Job ID = 1295420 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,497,273 reads read : 4,994,546 reads written : 4,994,546 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: 00:06:33 2497273 reads; of these: 2497273 (100.00%) were paired; of these: 210252 (8.42%) aligned concordantly 0 times 1532955 (61.39%) aligned concordantly exactly 1 time 754066 (30.20%) aligned concordantly >1 times ---- 210252 pairs aligned concordantly 0 times; of these: 2024 (0.96%) aligned discordantly 1 time ---- 208228 pairs aligned 0 times concordantly or discordantly; of these: 416456 mates make up the pairs; of these: 309351 (74.28%) aligned 0 times 61506 (14.77%) aligned exactly 1 time 45599 (10.95%) aligned >1 times 93.81% overall alignment rate Time searching: 00:06:33 Overall time: 00:06:33 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_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] 28449 / 2287811 = 0.0124 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 13:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.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 13:45:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:45:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.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 13:45:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:45:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:45:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.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 13:45:08: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:45:08: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:45:16: 1000000 INFO @ Mon, 03 Jun 2019 13:45:17: 1000000 INFO @ Mon, 03 Jun 2019 13:45:17: 1000000 INFO @ Mon, 03 Jun 2019 13:45:24: 2000000 INFO @ Mon, 03 Jun 2019 13:45:25: 2000000 INFO @ Mon, 03 Jun 2019 13:45:25: 2000000 INFO @ Mon, 03 Jun 2019 13:45:31: 3000000 INFO @ Mon, 03 Jun 2019 13:45:32: 3000000 INFO @ Mon, 03 Jun 2019 13:45:34: 3000000 INFO @ Mon, 03 Jun 2019 13:45:38: 4000000 INFO @ Mon, 03 Jun 2019 13:45:40: 4000000 INFO @ Mon, 03 Jun 2019 13:45:42: 4000000 INFO @ Mon, 03 Jun 2019 13:45:43: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 13:45:43: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 13:45:43: #1 total tags in treatment: 2258587 INFO @ Mon, 03 Jun 2019 13:45:43: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:45:43: #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 13:45:43: #1 tags after filtering in treatment: 2191647 INFO @ Mon, 03 Jun 2019 13:45:43: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 13:45:43: #1 finished! INFO @ Mon, 03 Jun 2019 13:45:43: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:45:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:45:43: #2 number of paired peaks: 1384 INFO @ Mon, 03 Jun 2019 13:45:43: start model_add_line... INFO @ Mon, 03 Jun 2019 13:45:43: start X-correlation... INFO @ Mon, 03 Jun 2019 13:45:43: end of X-cor INFO @ Mon, 03 Jun 2019 13:45:43: #2 finished! INFO @ Mon, 03 Jun 2019 13:45:43: #2 predicted fragment length is 153 bps INFO @ Mon, 03 Jun 2019 13:45:43: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 03 Jun 2019 13:45:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.10_model.r INFO @ Mon, 03 Jun 2019 13:45:43: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:45:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:45:45: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 13:45:45: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 13:45:45: #1 total tags in treatment: 2258587 INFO @ Mon, 03 Jun 2019 13:45:45: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:45:45: #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 13:45:45: #1 tags after filtering in treatment: 2191647 INFO @ Mon, 03 Jun 2019 13:45:45: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 13:45:45: #1 finished! INFO @ Mon, 03 Jun 2019 13:45:45: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:45:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:45:45: #2 number of paired peaks: 1384 INFO @ Mon, 03 Jun 2019 13:45:45: start model_add_line... INFO @ Mon, 03 Jun 2019 13:45:45: start X-correlation... INFO @ Mon, 03 Jun 2019 13:45:45: end of X-cor INFO @ Mon, 03 Jun 2019 13:45:45: #2 finished! INFO @ Mon, 03 Jun 2019 13:45:45: #2 predicted fragment length is 153 bps INFO @ Mon, 03 Jun 2019 13:45:45: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 03 Jun 2019 13:45:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.20_model.r INFO @ Mon, 03 Jun 2019 13:45:45: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:45:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:45:47: #1 tag size is determined as 42 bps INFO @ Mon, 03 Jun 2019 13:45:47: #1 tag size = 42 INFO @ Mon, 03 Jun 2019 13:45:47: #1 total tags in treatment: 2258587 INFO @ Mon, 03 Jun 2019 13:45:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:45:47: #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 13:45:47: #1 tags after filtering in treatment: 2191647 INFO @ Mon, 03 Jun 2019 13:45:47: #1 Redundant rate of treatment: 0.03 INFO @ Mon, 03 Jun 2019 13:45:47: #1 finished! INFO @ Mon, 03 Jun 2019 13:45:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:45:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:45:47: #2 number of paired peaks: 1384 INFO @ Mon, 03 Jun 2019 13:45:47: start model_add_line... INFO @ Mon, 03 Jun 2019 13:45:47: start X-correlation... INFO @ Mon, 03 Jun 2019 13:45:47: end of X-cor INFO @ Mon, 03 Jun 2019 13:45:47: #2 finished! INFO @ Mon, 03 Jun 2019 13:45:47: #2 predicted fragment length is 153 bps INFO @ Mon, 03 Jun 2019 13:45:47: #2 alternative fragment length(s) may be 153 bps INFO @ Mon, 03 Jun 2019 13:45:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.05_model.r INFO @ Mon, 03 Jun 2019 13:45:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:45:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:45:50: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:45:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:45:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:45:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:45:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.10_summits.bed INFO @ Mon, 03 Jun 2019 13:45:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (540 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:45:55: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:45:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:45:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:45:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.20_summits.bed INFO @ Mon, 03 Jun 2019 13:45:56: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:45:58: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:45:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:45:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3393640/SRX3393640.05_summits.bed INFO @ Mon, 03 Jun 2019 13:45:58: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1115 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。