Job ID = 2589999 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,886,714 reads read : 8,886,714 reads written : 8,886,714 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: 00:01:26 8886714 reads; of these: 8886714 (100.00%) were unpaired; of these: 2903404 (32.67%) aligned 0 times 5060484 (56.94%) aligned exactly 1 time 922826 (10.38%) aligned >1 times 67.33% overall alignment rate Time searching: 00:01:26 Overall time: 00:01:26 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] 847037 / 5983310 = 0.1416 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 19:02:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.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 19:02:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:02:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:02:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.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 19:02:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:02:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:02:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.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 19:02:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:02:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:02:07: 1000000 INFO @ Mon, 12 Aug 2019 19:02:08: 1000000 INFO @ Mon, 12 Aug 2019 19:02:09: 1000000 INFO @ Mon, 12 Aug 2019 19:02:13: 2000000 INFO @ Mon, 12 Aug 2019 19:02:14: 2000000 INFO @ Mon, 12 Aug 2019 19:02:15: 2000000 INFO @ Mon, 12 Aug 2019 19:02:20: 3000000 INFO @ Mon, 12 Aug 2019 19:02:20: 3000000 INFO @ Mon, 12 Aug 2019 19:02:22: 3000000 INFO @ Mon, 12 Aug 2019 19:02:26: 4000000 INFO @ Mon, 12 Aug 2019 19:02:27: 4000000 INFO @ Mon, 12 Aug 2019 19:02:28: 4000000 INFO @ Mon, 12 Aug 2019 19:02:32: 5000000 INFO @ Mon, 12 Aug 2019 19:02:33: 5000000 INFO @ Mon, 12 Aug 2019 19:02:33: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:02:33: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:02:33: #1 total tags in treatment: 5136273 INFO @ Mon, 12 Aug 2019 19:02:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:02:33: #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 19:02:33: #1 tags after filtering in treatment: 5136273 INFO @ Mon, 12 Aug 2019 19:02:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:02:33: #1 finished! INFO @ Mon, 12 Aug 2019 19:02:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:02:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:02:34: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:02:34: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:02:34: #1 total tags in treatment: 5136273 INFO @ Mon, 12 Aug 2019 19:02:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:02:34: #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 19:02:34: #2 number of paired peaks: 1703 INFO @ Mon, 12 Aug 2019 19:02:34: start model_add_line... INFO @ Mon, 12 Aug 2019 19:02:34: #1 tags after filtering in treatment: 5136273 INFO @ Mon, 12 Aug 2019 19:02:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:02:34: #1 finished! INFO @ Mon, 12 Aug 2019 19:02:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:02:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:02:34: start X-correlation... INFO @ Mon, 12 Aug 2019 19:02:34: end of X-cor INFO @ Mon, 12 Aug 2019 19:02:34: #2 finished! INFO @ Mon, 12 Aug 2019 19:02:34: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 19:02:34: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 19:02:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.05_model.r INFO @ Mon, 12 Aug 2019 19:02:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:02:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:02:34: 5000000 INFO @ Mon, 12 Aug 2019 19:02:35: #2 number of paired peaks: 1703 INFO @ Mon, 12 Aug 2019 19:02:35: start model_add_line... INFO @ Mon, 12 Aug 2019 19:02:35: start X-correlation... INFO @ Mon, 12 Aug 2019 19:02:35: end of X-cor INFO @ Mon, 12 Aug 2019 19:02:35: #2 finished! INFO @ Mon, 12 Aug 2019 19:02:35: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 19:02:35: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 19:02:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.10_model.r INFO @ Mon, 12 Aug 2019 19:02:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:02:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:02:35: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:02:35: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:02:35: #1 total tags in treatment: 5136273 INFO @ Mon, 12 Aug 2019 19:02:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:02:35: #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 19:02:35: #1 tags after filtering in treatment: 5136273 INFO @ Mon, 12 Aug 2019 19:02:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:02:35: #1 finished! INFO @ Mon, 12 Aug 2019 19:02:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:02:36: #2 number of paired peaks: 1703 INFO @ Mon, 12 Aug 2019 19:02:36: start model_add_line... INFO @ Mon, 12 Aug 2019 19:02:36: start X-correlation... INFO @ Mon, 12 Aug 2019 19:02:36: end of X-cor INFO @ Mon, 12 Aug 2019 19:02:36: #2 finished! INFO @ Mon, 12 Aug 2019 19:02:36: #2 predicted fragment length is 139 bps INFO @ Mon, 12 Aug 2019 19:02:36: #2 alternative fragment length(s) may be 139 bps INFO @ Mon, 12 Aug 2019 19:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.20_model.r INFO @ Mon, 12 Aug 2019 19:02:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:02:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.05_summits.bed INFO @ Mon, 12 Aug 2019 19:02:58: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5202 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:02:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.10_summits.bed INFO @ Mon, 12 Aug 2019 19:02:59: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3744 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:03:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:03:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:03:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467177/SRX467177.20_summits.bed INFO @ Mon, 12 Aug 2019 19:03:00: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2493 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。