Job ID = 2590169 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,122,451 reads read : 24,122,451 reads written : 24,122,451 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: 00:04:22 24122451 reads; of these: 24122451 (100.00%) were unpaired; of these: 8419219 (34.90%) aligned 0 times 13884572 (57.56%) aligned exactly 1 time 1818660 (7.54%) aligned >1 times 65.10% overall alignment rate Time searching: 00:04:22 Overall time: 00:04:22 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] 14304272 / 15703232 = 0.9109 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 20:10:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.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 20:10:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.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 20:10:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.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 20:10:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:10:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:10:59: 1000000 INFO @ Mon, 12 Aug 2019 20:11:02: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:11:02: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:11:02: #1 total tags in treatment: 1398960 INFO @ Mon, 12 Aug 2019 20:11:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:11:02: #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 20:11:02: #1 tags after filtering in treatment: 1398960 INFO @ Mon, 12 Aug 2019 20:11:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:11:02: #1 finished! INFO @ Mon, 12 Aug 2019 20:11:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:11:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:11:03: 1000000 INFO @ Mon, 12 Aug 2019 20:11:03: #2 number of paired peaks: 1587 INFO @ Mon, 12 Aug 2019 20:11:03: start model_add_line... INFO @ Mon, 12 Aug 2019 20:11:03: start X-correlation... INFO @ Mon, 12 Aug 2019 20:11:03: end of X-cor INFO @ Mon, 12 Aug 2019 20:11:03: #2 finished! INFO @ Mon, 12 Aug 2019 20:11:03: #2 predicted fragment length is 122 bps INFO @ Mon, 12 Aug 2019 20:11:03: #2 alternative fragment length(s) may be 64,122 bps INFO @ Mon, 12 Aug 2019 20:11:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.05_model.r INFO @ Mon, 12 Aug 2019 20:11:03: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:11:03: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:11:03: 1000000 INFO @ Mon, 12 Aug 2019 20:11:06: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:11:06: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:11:06: #1 total tags in treatment: 1398960 INFO @ Mon, 12 Aug 2019 20:11:06: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:11:06: #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 20:11:06: #1 tags after filtering in treatment: 1398960 INFO @ Mon, 12 Aug 2019 20:11:06: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:11:06: #1 finished! INFO @ Mon, 12 Aug 2019 20:11:06: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:11:06: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:11:06: #2 number of paired peaks: 1587 INFO @ Mon, 12 Aug 2019 20:11:06: start model_add_line... INFO @ Mon, 12 Aug 2019 20:11:06: start X-correlation... INFO @ Mon, 12 Aug 2019 20:11:06: end of X-cor INFO @ Mon, 12 Aug 2019 20:11:06: #2 finished! INFO @ Mon, 12 Aug 2019 20:11:06: #2 predicted fragment length is 122 bps INFO @ Mon, 12 Aug 2019 20:11:06: #2 alternative fragment length(s) may be 64,122 bps INFO @ Mon, 12 Aug 2019 20:11:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.20_model.r INFO @ Mon, 12 Aug 2019 20:11:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:11:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:11:07: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:11:07: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:11:07: #1 total tags in treatment: 1398960 INFO @ Mon, 12 Aug 2019 20:11:07: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:11:07: #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 20:11:07: #1 tags after filtering in treatment: 1398960 INFO @ Mon, 12 Aug 2019 20:11:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:11:07: #1 finished! INFO @ Mon, 12 Aug 2019 20:11:07: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:11:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:11:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:11:07: #2 number of paired peaks: 1587 INFO @ Mon, 12 Aug 2019 20:11:07: start model_add_line... INFO @ Mon, 12 Aug 2019 20:11:07: start X-correlation... INFO @ Mon, 12 Aug 2019 20:11:07: end of X-cor INFO @ Mon, 12 Aug 2019 20:11:07: #2 finished! INFO @ Mon, 12 Aug 2019 20:11:07: #2 predicted fragment length is 122 bps INFO @ Mon, 12 Aug 2019 20:11:07: #2 alternative fragment length(s) may be 64,122 bps INFO @ Mon, 12 Aug 2019 20:11:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.10_model.r INFO @ Mon, 12 Aug 2019 20:11:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:11:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:11:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:11:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:11:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.05_summits.bed INFO @ Mon, 12 Aug 2019 20:11:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (660 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:11:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:11:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:11:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:11:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:11:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.20_summits.bed INFO @ Mon, 12 Aug 2019 20:11:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (77 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:11:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:11:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:11:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495043/SRX495043.10_summits.bed INFO @ Mon, 12 Aug 2019 20:11:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (233 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。