Job ID = 1294339 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 11,327,322 reads read : 22,654,644 reads written : 22,654,644 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: 00:12:31 11327322 reads; of these: 11327322 (100.00%) were paired; of these: 2501736 (22.09%) aligned concordantly 0 times 7895336 (69.70%) aligned concordantly exactly 1 time 930250 (8.21%) aligned concordantly >1 times ---- 2501736 pairs aligned concordantly 0 times; of these: 5015 (0.20%) aligned discordantly 1 time ---- 2496721 pairs aligned 0 times concordantly or discordantly; of these: 4993442 mates make up the pairs; of these: 4872196 (97.57%) aligned 0 times 93740 (1.88%) aligned exactly 1 time 27506 (0.55%) aligned >1 times 78.49% overall alignment rate Time searching: 00:12:31 Overall time: 00:12:31 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 8 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] 1177754 / 8827624 = 0.1334 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 06:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.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 06:52:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:52:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.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 06:52:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:52:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:52:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.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 06:52:10: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:52:10: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:52:18: 1000000 INFO @ Mon, 03 Jun 2019 06:52:19: 1000000 INFO @ Mon, 03 Jun 2019 06:52:20: 1000000 INFO @ Mon, 03 Jun 2019 06:52:26: 2000000 INFO @ Mon, 03 Jun 2019 06:52:29: 2000000 INFO @ Mon, 03 Jun 2019 06:52:29: 2000000 INFO @ Mon, 03 Jun 2019 06:52:34: 3000000 INFO @ Mon, 03 Jun 2019 06:52:38: 3000000 INFO @ Mon, 03 Jun 2019 06:52:39: 3000000 INFO @ Mon, 03 Jun 2019 06:52:41: 4000000 INFO @ Mon, 03 Jun 2019 06:52:47: 4000000 INFO @ Mon, 03 Jun 2019 06:52:48: 4000000 INFO @ Mon, 03 Jun 2019 06:52:49: 5000000 INFO @ Mon, 03 Jun 2019 06:52:57: 5000000 INFO @ Mon, 03 Jun 2019 06:52:57: 6000000 INFO @ Mon, 03 Jun 2019 06:52:58: 5000000 INFO @ Mon, 03 Jun 2019 06:53:05: 7000000 INFO @ Mon, 03 Jun 2019 06:53:06: 6000000 INFO @ Mon, 03 Jun 2019 06:53:08: 6000000 INFO @ Mon, 03 Jun 2019 06:53:13: 8000000 INFO @ Mon, 03 Jun 2019 06:53:15: 7000000 INFO @ Mon, 03 Jun 2019 06:53:18: 7000000 INFO @ Mon, 03 Jun 2019 06:53:20: 9000000 INFO @ Mon, 03 Jun 2019 06:53:24: 8000000 INFO @ Mon, 03 Jun 2019 06:53:27: 8000000 INFO @ Mon, 03 Jun 2019 06:53:28: 10000000 INFO @ Mon, 03 Jun 2019 06:53:33: 9000000 INFO @ Mon, 03 Jun 2019 06:53:36: 11000000 INFO @ Mon, 03 Jun 2019 06:53:36: 9000000 INFO @ Mon, 03 Jun 2019 06:53:42: 10000000 INFO @ Mon, 03 Jun 2019 06:53:44: 12000000 INFO @ Mon, 03 Jun 2019 06:53:46: 10000000 INFO @ Mon, 03 Jun 2019 06:53:51: 11000000 INFO @ Mon, 03 Jun 2019 06:53:52: 13000000 INFO @ Mon, 03 Jun 2019 06:53:55: 11000000 INFO @ Mon, 03 Jun 2019 06:53:59: 14000000 INFO @ Mon, 03 Jun 2019 06:54:00: 12000000 INFO @ Mon, 03 Jun 2019 06:54:05: 12000000 INFO @ Mon, 03 Jun 2019 06:54:08: 15000000 INFO @ Mon, 03 Jun 2019 06:54:10: 13000000 INFO @ Mon, 03 Jun 2019 06:54:11: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:54:11: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:54:11: #1 total tags in treatment: 7648043 INFO @ Mon, 03 Jun 2019 06:54:11: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:54:11: #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 06:54:11: #1 tags after filtering in treatment: 5444604 INFO @ Mon, 03 Jun 2019 06:54:11: #1 Redundant rate of treatment: 0.29 INFO @ Mon, 03 Jun 2019 06:54:11: #1 finished! INFO @ Mon, 03 Jun 2019 06:54:11: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:54:12: #2 number of paired peaks: 8009 INFO @ Mon, 03 Jun 2019 06:54:12: start model_add_line... INFO @ Mon, 03 Jun 2019 06:54:12: start X-correlation... INFO @ Mon, 03 Jun 2019 06:54:13: end of X-cor INFO @ Mon, 03 Jun 2019 06:54:13: #2 finished! INFO @ Mon, 03 Jun 2019 06:54:13: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 