Job ID = 1293165 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,353,821 reads read : 24,353,821 reads written : 24,353,821 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:31 24353821 reads; of these: 24353821 (100.00%) were unpaired; of these: 3666007 (15.05%) aligned 0 times 18498605 (75.96%) aligned exactly 1 time 2189209 (8.99%) aligned >1 times 84.95% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 11637023 / 20687814 = 0.5625 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 22:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.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 22:26:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:26:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.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 22:26:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:26:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:26:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.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 22:26:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:26:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:26:27: 1000000 INFO @ Sun, 02 Jun 2019 22:26:28: 1000000 INFO @ Sun, 02 Jun 2019 22:26:29: 1000000 INFO @ Sun, 02 Jun 2019 22:26:35: 2000000 INFO @ Sun, 02 Jun 2019 22:26:38: 2000000 INFO @ Sun, 02 Jun 2019 22:26:39: 2000000 INFO @ Sun, 02 Jun 2019 22:26:44: 3000000 INFO @ Sun, 02 Jun 2019 22:26:47: 3000000 INFO @ Sun, 02 Jun 2019 22:26:50: 3000000 INFO @ Sun, 02 Jun 2019 22:26:53: 4000000 INFO @ Sun, 02 Jun 2019 22:26:57: 4000000 INFO @ Sun, 02 Jun 2019 22:27:01: 4000000 INFO @ Sun, 02 Jun 2019 22:27:01: 5000000 INFO @ Sun, 02 Jun 2019 22:27:06: 5000000 INFO @ Sun, 02 Jun 2019 22:27:10: 6000000 INFO @ Sun, 02 Jun 2019 22:27:12: 5000000 INFO @ Sun, 02 Jun 2019 22:27:16: 6000000 INFO @ Sun, 02 Jun 2019 22:27:18: 7000000 INFO @ Sun, 02 Jun 2019 22:27:23: 6000000 INFO @ Sun, 02 Jun 2019 22:27:26: 7000000 INFO @ Sun, 02 Jun 2019 22:27:27: 8000000 INFO @ Sun, 02 Jun 2019 22:27:35: 7000000 INFO @ Sun, 02 Jun 2019 22:27:35: 8000000 INFO @ Sun, 02 Jun 2019 22:27:36: 9000000 INFO @ Sun, 02 Jun 2019 22:27:36: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:27:36: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:27:36: #1 total tags in treatment: 9050791 INFO @ Sun, 02 Jun 2019 22:27:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:27:36: #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 22:27:37: #1 tags after filtering in treatment: 9050791 INFO @ Sun, 02 Jun 2019 22:27:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:27:37: #1 finished! INFO @ Sun, 02 Jun 2019 22:27:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:27:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:27:38: #2 number of paired peaks: 4885 INFO @ Sun, 02 Jun 2019 22:27:38: start model_add_line... INFO @ Sun, 02 Jun 2019 22:27:38: start X-correlation... INFO @ Sun, 02 Jun 2019 22:27:38: end of X-cor INFO @ Sun, 02 Jun 2019 22:27:38: #2 finished! INFO @ Sun, 02 Jun 2019 22:27:38: #2 predicted fragment length is 189 bps INFO @ Sun, 02 Jun 2019 22:27:38: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 02 Jun 2019 22:27:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.10_model.r INFO @ Sun, 02 Jun 2019 22:27:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:27:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:27:44: 9000000 INFO @ Sun, 02 Jun 2019 22:27:45: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:27:45: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:27:45: #1 total tags in treatment: 9050791 INFO @ Sun, 02 Jun 2019 22:27:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:27:45: #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 22:27:45: #1 tags after filtering in treatment: 9050791 INFO @ Sun, 02 Jun 2019 22:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:27:45: #1 finished! INFO @ Sun, 02 Jun 2019 22:27:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:27:45: 8000000 INFO @ Sun, 02 Jun 2019 22:27:46: #2 number of paired peaks: 4885 INFO @ Sun, 02 Jun 2019 22:27:46: start model_add_line... INFO @ Sun, 02 Jun 2019 22:27:46: start X-correlation... INFO @ Sun, 02 Jun 2019 22:27:46: end of X-cor INFO @ Sun, 02 Jun 2019 22:27:46: #2 finished! INFO @ Sun, 02 Jun 2019 22:27:46: #2 predicted fragment length is 189 bps INFO @ Sun, 02 Jun 2019 22:27:46: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 02 Jun 2019 22:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.20_model.r INFO @ Sun, 02 Jun 2019 22:27:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:27:55: 9000000 INFO @ Sun, 02 Jun 2019 22:27:56: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:27:56: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:27:56: #1 total tags in treatment: 9050791 INFO @ Sun, 02 Jun 2019 22:27:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:27:56: #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 22:27:56: #1 tags after filtering in treatment: 9050791 INFO @ Sun, 02 Jun 2019 22:27:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:27:56: #1 finished! INFO @ Sun, 02 Jun 2019 22:27:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:27:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:27:57: #2 number of paired peaks: 4885 INFO @ Sun, 02 Jun 2019 22:27:57: start model_add_line... INFO @ Sun, 02 Jun 2019 22:27:58: start X-correlation... INFO @ Sun, 02 Jun 2019 22:27:58: end of X-cor INFO @ Sun, 02 Jun 2019 22:27:58: #2 finished! INFO @ Sun, 02 Jun 2019 22:27:58: #2 predicted fragment length is 189 bps INFO @ Sun, 02 Jun 2019 22:27:58: #2 alternative fragment length(s) may be 189 bps INFO @ Sun, 02 Jun 2019 22:27:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.05_model.r INFO @ Sun, 02 Jun 2019 22:27:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:27:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:28:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:28:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:28:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:28:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:28:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.10_summits.bed INFO @ Sun, 02 Jun 2019 22:28:24: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5343 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:28:29: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.20_summits.bed INFO @ Sun, 02 Jun 2019 22:28:32: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4298 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:28:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:28:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:28:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402730/SRX5402730.05_summits.bed INFO @ Sun, 02 Jun 2019 22:28:43: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6607 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。