Job ID = 2640411 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,123,682 reads read : 6,123,682 reads written : 6,123,682 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR399328.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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:02:19 6123682 reads; of these: 6123682 (100.00%) were unpaired; of these: 257893 (4.21%) aligned 0 times 4307161 (70.34%) aligned exactly 1 time 1558628 (25.45%) aligned >1 times 95.79% overall alignment rate Time searching: 00:02:22 Overall time: 00:02:22 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_rmdupse_core] 2571321 / 5865789 = 0.4384 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 16:23:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:23:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:23:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:23:12: 1000000 INFO @ Sat, 24 Aug 2019 16:23:20: 2000000 INFO @ Sat, 24 Aug 2019 16:23:29: 3000000 INFO @ Sat, 24 Aug 2019 16:23:31: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:23:31: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:23:31: #1 total tags in treatment: 3294468 INFO @ Sat, 24 Aug 2019 16:23:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:23:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:23:32: #1 tags after filtering in treatment: 3294185 INFO @ Sat, 24 Aug 2019 16:23:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:23:32: #1 finished! INFO @ Sat, 24 Aug 2019 16:23:32: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:23:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:23:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:23:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:23:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:23:37: #2 number of paired peaks: 45694 INFO @ Sat, 24 Aug 2019 16:23:37: start model_add_line... INFO @ Sat, 24 Aug 2019 16:23:37: start X-correlation... INFO @ Sat, 24 Aug 2019 16:23:37: end of X-cor INFO @ Sat, 24 Aug 2019 16:23:37: #2 finished! INFO @ Sat, 24 Aug 2019 16:23:37: #2 predicted fragment length is 294 bps INFO @ Sat, 24 Aug 2019 16:23:37: #2 alternative fragment length(s) may be 294 bps INFO @ Sat, 24 Aug 2019 16:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.05_model.r INFO @ Sat, 24 Aug 2019 16:23:37: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:23:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:23:42: 1000000 INFO @ Sat, 24 Aug 2019 16:23:49: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:23:50: 2000000 INFO @ Sat, 24 Aug 2019 16:23:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.05_peaks.xls INFO @ Sat, 24 Aug 2019 16:23:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:23:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.05_summits.bed INFO @ Sat, 24 Aug 2019 16:23:56: Done! pass1 - making usageList (27 chroms): 2 millis pass2 - checking and writing primary data (271 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:23:59: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 16:24:01: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:24:01: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:24:01: #1 total tags in treatment: 3294468 INFO @ Sat, 24 Aug 2019 16:24:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:24:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:24:02: #1 tags after filtering in treatment: 3294185 INFO @ Sat, 24 Aug 2019 16:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:24:02: #1 finished! INFO @ Sat, 24 Aug 2019 16:24:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:24:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 24 Aug 2019 16:24:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:24:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:24:07: #2 number of paired peaks: 45694 INFO @ Sat, 24 Aug 2019 16:24:07: start model_add_line... INFO @ Sat, 24 Aug 2019 16:24:07: start X-correlation... INFO @ Sat, 24 Aug 2019 16:24:07: end of X-cor INFO @ Sat, 24 Aug 2019 16:24:07: #2 finished! INFO @ Sat, 24 Aug 2019 16:24:07: #2 predicted fragment length is 294 bps INFO @ Sat, 24 Aug 2019 16:24:07: #2 alternative fragment length(s) may be 294 bps INFO @ Sat, 24 Aug 2019 16:24:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.10_model.r INFO @ Sat, 24 Aug 2019 16:24:07: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:24:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:24:11: 1000000 INFO @ Sat, 24 Aug 2019 16:24:18: 2000000 INFO @ Sat, 24 Aug 2019 16:24:18: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:24:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.10_peaks.xls INFO @ Sat, 24 Aug 2019 16:24:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:24:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.10_summits.bed INFO @ Sat, 24 Aug 2019 16:24:24: Done! pass1 - making usageList (21 chroms): 2 millis pass2 - checking and writing primary data (147 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:24:25: 3000000 INFO @ Sat, 24 Aug 2019 16:24:27: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:24:27: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:24:27: #1 total tags in treatment: 3294468 INFO @ Sat, 24 Aug 2019 16:24:27: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:24:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:24:27: #1 tags after filtering in treatment: 3294185 INFO @ Sat, 24 Aug 2019 16:24:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:24:27: #1 finished! INFO @ Sat, 24 Aug 2019 16:24:27: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:24:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:24:32: #2 number of paired peaks: 45694 INFO @ Sat, 24 Aug 2019 16:24:32: start model_add_line... INFO @ Sat, 24 Aug 2019 16:24:32: start X-correlation... INFO @ Sat, 24 Aug 2019 16:24:32: end of X-cor INFO @ Sat, 24 Aug 2019 16:24:32: #2 finished! INFO @ Sat, 24 Aug 2019 16:24:32: #2 predicted fragment length is 294 bps INFO @ Sat, 24 Aug 2019 16:24:32: #2 alternative fragment length(s) may be 294 bps INFO @ Sat, 24 Aug 2019 16:24:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.20_model.r INFO @ Sat, 24 Aug 2019 16:24:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:24:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:24:43: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:24:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.20_peaks.xls INFO @ Sat, 24 Aug 2019 16:24:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:24:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116050/SRX116050.20_summits.bed INFO @ Sat, 24 Aug 2019 16:24:49: Done! pass1 - making usageList (9 chroms): 2 millis pass2 - checking and writing primary data (54 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。