Job ID = 1292764 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,613,870 reads read : 13,613,870 reads written : 13,613,870 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: 00:02:27 13613870 reads; of these: 13613870 (100.00%) were unpaired; of these: 795287 (5.84%) aligned 0 times 11685018 (85.83%) aligned exactly 1 time 1133565 (8.33%) aligned >1 times 94.16% overall alignment rate Time searching: 00:02:27 Overall time: 00:02:27 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] 4221903 / 12818583 = 0.3294 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 20:17:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.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 20:17:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:17:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:17:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.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 20:17:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:17:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:17:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.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 20:17:59: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:17:59: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:18:06: 1000000 INFO @ Sun, 02 Jun 2019 20:18:07: 1000000 INFO @ Sun, 02 Jun 2019 20:18:09: 1000000 INFO @ Sun, 02 Jun 2019 20:18:13: 2000000 INFO @ Sun, 02 Jun 2019 20:18:15: 2000000 INFO @ Sun, 02 Jun 2019 20:18:19: 2000000 INFO @ Sun, 02 Jun 2019 20:18:20: 3000000 INFO @ Sun, 02 Jun 2019 20:18:23: 3000000 INFO @ Sun, 02 Jun 2019 20:18:27: 4000000 INFO @ Sun, 02 Jun 2019 20:18:28: 3000000 INFO @ Sun, 02 Jun 2019 20:18:31: 4000000 INFO @ Sun, 02 Jun 2019 20:18:34: 5000000 INFO @ Sun, 02 Jun 2019 20:18:38: 4000000 INFO @ Sun, 02 Jun 2019 20:18:38: 5000000 INFO @ Sun, 02 Jun 2019 20:18:41: 6000000 INFO @ Sun, 02 Jun 2019 20:18:46: 6000000 INFO @ Sun, 02 Jun 2019 20:18:47: 5000000 INFO @ Sun, 02 Jun 2019 20:18:48: 7000000 INFO @ Sun, 02 Jun 2019 20:18:54: 7000000 INFO @ Sun, 02 Jun 2019 20:18:55: 8000000 INFO @ Sun, 02 Jun 2019 20:18:56: 6000000 INFO @ Sun, 02 Jun 2019 20:18:59: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:18:59: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:18:59: #1 total tags in treatment: 8596680 INFO @ Sun, 02 Jun 2019 20:18:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:18:59: #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 20:18:59: #1 tags after filtering in treatment: 8596680 INFO @ Sun, 02 Jun 2019 20:18:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:18:59: #1 finished! INFO @ Sun, 02 Jun 2019 20:18:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:18:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:19:00: #2 number of paired peaks: 3494 INFO @ Sun, 02 Jun 2019 20:19:00: start model_add_line... INFO @ Sun, 02 Jun 2019 20:19:01: start X-correlation... INFO @ Sun, 02 Jun 2019 20:19:01: end of X-cor INFO @ Sun, 02 Jun 2019 20:19:01: #2 finished! INFO @ Sun, 02 Jun 2019 20:19:01: #2 predicted fragment length is 211 bps INFO @ Sun, 02 Jun 2019 20:19:01: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 02 Jun 2019 20:19:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.20_model.r INFO @ Sun, 02 Jun 2019 20:19:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:19:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:19:01: 8000000 INFO @ Sun, 02 Jun 2019 20:19:06: 7000000 INFO @ Sun, 02 Jun 2019 20:19:06: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:19:06: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:19:06: #1 total tags in treatment: 8596680 INFO @ Sun, 02 Jun 2019 20:19:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:19:06: #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 20:19:06: #1 tags after filtering in treatment: 8596680 INFO @ Sun, 02 Jun 2019 20:19:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:19:06: #1 finished! INFO @ Sun, 02 Jun 2019 20:19:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:19:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:19:07: #2 number of paired peaks: 3494 INFO @ Sun, 02 Jun 2019 20:19:07: start model_add_line... INFO @ Sun, 02 Jun 2019 20:19:07: start X-correlation... INFO @ Sun, 02 Jun 2019 20:19:07: end of X-cor INFO @ Sun, 02 Jun 2019 20:19:07: #2 finished! INFO @ Sun, 02 Jun 2019 20:19:07: #2 predicted fragment length is 211 bps INFO @ Sun, 02 Jun 2019 20:19:07: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 02 Jun 2019 20:19:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.10_model.r INFO @ Sun, 02 Jun 2019 20:19:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:19:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:19:15: 8000000 INFO @ Sun, 02 Jun 2019 20:19:20: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:19:20: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:19:20: #1 total tags in treatment: 8596680 INFO @ Sun, 02 Jun 2019 20:19:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:19:20: #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 20:19:20: #1 tags after filtering in treatment: 8596680 INFO @ Sun, 02 Jun 2019 20:19:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:19:20: #1 finished! INFO @ Sun, 02 Jun 2019 20:19:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:19:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:19:21: #2 number of paired peaks: 3494 INFO @ Sun, 02 Jun 2019 20:19:21: start model_add_line... INFO @ Sun, 02 Jun 2019 20:19:22: start X-correlation... INFO @ Sun, 02 Jun 2019 20:19:22: end of X-cor INFO @ Sun, 02 Jun 2019 20:19:22: #2 finished! INFO @ Sun, 02 Jun 2019 20:19:22: #2 predicted fragment length is 211 bps INFO @ Sun, 02 Jun 2019 20:19:22: #2 alternative fragment length(s) may be 211 bps INFO @ Sun, 02 Jun 2019 20:19:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.05_model.r INFO @ Sun, 02 Jun 2019 20:19:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:19:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:19:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:19:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:19:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:19:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:19:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.20_summits.bed INFO @ Sun, 02 Jun 2019 20:19:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4405 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:19:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:19:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:19:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.10_summits.bed INFO @ Sun, 02 Jun 2019 20:19:53: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (6427 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:19:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:20:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:20:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:20:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494989/SRX494989.05_summits.bed INFO @ Sun, 02 Jun 2019 20:20:08: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (8710 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。