Job ID = 1293151 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,963,731 reads read : 15,927,462 reads written : 7,963,731 reads 0-length : 7,963,731 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: 00:02:00 7963731 reads; of these: 7963731 (100.00%) were unpaired; of these: 36809 (0.46%) aligned 0 times 7189390 (90.28%) aligned exactly 1 time 737532 (9.26%) aligned >1 times 99.54% overall alignment rate Time searching: 00:02:00 Overall time: 00:02:00 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] 1716618 / 7926922 = 0.2166 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 22:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.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 22:04:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:04:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.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 22:04:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:04:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:04:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.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 22:04:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:04:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:05: 1000000 INFO @ Sun, 02 Jun 2019 22:05:05: 1000000 INFO @ Sun, 02 Jun 2019 22:05:05: 1000000 INFO @ Sun, 02 Jun 2019 22:05:14: 2000000 INFO @ Sun, 02 Jun 2019 22:05:14: 2000000 INFO @ Sun, 02 Jun 2019 22:05:14: 2000000 INFO @ Sun, 02 Jun 2019 22:05:22: 3000000 INFO @ Sun, 02 Jun 2019 22:05:24: 3000000 INFO @ Sun, 02 Jun 2019 22:05:24: 3000000 INFO @ Sun, 02 Jun 2019 22:05:31: 4000000 INFO @ Sun, 02 Jun 2019 22:05:33: 4000000 INFO @ Sun, 02 Jun 2019 22:05:33: 4000000 INFO @ Sun, 02 Jun 2019 22:05:40: 5000000 INFO @ Sun, 02 Jun 2019 22:05:42: 5000000 INFO @ Sun, 02 Jun 2019 22:05:42: 5000000 INFO @ Sun, 02 Jun 2019 22:05:49: 6000000 INFO @ Sun, 02 Jun 2019 22:05:50: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:05:50: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:05:50: #1 total tags in treatment: 6210304 INFO @ Sun, 02 Jun 2019 22:05:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:50: #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 22:05:51: #1 tags after filtering in treatment: 6210304 INFO @ Sun, 02 Jun 2019 22:05:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:51: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:51: 6000000 INFO @ Sun, 02 Jun 2019 22:05:52: 6000000 INFO @ Sun, 02 Jun 2019 22:05:52: #2 number of paired peaks: 4253 INFO @ Sun, 02 Jun 2019 22:05:52: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:52: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:52: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:52: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:52: #2 predicted fragment length is 188 bps INFO @ Sun, 02 Jun 2019 22:05:52: #2 alternative fragment length(s) may be 4,188 bps INFO @ Sun, 02 Jun 2019 22:05:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.05_model.r INFO @ Sun, 02 Jun 2019 22:05:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:53: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:05:53: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:05:53: #1 total tags in treatment: 6210304 INFO @ Sun, 02 Jun 2019 22:05:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:53: #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 22:05:53: #1 tags after filtering in treatment: 6210304 INFO @ Sun, 02 Jun 2019 22:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:53: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:53: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:05:53: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:05:53: #1 total tags in treatment: 6210304 INFO @ Sun, 02 Jun 2019 22:05:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:53: #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 22:05:53: #1 tags after filtering in treatment: 6210304 INFO @ Sun, 02 Jun 2019 22:05:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:53: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:54: #2 number of paired peaks: 4253 INFO @ Sun, 02 Jun 2019 22:05:54: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:54: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:54: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:54: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:54: #2 predicted fragment length is 188 bps INFO @ Sun, 02 Jun 2019 22:05:54: #2 alternative fragment length(s) may be 4,188 bps INFO @ Sun, 02 Jun 2019 22:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.20_model.r INFO @ Sun, 02 Jun 2019 22:05:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:54: #2 number of paired peaks: 4253 INFO @ Sun, 02 Jun 2019 22:05:54: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:54: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:54: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:54: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:54: #2 predicted fragment length is 188 bps INFO @ Sun, 02 Jun 2019 22:05:54: #2 alternative fragment length(s) may be 4,188 bps INFO @ Sun, 02 Jun 2019 22:05:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.10_model.r INFO @ Sun, 02 Jun 2019 22:05:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:06:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:06:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:06:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:06:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:06:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:06:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.05_summits.bed INFO @ Sun, 02 Jun 2019 22:06:21: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6500 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:06:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:06:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:06:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.20_summits.bed INFO @ Sun, 02 Jun 2019 22:06:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (812 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:06:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:06:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:06:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402719/SRX5402719.10_summits.bed INFO @ Sun, 02 Jun 2019 22:06:25: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3170 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。