Job ID = 2590001 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,588,464 reads read : 7,588,464 reads written : 7,588,464 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: 00:01:06 7588464 reads; of these: 7588464 (100.00%) were unpaired; of these: 2778755 (36.62%) aligned 0 times 4041565 (53.26%) aligned exactly 1 time 768144 (10.12%) aligned >1 times 63.38% overall alignment rate Time searching: 00:01:06 Overall time: 00:01:06 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] 539460 / 4809709 = 0.1122 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 19:01:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.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 19:01:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:01:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.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 19:01:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:01:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.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 19:01:04: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:04: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:01:08: 1000000 INFO @ Mon, 12 Aug 2019 19:01:10: 1000000 INFO @ Mon, 12 Aug 2019 19:01:14: 1000000 INFO @ Mon, 12 Aug 2019 19:01:14: 2000000 INFO @ Mon, 12 Aug 2019 19:01:16: 2000000 INFO @ Mon, 12 Aug 2019 19:01:20: 3000000 INFO @ Mon, 12 Aug 2019 19:01:23: 3000000 INFO @ Mon, 12 Aug 2019 19:01:23: 2000000 INFO @ Mon, 12 Aug 2019 19:01:26: 4000000 INFO @ Mon, 12 Aug 2019 19:01:28: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:01:28: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:01:28: #1 total tags in treatment: 4270249 INFO @ Mon, 12 Aug 2019 19:01:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:28: #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 19:01:28: #1 tags after filtering in treatment: 4270249 INFO @ Mon, 12 Aug 2019 19:01:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:28: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:28: #2 number of paired peaks: 1514 INFO @ Mon, 12 Aug 2019 19:01:28: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:28: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:28: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:28: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:28: #2 predicted fragment length is 137 bps INFO @ Mon, 12 Aug 2019 19:01:28: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 12 Aug 2019 19:01:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.05_model.r INFO @ Mon, 12 Aug 2019 19:01:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:29: 4000000 INFO @ Mon, 12 Aug 2019 19:01:31: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:01:31: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:01:31: #1 total tags in treatment: 4270249 INFO @ Mon, 12 Aug 2019 19:01:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:31: #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 19:01:31: #1 tags after filtering in treatment: 4270249 INFO @ Mon, 12 Aug 2019 19:01:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:31: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:31: #2 number of paired peaks: 1514 INFO @ Mon, 12 Aug 2019 19:01:31: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:31: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:31: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:31: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:31: #2 predicted fragment length is 137 bps INFO @ Mon, 12 Aug 2019 19:01:31: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 12 Aug 2019 19:01:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.10_model.r INFO @ Mon, 12 Aug 2019 19:01:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:33: 3000000 INFO @ Mon, 12 Aug 2019 19:01:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:42: 4000000 INFO @ Mon, 12 Aug 2019 19:01:44: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:01:44: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:01:44: #1 total tags in treatment: 4270249 INFO @ Mon, 12 Aug 2019 19:01:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:44: #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 19:01:45: #1 tags after filtering in treatment: 4270249 INFO @ Mon, 12 Aug 2019 19:01:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:45: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:45: #2 number of paired peaks: 1514 INFO @ Mon, 12 Aug 2019 19:01:45: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:45: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:45: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:45: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:45: #2 predicted fragment length is 137 bps INFO @ Mon, 12 Aug 2019 19:01:45: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 12 Aug 2019 19:01:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.20_model.r INFO @ Mon, 12 Aug 2019 19:01:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:01:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:01:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.05_summits.bed INFO @ Mon, 12 Aug 2019 19:01:48: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4191 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:01:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:01:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:01:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.10_summits.bed INFO @ Mon, 12 Aug 2019 19:01:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2956 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:01:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467179/SRX467179.20_summits.bed INFO @ Mon, 12 Aug 2019 19:02:05: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1802 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。