1000000 INFO @ Mon, 03 Jun 2019 16:21:24: 1000000 INFO @ Mon, 03 Jun 2019 16:21:25: 1000000 INFO @ Mon, 03 Jun 2019 16:21:32: 2000000 INFO @ Mon, 03 Jun 2019 16:21:32: 2000000 INFO @ Mon, 03 Jun 2019 16:21:32: 2000000 INFO @ Mon, 03 Jun 2019 16:21:39: 3000000 INFO @ Mon, 03 Jun 2019 16:21:40: 3000000 INFO @ Mon, 03 Jun 2019 16:21:40: 3000000 INFO @ Mon, 03 Jun 2019 16:21:46: 4000000 INFO @ Mon, 03 Jun 2019 16:21:47: 4000000 INFO @ Mon, 03 Jun 2019 16:21:48: 4000000 INFO @ Mon, 03 Jun 2019 16:21:52: 5000000 INFO @ Mon, 03 Jun 2019 16:21:54: 5000000 INFO @ Mon, 03 Jun 2019 16:21:55: 5000000 INFO @ Mon, 03 Jun 2019 16:21:59: 6000000 INFO @ Mon, 03 Jun 2019 16:22:02: 6000000 INFO @ Mon, 03 Jun 2019 16:22:02: 6000000 INFO @ Mon, 03 Jun 2019 16:22:06: 7000000 INFO @ Mon, 03 Jun 2019 16:22:09: 7000000 INFO @ Mon, 03 Jun 2019 16:22:09: 7000000 INFO @ Mon, 03 Jun 2019 16:22:13: 8000000 INFO @ Mon, 03 Jun 2019 16:22:17: 8000000 INFO @ Mon, 03 Jun 2019 16:22:17: 8000000 INFO @ Mon, 03 Jun 2019 16:22:19: 9000000 INFO @ Mon, 03 Jun 2019 16:22:24: 9000000 INFO @ Mon, 03 Jun 2019 16:22:24: 9000000 INFO @ Mon, 03 Jun 2019 16:22:26: 10000000 INFO @ Mon, 03 Jun 2019 16:22:31: 10000000 INFO @ Mon, 03 Jun 2019 16:22:32: 10000000 INFO @ Mon, 03 Jun 2019 16:22:33: 11000000 INFO @ Mon, 03 Jun 2019 16:22:39: 11000000 INFO @ Mon, 03 Jun 2019 16:22:39: 11000000 INFO @ Mon, 03 Jun 2019 16:22:40: 12000000 INFO @ Mon, 03 Jun 2019 16:22:46: 12000000 INFO @ Mon, 03 Jun 2019 16:22:46: 12000000 INFO @ Mon, 03 Jun 2019 16:22:46: 13000000 INFO @ Mon, 03 Jun 2019 16:22:53: 13000000 INFO @ Mon, 03 Jun 2019 16:22:53: 14000000 INFO @ Mon, 03 Jun 2019 16:22:53: 13000000 INFO @ Mon, 03 Jun 2019 16:22:59: 14000000 INFO @ Mon, 03 Jun 2019 16:23:00: 15000000 INFO @ Mon, 03 Jun 2019 16:23:01: 14000000 INFO @ Mon, 03 Jun 2019 16:23:06: 16000000 INFO @ Mon, 03 Jun 2019 16:23:07: 15000000 INFO @ Mon, 03 Jun 2019 16:23:08: 15000000 INFO @ Mon, 03 Jun 2019 16:23:13: 17000000 INFO @ Mon, 03 Jun 2019 16:23:14: 16000000 INFO @ Mon, 03 Jun 2019 16:23:15: 16000000 INFO @ Mon, 03 Jun 2019 16:23:20: 18000000 INFO @ Mon, 03 Jun 2019 16:23:20: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:23:20: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:23:20: #1 total tags in treatment: 8293039 INFO @ Mon, 03 Jun 2019 16:23:20: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:23:20: #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 16:23:20: #1 tags after filtering in treatment: 7170067 INFO @ Mon, 03 Jun 2019 16:23:20: #1 Redundant rate of treatment: 0.14 INFO @ Mon, 03 Jun 2019 16:23:20: #1 finished! INFO @ Mon, 03 Jun 2019 16:23:20: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:23:21: #2 number of paired peaks: 4759 INFO @ Mon, 03 Jun 2019 16:23:21: start model_add_line... INFO @ Mon, 03 Jun 2019 16:23:21: start X-correlation... INFO @ Mon, 03 Jun 2019 16:23:21: end of X-cor INFO @ Mon, 03 Jun 2019 16:23:21: #2 finished! INFO @ Mon, 03 Jun 2019 16:23:21: #2 predicted fragment length is 174 bps INFO @ Mon, 03 Jun 2019 16:23:21: #2 alternative fragment length(s) may be 174 bps INFO @ Mon, 03 Jun 2019 16:23:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.20_model.r INFO @ Mon, 03 Jun 2019 16:23:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:23:22: 17000000 INFO @ Mon, 03 Jun 2019 16:23:22: 17000000 INFO @ Mon, 03 Jun 2019 16:23:28: 18000000 INFO @ Mon, 03 Jun 2019 16:23:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:23:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:23:29: #1 total tags in treatment: 8293039 INFO @ Mon, 03 Jun 2019 16:23:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:23:29: #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 16:23:29: #1 tags after filtering in treatment: 7170067 INFO @ Mon, 03 Jun 2019 16:23:29: #1 Redundant rate of treatment: 0.14 INFO @ Mon, 03 Jun 2019 16:23:29: #1 finished! INFO @ Mon, 03 Jun 2019 16:23:29: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:23:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:23:29: 18000000 INFO @ Mon, 03 Jun 2019 16:23:29: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 16:23:29: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 16:23:29: #1 total tags in treatment: 8293039 INFO @ Mon, 03 Jun 2019 16:23:29: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:23:29: #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 16:23:30: #1 tags after filtering in treatment: 7170067 INFO @ Mon, 03 Jun 2019 16:23:30: #1 Redundant rate of treatment: 0.14 INFO @ Mon, 03 Jun 2019 16:23:30: #1 finished! INFO @ Mon, 03 Jun 2019 16:23:30: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:23:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:23:30: #2 number of paired peaks: 4759 INFO @ Mon, 03 Jun 2019 16:23:30: start model_add_line... INFO @ Mon, 03 Jun 2019 16:23:30: start X-correlation... INFO @ Mon, 03 Jun 2019 16:23:30: end of X-cor INFO @ Mon, 03 Jun 2019 16:23:30: #2 finished! INFO @ Mon, 03 Jun 2019 16:23:30: #2 predicted fragment length is 174 bps INFO @ Mon, 03 Jun 2019 16:23:30: #2 alternative fragment length(s) may be 174 bps INFO @ Mon, 03 Jun 2019 16:23:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.05_model.r INFO @ Mon, 03 Jun 2019 16:23:30: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:23:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:23:31: #2 number of paired peaks: 4759 INFO @ Mon, 03 Jun 2019 16:23:31: start model_add_line... INFO @ Mon, 03 Jun 2019 16:23:31: start X-correlation... INFO @ Mon, 03 Jun 2019 16:23:31: end of X-cor INFO @ Mon, 03 Jun 2019 16:23:31: #2 finished! INFO @ Mon, 03 Jun 2019 16:23:31: #2 predicted fragment length is 174 bps INFO @ Mon, 03 Jun 2019 16:23:31: #2 alternative fragment length(s) may be 174 bps INFO @ Mon, 03 Jun 2019 16:23:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.10_model.r INFO @ Mon, 03 Jun 2019 16:23:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:23:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:23:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:23:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:23:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:23:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:23:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:23:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.20_summits.bed INFO @ Mon, 03 Jun 2019 16:23:58: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3834 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.05_summits.bed INFO @ Mon, 03 Jun 2019 16:24:07: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (7524 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:24:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:24:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:24:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4577938/SRX4577938.10_summits.bed INFO @ Mon, 03 Jun 2019 16:24:08: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5774 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。