Job ID = 2640675 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,916,478 reads read : 11,832,956 reads written : 5,916,478 reads 0-length : 5,916,478 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:18 5916478 reads; of these: 5916478 (100.00%) were unpaired; of these: 327381 (5.53%) aligned 0 times 4141495 (70.00%) aligned exactly 1 time 1447602 (24.47%) aligned >1 times 94.47% overall alignment rate Time searching: 00:05:21 Overall time: 00:05:21 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] 237824 / 5589097 = 0.0426 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:14:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.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 18:14:23: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:14:23: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:14:29: 1000000 INFO @ Sat, 24 Aug 2019 18:14:36: 2000000 INFO @ Sat, 24 Aug 2019 18:14:43: 3000000 INFO @ Sat, 24 Aug 2019 18:14:51: 4000000 INFO @ Sat, 24 Aug 2019 18:14:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.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 18:14:53: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:14:53: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:14:58: 5000000 INFO @ Sat, 24 Aug 2019 18:15:00: 1000000 INFO @ Sat, 24 Aug 2019 18:15:01: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:15:01: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:15:01: #1 total tags in treatment: 5351273 INFO @ Sat, 24 Aug 2019 18:15:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:15:01: #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 18:15:01: #1 tags after filtering in treatment: 5351021 INFO @ Sat, 24 Aug 2019 18:15:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:15:01: #1 finished! INFO @ Sat, 24 Aug 2019 18:15:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:15:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:15:03: #2 number of paired peaks: 19357 INFO @ Sat, 24 Aug 2019 18:15:03: start model_add_line... INFO @ Sat, 24 Aug 2019 18:15:03: start X-correlation... INFO @ Sat, 24 Aug 2019 18:15:03: end of X-cor INFO @ Sat, 24 Aug 2019 18:15:03: #2 finished! INFO @ Sat, 24 Aug 2019 18:15:03: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:15:03: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:15:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.05_model.r INFO @ Sat, 24 Aug 2019 18:15:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:15:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:15:07: 2000000 INFO @ Sat, 24 Aug 2019 18:15:14: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:15:21: 4000000 INFO @ Sat, 24 Aug 2019 18:15:21: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:15:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.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 18:15:22: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:15:22: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:15:28: 5000000 INFO @ Sat, 24 Aug 2019 18:15:30: 1000000 INFO @ Sat, 24 Aug 2019 18:15:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.05_summits.bed INFO @ Sat, 24 Aug 2019 18:15:30: Done! INFO @ Sat, 24 Aug 2019 18:15:30: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:15:30: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:15:30: #1 total tags in treatment: 5351273 INFO @ Sat, 24 Aug 2019 18:15:30: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:15:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (3421 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:15:30: #1 tags after filtering in treatment: 5351021 INFO @ Sat, 24 Aug 2019 18:15:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:15:30: #1 finished! INFO @ Sat, 24 Aug 2019 18:15:30: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:15:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:15:32: #2 number of paired peaks: 19357 INFO @ Sat, 24 Aug 2019 18:15:32: start model_add_line... INFO @ Sat, 24 Aug 2019 18:15:32: start X-correlation... INFO @ Sat, 24 Aug 2019 18:15:32: end of X-cor INFO @ Sat, 24 Aug 2019 18:15:32: #2 finished! INFO @ Sat, 24 Aug 2019 18:15:32: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:15:32: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:15:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.10_model.r INFO @ Sat, 24 Aug 2019 18:15:32: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:15:37: 2000000 INFO @ Sat, 24 Aug 2019 18:15:44: 3000000 INFO @ Sat, 24 Aug 2019 18:15:51: 4000000 INFO @ Sat, 24 Aug 2019 18:15:51: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:15:57: 5000000 INFO @ Sat, 24 Aug 2019 18:16:00: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:16:00: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:16:00: #1 total tags in treatment: 5351273 INFO @ Sat, 24 Aug 2019 18:16:00: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:16:00: #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 18:16:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:16:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:16:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.10_summits.bed INFO @ Sat, 24 Aug 2019 18:16:00: Done! INFO @ Sat, 24 Aug 2019 18:16:00: #1 tags after filtering in treatment: 5351021 INFO @ Sat, 24 Aug 2019 18:16:00: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:16:00: #1 finished! INFO @ Sat, 24 Aug 2019 18:16:00: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:16:00: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (35 chroms): 3 millis pass2 - checking and writing primary data (1774 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:16:02: #2 number of paired peaks: 19357 INFO @ Sat, 24 Aug 2019 18:16:02: start model_add_line... INFO @ Sat, 24 Aug 2019 18:16:02: start X-correlation... INFO @ Sat, 24 Aug 2019 18:16:03: end of X-cor INFO @ Sat, 24 Aug 2019 18:16:03: #2 finished! INFO @ Sat, 24 Aug 2019 18:16:03: #2 predicted fragment length is 150 bps INFO @ Sat, 24 Aug 2019 18:16:03: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 24 Aug 2019 18:16:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.20_model.r INFO @ Sat, 24 Aug 2019 18:16:03: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:16:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:16:21: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:16:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:16:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:16:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375042/SRX5375042.20_summits.bed INFO @ Sat, 24 Aug 2019 18:16:31: Done! pass1 - making usageList (25 chroms): 2 millis pass2 - checking and writing primary data (740 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。