Job ID = 1291669 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 53,147,964 reads read : 53,147,964 reads written : 53,147,964 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:08:09 53147964 reads; of these: 53147964 (100.00%) were unpaired; of these: 32409269 (60.98%) aligned 0 times 17106108 (32.19%) aligned exactly 1 time 3632587 (6.83%) aligned >1 times 39.02% overall alignment rate Time searching: 00:08:09 Overall time: 00:08:09 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 12 files... [bam_rmdupse_core] 10701288 / 20738695 = 0.5160 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 @ Sun, 02 Jun 2019 16:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.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 @ Sun, 02 Jun 2019 16:29:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:29:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.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 @ Sun, 02 Jun 2019 16:29:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:29:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:29:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.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 @ Sun, 02 Jun 2019 16:29:56: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:29:56: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:30:05: 1000000 INFO @ Sun, 02 Jun 2019 16:30:05: 1000000 INFO @ Sun, 02 Jun 2019 16:30:05: 1000000 INFO @ Sun, 02 Jun 2019 16:30:14: 2000000 INFO @ Sun, 02 Jun 2019 16:30:14: 2000000 INFO @ Sun, 02 Jun 2019 16:30:14: 2000000 INFO @ Sun, 02 Jun 2019 16:30:23: 3000000 INFO @ Sun, 02 Jun 2019 16:30:23: 3000000 INFO @ Sun, 02 Jun 2019 16:30:24: 3000000 INFO @ Sun, 02 Jun 2019 16:30:31: 4000000 INFO @ Sun, 02 Jun 2019 16:30:31: 4000000 INFO @ Sun, 02 Jun 2019 16:30:32: 4000000 INFO @ Sun, 02 Jun 2019 16:30:39: 5000000 INFO @ Sun, 02 Jun 2019 16:30:39: 5000000 INFO @ Sun, 02 Jun 2019 16:30:41: 5000000 INFO @ Sun, 02 Jun 2019 16:30:46: 6000000 INFO @ Sun, 02 Jun 2019 16:30:47: 6000000 INFO @ Sun, 02 Jun 2019 16:30:50: 6000000 INFO @ Sun, 02 Jun 2019 16:30:54: 7000000 INFO @ Sun, 02 Jun 2019 16:30:54: 7000000 INFO @ Sun, 02 Jun 2019 16:30:58: 7000000 INFO @ Sun, 02 Jun 2019 16:31:02: 8000000 INFO @ Sun, 02 Jun 2019 16:31:02: 8000000 INFO @ Sun, 02 Jun 2019 16:31:07: 8000000 INFO @ Sun, 02 Jun 2019 16:31:10: 9000000 INFO @ Sun, 02 Jun 2019 16:31:10: 9000000 INFO @ Sun, 02 Jun 2019 16:31:15: 9000000 INFO @ Sun, 02 Jun 2019 16:31:18: 10000000 INFO @ Sun, 02 Jun 2019 16:31:18: 10000000 INFO @ Sun, 02 Jun 2019 16:31:18: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:31:18: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:31:18: #1 total tags in treatment: 10037407 INFO @ Sun, 02 Jun 2019 16:31:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:31:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:31:18: #1 tags after filtering in treatment: 10037407 INFO @ Sun, 02 Jun 2019 16:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:31:18: #1 finished! INFO @ Sun, 02 Jun 2019 16:31:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:31:18: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:31:18: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:31:18: #1 total tags in treatment: 10037407 INFO @ Sun, 02 Jun 2019 16:31:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:31:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:31:18: #1 tags after filtering in treatment: 10037407 INFO @ Sun, 02 Jun 2019 16:31:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:31:18: #1 finished! INFO @ Sun, 02 Jun 2019 16:31:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:31:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:31:19: #2 number of paired peaks: 3218 INFO @ Sun, 02 Jun 2019 16:31:19: start model_add_line... INFO @ Sun, 02 Jun 2019 16:31:20: start X-correlation... INFO @ Sun, 02 Jun 2019 16:31:20: end of X-cor INFO @ Sun, 02 Jun 2019 16:31:20: #2 finished! INFO @ Sun, 02 Jun 2019 16:31:20: #2 predicted fragment length is 406 bps INFO @ Sun, 02 Jun 2019 16:31:20: #2 alternative fragment length(s) may be 406 bps INFO @ Sun, 02 Jun 2019 16:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.05_model.r INFO @ Sun, 02 Jun 2019 16:31:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:31:20: #2 number of paired peaks: 3218 INFO @ Sun, 02 Jun 2019 16:31:20: start model_add_line... INFO @ Sun, 02 Jun 2019 16:31:20: start X-correlation... INFO @ Sun, 02 Jun 2019 16:31:20: end of X-cor INFO @ Sun, 02 Jun 2019 16:31:20: #2 finished! INFO @ Sun, 02 Jun 2019 16:31:20: #2 predicted fragment length is 406 bps INFO @ Sun, 02 Jun 2019 16:31:20: #2 alternative fragment length(s) may be 406 bps INFO @ Sun, 02 Jun 2019 16:31:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.10_model.r INFO @ Sun, 02 Jun 2019 16:31:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:31:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:31:24: 10000000 INFO @ Sun, 02 Jun 2019 16:31:24: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:31:24: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:31:24: #1 total tags in treatment: 10037407 INFO @ Sun, 02 Jun 2019 16:31:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:31:24: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 16:31:24: #1 tags after filtering in treatment: 10037407 INFO @ Sun, 02 Jun 2019 16:31:24: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:31:24: #1 finished! INFO @ Sun, 02 Jun 2019 16:31:24: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:31:24: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:31:26: #2 number of paired peaks: 3218 INFO @ Sun, 02 Jun 2019 16:31:26: start model_add_line... INFO @ Sun, 02 Jun 2019 16:31:26: start X-correlation... INFO @ Sun, 02 Jun 2019 16:31:26: end of X-cor INFO @ Sun, 02 Jun 2019 16:31:26: #2 finished! INFO @ Sun, 02 Jun 2019 16:31:26: #2 predicted fragment length is 406 bps INFO @ Sun, 02 Jun 2019 16:31:26: #2 alternative fragment length(s) may be 406 bps INFO @ Sun, 02 Jun 2019 16:31:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.20_model.r INFO @ Sun, 02 Jun 2019 16:31:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:31:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:32:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:32:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:32:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:32:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:32:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.10_summits.bed INFO @ Sun, 02 Jun 2019 16:32:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.05_summits.bed INFO @ Sun, 02 Jun 2019 16:32:22: Done! INFO @ Sun, 02 Jun 2019 16:32:22: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5115 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6312 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:32:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:32:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:32:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769997/SRX1769997.20_summits.bed INFO @ Sun, 02 Jun 2019 16:32:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3850 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。