Job ID = 1292607 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,666,051 reads read : 8,666,051 reads written : 8,666,051 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: 00:01:20 8666051 reads; of these: 8666051 (100.00%) were unpaired; of these: 993583 (11.47%) aligned 0 times 6677133 (77.05%) aligned exactly 1 time 995335 (11.49%) aligned >1 times 88.53% overall alignment rate Time searching: 00:01:20 Overall time: 00:01:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 1694861 / 7672468 = 0.2209 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 @ Sun, 02 Jun 2019 19:45:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:45:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:45:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:45:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:45:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:45:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:45:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.bam'] # control file = None # effective genome size = 9.00e+07 # 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 @ Sun, 02 Jun 2019 19:45:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:45:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:45:58: 1000000 INFO @ Sun, 02 Jun 2019 19:45:58: 1000000 INFO @ Sun, 02 Jun 2019 19:45:59: 1000000 INFO @ Sun, 02 Jun 2019 19:46:05: 2000000 INFO @ Sun, 02 Jun 2019 19:46:06: 2000000 INFO @ Sun, 02 Jun 2019 19:46:08: 2000000 INFO @ Sun, 02 Jun 2019 19:46:13: 3000000 INFO @ Sun, 02 Jun 2019 19:46:13: 3000000 INFO @ Sun, 02 Jun 2019 19:46:16: 3000000 INFO @ Sun, 02 Jun 2019 19:46:20: 4000000 INFO @ Sun, 02 Jun 2019 19:46:20: 4000000 INFO @ Sun, 02 Jun 2019 19:46:24: 4000000 INFO @ Sun, 02 Jun 2019 19:46:27: 5000000 INFO @ Sun, 02 Jun 2019 19:46:27: 5000000 INFO @ Sun, 02 Jun 2019 19:46:32: 5000000 INFO @ Sun, 02 Jun 2019 19:46:34: #1 tag size is determined as 29 bps INFO @ Sun, 02 Jun 2019 19:46:34: #1 tag size = 29 INFO @ Sun, 02 Jun 2019 19:46:34: #1 total tags in treatment: 5977607 INFO @ Sun, 02 Jun 2019 19:46:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:46:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:46:34: #1 tags after filtering in treatment: 5977607 INFO @ Sun, 02 Jun 2019 19:46:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:46:34: #1 finished! INFO @ Sun, 02 Jun 2019 19:46:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:46:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:46:34: #1 tag size is determined as 29 bps INFO @ Sun, 02 Jun 2019 19:46:34: #1 tag size = 29 INFO @ Sun, 02 Jun 2019 19:46:34: #1 total tags in treatment: 5977607 INFO @ Sun, 02 Jun 2019 19:46:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:46:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:46:35: #1 tags after filtering in treatment: 5977607 INFO @ Sun, 02 Jun 2019 19:46:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:46:35: #1 finished! INFO @ Sun, 02 Jun 2019 19:46:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:46:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:46:35: #2 number of paired peaks: 1804 INFO @ Sun, 02 Jun 2019 19:46:35: start model_add_line... INFO @ Sun, 02 Jun 2019 19:46:35: start X-correlation... INFO @ Sun, 02 Jun 2019 19:46:35: end of X-cor INFO @ Sun, 02 Jun 2019 19:46:35: #2 finished! INFO @ Sun, 02 Jun 2019 19:46:35: #2 predicted fragment length is 204 bps INFO @ Sun, 02 Jun 2019 19:46:35: #2 alternative fragment length(s) may be 4,204 bps INFO @ Sun, 02 Jun 2019 19:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.10_model.r INFO @ Sun, 02 Jun 2019 19:46:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:46:35: #2 number of paired peaks: 1804 INFO @ Sun, 02 Jun 2019 19:46:35: start model_add_line... INFO @ Sun, 02 Jun 2019 19:46:35: start X-correlation... INFO @ Sun, 02 Jun 2019 19:46:35: end of X-cor INFO @ Sun, 02 Jun 2019 19:46:35: #2 finished! INFO @ Sun, 02 Jun 2019 19:46:35: #2 predicted fragment length is 204 bps INFO @ Sun, 02 Jun 2019 19:46:35: #2 alternative fragment length(s) may be 4,204 bps INFO @ Sun, 02 Jun 2019 19:46:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.20_model.r INFO @ Sun, 02 Jun 2019 19:46:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:46:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:46:39: #1 tag size is determined as 29 bps INFO @ Sun, 02 Jun 2019 19:46:39: #1 tag size = 29 INFO @ Sun, 02 Jun 2019 19:46:39: #1 total tags in treatment: 5977607 INFO @ Sun, 02 Jun 2019 19:46:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:46:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:46:40: #1 tags after filtering in treatment: 5977607 INFO @ Sun, 02 Jun 2019 19:46:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:46:40: #1 finished! INFO @ Sun, 02 Jun 2019 19:46:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:46:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:46:40: #2 number of paired peaks: 1804 INFO @ Sun, 02 Jun 2019 19:46:40: start model_add_line... INFO @ Sun, 02 Jun 2019 19:46:40: start X-correlation... INFO @ Sun, 02 Jun 2019 19:46:40: end of X-cor INFO @ Sun, 02 Jun 2019 19:46:40: #2 finished! INFO @ Sun, 02 Jun 2019 19:46:40: #2 predicted fragment length is 204 bps INFO @ Sun, 02 Jun 2019 19:46:40: #2 alternative fragment length(s) may be 4,204 bps INFO @ Sun, 02 Jun 2019 19:46:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.05_model.r INFO @ Sun, 02 Jun 2019 19:46:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:46:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:46:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:46:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:47:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:47:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:47:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:47:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.10_summits.bed INFO @ Sun, 02 Jun 2019 19:47:03: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1307 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:47:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:47:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:47:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.20_summits.bed INFO @ Sun, 02 Jun 2019 19:47:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:47:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:47:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:47:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494854/SRX494854.05_summits.bed INFO @ Sun, 02 Jun 2019 19:47:09: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3780 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。