Job ID = 1294055 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 6,031,642 reads read : 12,063,284 reads written : 12,063,284 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: 00:14:15 6031642 reads; of these: 6031642 (100.00%) were paired; of these: 1343548 (22.27%) aligned concordantly 0 times 3913614 (64.88%) aligned concordantly exactly 1 time 774480 (12.84%) aligned concordantly >1 times ---- 1343548 pairs aligned concordantly 0 times; of these: 451788 (33.63%) aligned discordantly 1 time ---- 891760 pairs aligned 0 times concordantly or discordantly; of these: 1783520 mates make up the pairs; of these: 1400165 (78.51%) aligned 0 times 175925 (9.86%) aligned exactly 1 time 207430 (11.63%) aligned >1 times 88.39% overall alignment rate Time searching: 00:14:15 Overall time: 00:14:15 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] 168168 / 5134018 = 0.0328 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 04:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.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 04:52:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:52:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.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 04:52:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:52:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:52:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.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 04:52:09: #1 read tag files... INFO @ Mon, 03 Jun 2019 04:52:09: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 04:52:17: 1000000 INFO @ Mon, 03 Jun 2019 04:52:17: 1000000 INFO @ Mon, 03 Jun 2019 04:52:20: 1000000 INFO @ Mon, 03 Jun 2019 04:52:24: 2000000 INFO @ Mon, 03 Jun 2019 04:52:26: 2000000 INFO @ Mon, 03 Jun 2019 04:52:31: 2000000 INFO @ Mon, 03 Jun 2019 04:52:32: 3000000 INFO @ Mon, 03 Jun 2019 04:52:34: 3000000 INFO @ Mon, 03 Jun 2019 04:52:40: 4000000 INFO @ Mon, 03 Jun 2019 04:52:42: 3000000 INFO @ Mon, 03 Jun 2019 04:52:43: 4000000 INFO @ Mon, 03 Jun 2019 04:52:48: 5000000 INFO @ Mon, 03 Jun 2019 04:52:51: 5000000 INFO @ Mon, 03 Jun 2019 04:52:53: 4000000 INFO @ Mon, 03 Jun 2019 04:52:55: 6000000 INFO @ Mon, 03 Jun 2019 04:53:00: 6000000 INFO @ Mon, 03 Jun 2019 04:53:03: 5000000 INFO @ Mon, 03 Jun 2019 04:53:03: 7000000 INFO @ Mon, 03 Jun 2019 04:53:08: 7000000 INFO @ Mon, 03 Jun 2019 04:53:12: 8000000 INFO @ Mon, 03 Jun 2019 04:53:14: 6000000 INFO @ Mon, 03 Jun 2019 04:53:17: 8000000 INFO @ Mon, 03 Jun 2019 04:53:20: 9000000 INFO @ Mon, 03 Jun 2019 04:53:25: 7000000 INFO @ Mon, 03 Jun 2019 04:53:26: 9000000 INFO @ Mon, 03 Jun 2019 04:53:28: 10000000 INFO @ Mon, 03 Jun 2019 04:53:30: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:53:30: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:53:30: #1 total tags in treatment: 4527306 INFO @ Mon, 03 Jun 2019 04:53:30: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:53:30: #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 04:53:31: #1 tags after filtering in treatment: 4304942 INFO @ Mon, 03 Jun 2019 04:53:31: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:53:31: #1 finished! INFO @ Mon, 03 Jun 2019 04:53:31: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:53:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:53:31: #2 number of paired peaks: 3515 INFO @ Mon, 03 Jun 2019 04:53:31: start model_add_line... INFO @ Mon, 03 Jun 2019 04:53:31: start X-correlation... INFO @ Mon, 03 Jun 2019 04:53:31: end of X-cor INFO @ Mon, 03 Jun 2019 04:53:31: #2 finished! INFO @ Mon, 03 Jun 2019 04:53:31: #2 predicted fragment length is 225 bps INFO @ Mon, 03 Jun 2019 04:53:31: #2 alternative fragment length(s) may be 225 bps INFO @ Mon, 03 Jun 2019 04:53:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.05_model.r INFO @ Mon, 03 Jun 2019 04:53:31: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:53:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:53:34: 10000000 INFO @ Mon, 03 Jun 2019 04:53:36: 8000000 INFO @ Mon, 03 Jun 2019 04:53:37: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:53:37: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:53:37: #1 total tags in treatment: 4527306 INFO @ Mon, 03 Jun 2019 04:53:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:53:37: #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 04:53:37: #1 tags after filtering in treatment: 4304942 INFO @ Mon, 03 Jun 2019 04:53:37: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:53:37: #1 finished! INFO @ Mon, 03 Jun 2019 04:53:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:53:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:53:38: #2 number of paired peaks: 3515 INFO @ Mon, 03 Jun 2019 04:53:38: start model_add_line... INFO @ Mon, 03 Jun 2019 04:53:38: start X-correlation... INFO @ Mon, 03 Jun 2019 04:53:38: end of X-cor INFO @ Mon, 03 Jun 2019 04:53:38: #2 finished! INFO @ Mon, 03 Jun 2019 04:53:38: #2 predicted fragment length is 225 bps INFO @ Mon, 03 Jun 2019 04:53:38: #2 alternative fragment length(s) may be 225 bps INFO @ Mon, 03 Jun 2019 04:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.10_model.r INFO @ Mon, 03 Jun 2019 04:53:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:53:46: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:53:47: 9000000 INFO @ Mon, 03 Jun 2019 04:53:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:53:53: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.05_peaks.xls INFO @ Mon, 03 Jun 2019 04:53:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:53:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.05_summits.bed INFO @ Mon, 03 Jun 2019 04:53:53: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (5789 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:53:57: 10000000 INFO @ Mon, 03 Jun 2019 04:53:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.10_peaks.xls INFO @ Mon, 03 Jun 2019 04:53:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:53:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.10_summits.bed INFO @ Mon, 03 Jun 2019 04:53:59: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4088 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 04:54:00: #1 tag size is determined as 81 bps INFO @ Mon, 03 Jun 2019 04:54:00: #1 tag size = 81 INFO @ Mon, 03 Jun 2019 04:54:00: #1 total tags in treatment: 4527306 INFO @ Mon, 03 Jun 2019 04:54:00: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 04:54:00: #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 04:54:00: #1 tags after filtering in treatment: 4304942 INFO @ Mon, 03 Jun 2019 04:54:00: #1 Redundant rate of treatment: 0.05 INFO @ Mon, 03 Jun 2019 04:54:00: #1 finished! INFO @ Mon, 03 Jun 2019 04:54:00: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 04:54:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 04:54:01: #2 number of paired peaks: 3515 INFO @ Mon, 03 Jun 2019 04:54:01: start model_add_line... INFO @ Mon, 03 Jun 2019 04:54:01: start X-correlation... INFO @ Mon, 03 Jun 2019 04:54:01: end of X-cor INFO @ Mon, 03 Jun 2019 04:54:01: #2 finished! INFO @ Mon, 03 Jun 2019 04:54:01: #2 predicted fragment length is 225 bps INFO @ Mon, 03 Jun 2019 04:54:01: #2 alternative fragment length(s) may be 225 bps INFO @ Mon, 03 Jun 2019 04:54:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.20_model.r INFO @ Mon, 03 Jun 2019 04:54:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 04:54:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 04:54:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 04:54:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.20_peaks.xls INFO @ Mon, 03 Jun 2019 04:54:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 04:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1763416/SRX1763416.20_summits.bed INFO @ Mon, 03 Jun 2019 04:54:23: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (2475 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。