Job ID = 2589193 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,463,996 reads read : 3,463,996 reads written : 3,463,996 spots read : 3,517,937 reads read : 3,517,937 reads written : 3,517,937 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107581.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107582.sra.cache’: 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: 00:00:44 6981933 reads; of these: 6981933 (100.00%) were unpaired; of these: 4885861 (69.98%) aligned 0 times 1873391 (26.83%) aligned exactly 1 time 222681 (3.19%) aligned >1 times 30.02% overall alignment rate Time searching: 00:00:44 Overall time: 00:00:44 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] 523456 / 2096072 = 0.2497 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 17:08:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.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 17:08:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:08:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:08:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.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 17:08:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:08:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:08:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.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 17:08:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:08:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:08:39: 1000000 INFO @ Mon, 12 Aug 2019 17:08:41: 1000000 INFO @ Mon, 12 Aug 2019 17:08:42: 1000000 INFO @ Mon, 12 Aug 2019 17:08:43: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:08:43: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:08:43: #1 total tags in treatment: 1572616 INFO @ Mon, 12 Aug 2019 17:08:43: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:08:43: #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 17:08:43: #1 tags after filtering in treatment: 1572616 INFO @ Mon, 12 Aug 2019 17:08:43: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:08:43: #1 finished! INFO @ Mon, 12 Aug 2019 17:08:43: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:08:43: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:08:43: #2 number of paired peaks: 1774 INFO @ Mon, 12 Aug 2019 17:08:43: start model_add_line... INFO @ Mon, 12 Aug 2019 17:08:43: start X-correlation... INFO @ Mon, 12 Aug 2019 17:08:43: end of X-cor INFO @ Mon, 12 Aug 2019 17:08:43: #2 finished! INFO @ Mon, 12 Aug 2019 17:08:43: #2 predicted fragment length is 145 bps INFO @ Mon, 12 Aug 2019 17:08:43: #2 alternative fragment length(s) may be 145 bps INFO @ Mon, 12 Aug 2019 17:08:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.05_model.r INFO @ Mon, 12 Aug 2019 17:08:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:08:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:08:45: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:08:45: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:08:45: #1 total tags in treatment: 1572616 INFO @ Mon, 12 Aug 2019 17:08:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:08:45: #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 17:08:45: #1 tags after filtering in treatment: 1572616 INFO @ Mon, 12 Aug 2019 17:08:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:08:45: #1 finished! INFO @ Mon, 12 Aug 2019 17:08:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:08:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:08:45: #2 number of paired peaks: 1774 INFO @ Mon, 12 Aug 2019 17:08:45: start model_add_line... INFO @ Mon, 12 Aug 2019 17:08:45: start X-correlation... INFO @ Mon, 12 Aug 2019 17:08:45: end of X-cor INFO @ Mon, 12 Aug 2019 17:08:45: #2 finished! INFO @ Mon, 12 Aug 2019 17:08:45: #2 predicted fragment length is 145 bps INFO @ Mon, 12 Aug 2019 17:08:45: #2 alternative fragment length(s) may be 145 bps INFO @ Mon, 12 Aug 2019 17:08:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.20_model.r INFO @ Mon, 12 Aug 2019 17:08:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:08:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:08:47: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:08:47: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:08:47: #1 total tags in treatment: 1572616 INFO @ Mon, 12 Aug 2019 17:08:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:08:47: #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 17:08:47: #1 tags after filtering in treatment: 1572616 INFO @ Mon, 12 Aug 2019 17:08:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:08:47: #1 finished! INFO @ Mon, 12 Aug 2019 17:08:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:08:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:08:47: #2 number of paired peaks: 1774 INFO @ Mon, 12 Aug 2019 17:08:47: start model_add_line... INFO @ Mon, 12 Aug 2019 17:08:47: start X-correlation... INFO @ Mon, 12 Aug 2019 17:08:47: end of X-cor INFO @ Mon, 12 Aug 2019 17:08:47: #2 finished! INFO @ Mon, 12 Aug 2019 17:08:47: #2 predicted fragment length is 145 bps INFO @ Mon, 12 Aug 2019 17:08:47: #2 alternative fragment length(s) may be 145 bps INFO @ Mon, 12 Aug 2019 17:08:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.10_model.r INFO @ Mon, 12 Aug 2019 17:08:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:08:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:08:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:08:50: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:08:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:08:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:08:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.05_summits.bed INFO @ Mon, 12 Aug 2019 17:08:50: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3337 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:08:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:08:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:08:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:08:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.20_summits.bed INFO @ Mon, 12 Aug 2019 17:08:53: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (191 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:08:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:08:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:08:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX044000/SRX044000.10_summits.bed INFO @ Mon, 12 Aug 2019 17:08:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1324 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。