06:54:13: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 06:54:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.10_model.r INFO @ Mon, 03 Jun 2019 06:54:13: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:54:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:54:14: 13000000 INFO @ Mon, 03 Jun 2019 06:54:19: 14000000 INFO @ Mon, 03 Jun 2019 06:54:24: 14000000 INFO @ Mon, 03 Jun 2019 06:54:29: 15000000 INFO @ Mon, 03 Jun 2019 06:54:32: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:54:32: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:54:32: #1 total tags in treatment: 7648043 INFO @ Mon, 03 Jun 2019 06:54:32: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:54:32: #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 06:54:32: #1 tags after filtering in treatment: 5444604 INFO @ Mon, 03 Jun 2019 06:54:32: #1 Redundant rate of treatment: 0.29 INFO @ Mon, 03 Jun 2019 06:54:32: #1 finished! INFO @ Mon, 03 Jun 2019 06:54:32: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:54:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:54:33: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:54:34: #2 number of paired peaks: 8009 INFO @ Mon, 03 Jun 2019 06:54:34: start model_add_line... INFO @ Mon, 03 Jun 2019 06:54:34: start X-correlation... INFO @ Mon, 03 Jun 2019 06:54:34: end of X-cor INFO @ Mon, 03 Jun 2019 06:54:34: #2 finished! INFO @ Mon, 03 Jun 2019 06:54:34: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 06:54:34: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 06:54:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.05_model.r INFO @ Mon, 03 Jun 2019 06:54:34: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:54:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:54:34: 15000000 INFO @ Mon, 03 Jun 2019 06:54:38: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 06:54:38: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 06:54:38: #1 total tags in treatment: 7648043 INFO @ Mon, 03 Jun 2019 06:54:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:54:38: #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 06:54:38: #1 tags after filtering in treatment: 5444604 INFO @ Mon, 03 Jun 2019 06:54:38: #1 Redundant rate of treatment: 0.29 INFO @ Mon, 03 Jun 2019 06:54:38: #1 finished! INFO @ Mon, 03 Jun 2019 06:54:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:54:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:54:39: #2 number of paired peaks: 8009 INFO @ Mon, 03 Jun 2019 06:54:39: start model_add_line... INFO @ Mon, 03 Jun 2019 06:54:39: start X-correlation... INFO @ Mon, 03 Jun 2019 06:54:39: end of X-cor INFO @ Mon, 03 Jun 2019 06:54:39: #2 finished! INFO @ Mon, 03 Jun 2019 06:54:39: #2 predicted fragment length is 136 bps INFO @ Mon, 03 Jun 2019 06:54:39: #2 alternative fragment length(s) may be 136 bps INFO @ Mon, 03 Jun 2019 06:54:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.20_model.r INFO @ Mon, 03 Jun 2019 06:54:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:54:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:54:42: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:54:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:54:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.10_summits.bed INFO @ Mon, 03 Jun 2019 06:54:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7817 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:54:53: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:54:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:55:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:55:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:55:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.05_summits.bed INFO @ Mon, 03 Jun 2019 06:55:02: Done! pass1 - making usageList (14 chroms): 6 millis pass2 - checking and writing primary data (11284 records, 4 fields): 23 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 06:55:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:55:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:55:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX252229/SRX252229.20_summits.bed INFO @ Mon, 03 Jun 2019 06:55:08: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (5030 records, 4 fields): 12 millis CompletedMACS2peakCalling BigWig に変換しました。