Job ID = 4303093 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 16,485,911 reads read : 32,971,822 reads written : 32,971,822 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1151104.sra.cache’: 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:39:57 16485911 reads; of these: 16485911 (100.00%) were paired; of these: 825863 (5.01%) aligned concordantly 0 times 11665674 (70.76%) aligned concordantly exactly 1 time 3994374 (24.23%) aligned concordantly >1 times ---- 825863 pairs aligned concordantly 0 times; of these: 15213 (1.84%) aligned discordantly 1 time ---- 810650 pairs aligned 0 times concordantly or discordantly; of these: 1621300 mates make up the pairs; of these: 1143812 (70.55%) aligned 0 times 342168 (21.10%) aligned exactly 1 time 135320 (8.35%) aligned >1 times 96.53% overall alignment rate Time searching: 00:39:58 Overall time: 00:39:58 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 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] 9394733 / 15661491 = 0.5999 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:30:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.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 @ Thu, 12 Dec 2019 01:30:58: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:30:58: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:31:05: 1000000 INFO @ Thu, 12 Dec 2019 01:31:12: 2000000 INFO @ Thu, 12 Dec 2019 01:31:19: 3000000 INFO @ Thu, 12 Dec 2019 01:31:26: 4000000 INFO @ Thu, 12 Dec 2019 01:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.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 @ Thu, 12 Dec 2019 01:31:28: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:31:28: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:31:33: 5000000 INFO @ Thu, 12 Dec 2019 01:31:36: 1000000 INFO @ Thu, 12 Dec 2019 01:31:39: 6000000 INFO @ Thu, 12 Dec 2019 01:31:44: 2000000 INFO @ Thu, 12 Dec 2019 01:31:46: 7000000 INFO @ Thu, 12 Dec 2019 01:31:51: 3000000 INFO @ Thu, 12 Dec 2019 01:31:53: 8000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:31:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.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 @ Thu, 12 Dec 2019 01:31:58: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:31:58: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:31:59: 4000000 INFO @ Thu, 12 Dec 2019 01:32:00: 9000000 INFO @ Thu, 12 Dec 2019 01:32:06: 10000000 INFO @ Thu, 12 Dec 2019 01:32:07: 5000000 INFO @ Thu, 12 Dec 2019 01:32:07: 1000000 INFO @ Thu, 12 Dec 2019 01:32:13: 11000000 INFO @ Thu, 12 Dec 2019 01:32:14: 6000000 INFO @ Thu, 12 Dec 2019 01:32:16: 2000000 INFO @ Thu, 12 Dec 2019 01:32:20: 12000000 INFO @ Thu, 12 Dec 2019 01:32:22: 7000000 INFO @ Thu, 12 Dec 2019 01:32:25: 3000000 INFO @ Thu, 12 Dec 2019 01:32:28: 13000000 INFO @ Thu, 12 Dec 2019 01:32:28: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:32:28: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:32:28: #1 total tags in treatment: 6271747 INFO @ Thu, 12 Dec 2019 01:32:28: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:32:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:32:28: #1 tags after filtering in treatment: 5774749 INFO @ Thu, 12 Dec 2019 01:32:28: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 12 Dec 2019 01:32:28: #1 finished! INFO @ Thu, 12 Dec 2019 01:32:28: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:32:28: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:32:29: #2 number of paired peaks: 2282 INFO @ Thu, 12 Dec 2019 01:32:29: start model_add_line... INFO @ Thu, 12 Dec 2019 01:32:29: start X-correlation... INFO @ Thu, 12 Dec 2019 01:32:29: end of X-cor INFO @ Thu, 12 Dec 2019 01:32:29: #2 finished! INFO @ Thu, 12 Dec 2019 01:32:29: #2 predicted fragment length is 126 bps INFO @ Thu, 12 Dec 2019 01:32:29: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 12 Dec 2019 01:32:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.05_model.r INFO @ Thu, 12 Dec 2019 01:32:29: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:32:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:32:29: 8000000 INFO @ Thu, 12 Dec 2019 01:32:34: 4000000 INFO @ Thu, 12 Dec 2019 01:32:37: 9000000 INFO @ Thu, 12 Dec 2019 01:32:42: 5000000 INFO @ Thu, 12 Dec 