Job ID = 2589103 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,124,428 reads read : 16,124,428 reads written : 16,124,428 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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:11 16124428 reads; of these: 16124428 (100.00%) were unpaired; of these: 266247 (1.65%) aligned 0 times 7136264 (44.26%) aligned exactly 1 time 8721917 (54.09%) aligned >1 times 98.35% overall alignment rate Time searching: 00:05:11 Overall time: 00:05:11 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_sort_core] merging from 8 files... [bam_rmdupse_core] 10309284 / 15858181 = 0.6501 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 @ Mon, 12 Aug 2019 17:07:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.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 @ Mon, 12 Aug 2019 17:07:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:07:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:07:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.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 @ Mon, 12 Aug 2019 17:07:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:07:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:07:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.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 @ Mon, 12 Aug 2019 17:07:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:07:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:07:45: 1000000 INFO @ Mon, 12 Aug 2019 17:07:46: 1000000 INFO @ Mon, 12 Aug 2019 17:07:46: 1000000 INFO @ Mon, 12 Aug 2019 17:07:53: 2000000 INFO @ Mon, 12 Aug 2019 17:07:53: 2000000 INFO @ Mon, 12 Aug 2019 17:07:54: 2000000 INFO @ Mon, 12 Aug 2019 17:07:59: 3000000 INFO @ Mon, 12 Aug 2019 17:08:00: 3000000 INFO @ Mon, 12 Aug 2019 17:08:01: 3000000 INFO @ Mon, 12 Aug 2019 17:08:06: 4000000 INFO @ Mon, 12 Aug 2019 17:08:07: 4000000 INFO @ Mon, 12 Aug 2019 17:08:08: 4000000 INFO @ Mon, 12 Aug 2019 17:08:14: 5000000 INFO @ Mon, 12 Aug 2019 17:08:14: 5000000 INFO @ Mon, 12 Aug 2019 17:08:15: 5000000 INFO @ Mon, 12 Aug 2019 17:08:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 17:08:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 17:08:18: #1 total tags in treatment: 5548897 INFO @ Mon, 12 Aug 2019 17:08:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:08:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:08:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 17:08:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 17:08:18: #1 total tags in treatment: 5548897 INFO @ Mon, 12 Aug 2019 17:08:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:08:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:08:18: #1 tags after filtering in treatment: 5548897 INFO @ Mon, 12 Aug 2019 17:08:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:08:18: #1 finished! INFO @ Mon, 12 Aug 2019 17:08:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:08:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:08:18: #1 tags after filtering in treatment: 5548897 INFO @ Mon, 12 Aug 2019 17:08:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:08:18: #1 finished! INFO @ Mon, 12 Aug 2019 17:08:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:08:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:08:19: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 17:08:19: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 17:08:19: #1 total tags in treatment: 5548897 INFO @ Mon, 12 Aug 2019 17:08:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:08:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:08:19: #1 tags after filtering in treatment: 5548897 INFO @ Mon, 12 Aug 2019 17:08:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:08:19: #1 finished! INFO @ Mon, 12 Aug 2019 17:08:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:08:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:08:19: #2 number of paired peaks: 7522 INFO @ Mon, 12 Aug 2019 17:08:19: start model_add_line... INFO @ Mon, 12 Aug 2019 17:08:19: #2 number of paired peaks: 7522 INFO @ Mon, 12 Aug 2019 17:08:19: start model_add_line... INFO @ Mon, 12 Aug 2019 17:08:19: start X-correlation... INFO @ Mon, 12 Aug 2019 17:08:19: end of X-cor INFO @ Mon, 12 Aug 2019 17:08:19: #2 finished! INFO @ Mon, 12 Aug 2019 17:08:19: #2 predicted fragment length is 136 bps INFO @ Mon, 12 Aug 2019 17:08:19: #2 alternative fragment length(s) may be 3,136,168,172 bps INFO @ Mon, 12 Aug 2019 17:08:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.05_model.r INFO @ Mon, 12 Aug 2019 17:08:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:08:19: start X-correlation... INFO @ Mon, 12 Aug 2019 17:08:19: end of X-cor INFO @ Mon, 12 Aug 2019 17:08:19: #2 finished! INFO @ Mon, 12 Aug 2019 17:08:19: #2 predicted fragment length is 136 bps INFO @ Mon, 12 Aug 2019 17:08:19: #2 alternative fragment length(s) may be 3,136,168,172 bps INFO @ Mon, 12 Aug 2019 17:08:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.20_model.r INFO @ Mon, 12 Aug 2019 17:08:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:08:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:08:20: #2 number of paired peaks: 7522 INFO @ Mon, 12 Aug 2019 17:08:20: start model_add_line... INFO @ Mon, 12 Aug 2019 17:08:20: start X-correlation... INFO @ Mon, 12 Aug 2019 17:08:20: end of X-cor INFO @ Mon, 12 Aug 2019 17:08:20: #2 finished! INFO @ Mon, 12 Aug 2019 17:08:20: #2 predicted fragment length is 136 bps INFO @ Mon, 12 Aug 2019 17:08:20: #2 alternative fragment length(s) may be 3,136,168,172 bps INFO @ Mon, 12 Aug 2019 17:08:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.10_model.r INFO @ Mon, 12 Aug 2019 17:08:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:08:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:08:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:08:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:08:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.20_summits.bed INFO @ Mon, 12 Aug 2019 17:08:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:08:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:08:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.10_summits.bed INFO @ Mon, 12 Aug 2019 17:08:48: Done! INFO @ Mon, 12 Aug 2019 17:08:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/ERX1999202/ERX1999202.05_summits.bed INFO @ Mon, 12 Aug 2019 17:08:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1669 records, 4 fields): 4 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3832 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。