Job ID = 4303110 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,046,410 reads read : 13,046,410 reads written : 13,046,410 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1164525.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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:01 13046410 reads; of these: 13046410 (100.00%) were unpaired; of these: 2244566 (17.20%) aligned 0 times 8480755 (65.00%) aligned exactly 1 time 2321089 (17.79%) aligned >1 times 82.80% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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_rmdupse_core] 1010005 / 10801844 = 0.0935 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:49:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.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 00:49:21: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:49:21: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:49:25: 1000000 INFO @ Thu, 12 Dec 2019 00:49:29: 2000000 INFO @ Thu, 12 Dec 2019 00:49:33: 3000000 INFO @ Thu, 12 Dec 2019 00:49:38: 4000000 INFO @ Thu, 12 Dec 2019 00:49:42: 5000000 INFO @ Thu, 12 Dec 2019 00:49:46: 6000000 INFO @ Thu, 12 Dec 2019 00:49:50: 7000000 INFO @ Thu, 12 Dec 2019 00:49:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.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 00:49:51: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:49:51: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:49:54: 8000000 INFO @ Thu, 12 Dec 2019 00:49:55: 1000000 INFO @ Thu, 12 Dec 2019 00:49:58: 9000000 INFO @ Thu, 12 Dec 2019 00:49:59: 2000000 INFO @ Thu, 12 Dec 2019 00:50:02: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:50:02: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:50:02: #1 total tags in treatment: 9791839 INFO @ Thu, 12 Dec 2019 00:50:02: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:50:02: #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 00:50:02: #1 tags after filtering in treatment: 9791839 INFO @ Thu, 12 Dec 2019 00:50:02: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:50:02: #1 finished! INFO @ Thu, 12 Dec 2019 00:50:02: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:50:02: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:50:03: #2 number of paired peaks: 1116 INFO @ Thu, 12 Dec 2019 00:50:03: start model_add_line... INFO @ Thu, 12 Dec 2019 00:50:03: start X-correlation... INFO @ Thu, 12 Dec 2019 00:50:03: end of X-cor INFO @ Thu, 12 Dec 2019 00:50:03: #2 finished! INFO @ Thu, 12 Dec 2019 00:50:03: #2 predicted fragment length is 168 bps INFO @ Thu, 12 Dec 2019 00:50:03: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 12 Dec 2019 00:50:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.05_model.r INFO @ Thu, 12 Dec 2019 00:50:03: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:50:03: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:50:03: 3000000 INFO @ Thu, 12 Dec 2019 00:50:07: 4000000 INFO @ Thu, 12 Dec 2019 00:50:11: 5000000 INFO @ Thu, 12 Dec 2019 00:50:15: 6000000 INFO @ Thu, 12 Dec 2019 00:50:19: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:50:19: 7000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:50:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.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 00:50:21: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:50:21: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:50:23: 8000000 INFO @ Thu, 12 Dec 2019 00:50:25: 1000000 INFO @ Thu, 12 Dec 2019 00:50:27: 9000000 INFO @ Thu, 12 Dec 2019 00:50:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:50:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:50:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.05_summits.bed INFO @ Thu, 12 Dec 2019 00:50:28: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6160 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:50:29: 2000000 INFO @ Thu, 12 Dec 2019 00:50:30: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:50:30: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:50:30: #1 total tags in treatment: 9791839 INFO @ Thu, 12 Dec 2019 00:50:30: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:50:30: #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 00:50:30: #1 tags after filtering in treatment: 9791839 INFO @ Thu, 12 Dec 2019 00:50:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:50:30: #1 finished! INFO @ Thu, 12 Dec 2019 00:50:30: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:50:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:50:31: #2 number of paired peaks: 1116 INFO @ Thu, 12 Dec 2019 00:50:31: start model_add_line... INFO @ Thu, 12 Dec 2019 00:50:31: start X-correlation... INFO @ Thu, 12 Dec 2019 00:50:31: end of X-cor INFO @ Thu, 12 Dec 2019 00:50:31: #2 finished! INFO @ Thu, 12 Dec 2019 00:50:31: #2 predicted fragment length is 168 bps INFO @ Thu, 12 Dec 2019 00:50:31: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 12 Dec 2019 00:50:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.10_model.r INFO @ Thu, 12 Dec 2019 00:50:31: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:50:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:50:33: 3000000 INFO @ Thu, 12 Dec 2019 00:50:37: 4000000 INFO @ Thu, 12 Dec 2019 00:50:41: 5000000 INFO @ Thu, 12 Dec 2019 00:50:45: 6000000 INFO @ Thu, 12 Dec 2019 00:50:46: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:50:49: 7000000 INFO @ Thu, 12 Dec 2019 00:50:53: 8000000 INFO @ Thu, 12 Dec 2019 00:50:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:50:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:50:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.10_summits.bed INFO @ Thu, 12 Dec 2019 00:50:54: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (4425 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:50:57: 9000000 INFO @ Thu, 12 Dec 2019 00:51:00: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:51:00: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:51:00: #1 total tags in treatment: 9791839 INFO @ Thu, 12 Dec 2019 00:51:00: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:51:00: #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 00:51:00: #1 tags after filtering in treatment: 9791839 INFO @ Thu, 12 Dec 2019 00:51:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:51:00: #1 finished! INFO @ Thu, 12 Dec 2019 00:51:00: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:51:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:51:01: #2 number of paired peaks: 1116 INFO @ Thu, 12 Dec 2019 00:51:01: start model_add_line... INFO @ Thu, 12 Dec 2019 00:51:01: start X-correlation... INFO @ Thu, 12 Dec 2019 00:51:01: end of X-cor INFO @ Thu, 12 Dec 2019 00:51:01: #2 finished! INFO @ Thu, 12 Dec 2019 00:51:01: #2 predicted fragment length is 168 bps INFO @ Thu, 12 Dec 2019 00:51:01: #2 alternative fragment length(s) may be 168 bps INFO @ Thu, 12 Dec 2019 00:51:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.20_model.r INFO @ Thu, 12 Dec 2019 00:51:01: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:51:01: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:51:16: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:51:25: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:51:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:51:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467101/SRX467101.20_summits.bed INFO @ Thu, 12 Dec 2019 00:51:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2544 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。