2019 01:32:44: 10000000 INFO @ Thu, 12 Dec 2019 01:32:48: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:32:51: 6000000 INFO @ Thu, 12 Dec 2019 01:32:52: 11000000 INFO @ Thu, 12 Dec 2019 01:32:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:32:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:32:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.05_summits.bed INFO @ Thu, 12 Dec 2019 01:32:58: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4257 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:32:59: 12000000 INFO @ Thu, 12 Dec 2019 01:32:59: 7000000 INFO @ Thu, 12 Dec 2019 01:33:07: 13000000 INFO @ Thu, 12 Dec 2019 01:33:07: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:33:07: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:33:07: #1 total tags in treatment: 6271747 INFO @ Thu, 12 Dec 2019 01:33:07: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:33:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:33:07: #1 tags after filtering in treatment: 5774749 INFO @ Thu, 12 Dec 2019 01:33:07: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 12 Dec 2019 01:33:07: #1 finished! INFO @ Thu, 12 Dec 2019 01:33:07: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:33:07: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:33:08: #2 number of paired peaks: 2282 INFO @ Thu, 12 Dec 2019 01:33:08: start model_add_line... INFO @ Thu, 12 Dec 2019 01:33:08: 8000000 INFO @ Thu, 12 Dec 2019 01:33:08: start X-correlation... INFO @ Thu, 12 Dec 2019 01:33:08: end of X-cor INFO @ Thu, 12 Dec 2019 01:33:08: #2 finished! INFO @ Thu, 12 Dec 2019 01:33:08: #2 predicted fragment length is 126 bps INFO @ Thu, 12 Dec 2019 01:33:08: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 12 Dec 2019 01:33:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.10_model.r INFO @ Thu, 12 Dec 2019 01:33:08: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:33:08: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:33:16: 9000000 INFO @ Thu, 12 Dec 2019 01:33:25: 10000000 INFO @ Thu, 12 Dec 2019 01:33:27: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:33:33: 11000000 INFO @ Thu, 12 Dec 2019 01:33:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:33:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:33:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.10_summits.bed INFO @ Thu, 12 Dec 2019 01:33:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2123 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:33:42: 12000000 INFO @ Thu, 12 Dec 2019 01:33:50: 13000000 INFO @ Thu, 12 Dec 2019 01:33:51: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:33:51: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:33:51: #1 total tags in treatment: 6271747 INFO @ Thu, 12 Dec 2019 01:33:51: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:33:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:33:51: #1 tags after filtering in treatment: 5774749 INFO @ Thu, 12 Dec 2019 01:33:51: #1 Redundant rate of treatment: 0.08 INFO @ Thu, 12 Dec 2019 01:33:51: #1 finished! INFO @ Thu, 12 Dec 2019 01:33:51: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:33:51: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:33:51: #2 number of paired peaks: 2282 INFO @ Thu, 12 Dec 2019 01:33:51: start model_add_line... INFO @ Thu, 12 Dec 2019 01:33:52: start X-correlation... INFO @ Thu, 12 Dec 2019 01:33:52: end of X-cor INFO @ Thu, 12 Dec 2019 01:33:52: #2 finished! INFO @ Thu, 12 Dec 2019 01:33:52: #2 predicted fragment length is 126 bps INFO @ Thu, 12 Dec 2019 01:33:52: #2 alternative fragment length(s) may be 126 bps INFO @ Thu, 12 Dec 2019 01:33:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.20_model.r INFO @ Thu, 12 Dec 2019 01:33:52: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:33:52: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:34:11: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:34:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:34:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:34:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX456156/SRX456156.20_summits.bed INFO @ Thu, 12 Dec 2019 01:34:20: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (999 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。