Job ID = 1293175 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,227,271 reads read : 16,454,542 reads written : 8,227,271 reads 0-length : 8,227,271 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: 00:02:03 8227271 reads; of these: 8227271 (100.00%) were unpaired; of these: 121937 (1.48%) aligned 0 times 7305932 (88.80%) aligned exactly 1 time 799402 (9.72%) aligned >1 times 98.52% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 5881420 / 8105334 = 0.7256 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 22:12:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.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 22:12:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:12:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:12:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.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 22:12:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:12:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:12:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.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 22:12:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:12:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:12:52: 1000000 INFO @ Sun, 02 Jun 2019 22:12:54: 1000000 INFO @ Sun, 02 Jun 2019 22:12:54: 1000000 INFO @ Sun, 02 Jun 2019 22:12:59: 2000000 INFO @ Sun, 02 Jun 2019 22:13:01: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:13:01: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:13:01: #1 total tags in treatment: 2223914 INFO @ Sun, 02 Jun 2019 22:13:01: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:13:01: #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 22:13:01: #1 tags after filtering in treatment: 2223914 INFO @ Sun, 02 Jun 2019 22:13:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:13:01: #1 finished! INFO @ Sun, 02 Jun 2019 22:13:01: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:13:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:13:02: #2 number of paired peaks: 5308 INFO @ Sun, 02 Jun 2019 22:13:02: start model_add_line... INFO @ Sun, 02 Jun 2019 22:13:02: start X-correlation... INFO @ Sun, 02 Jun 2019 22:13:02: end of X-cor INFO @ Sun, 02 Jun 2019 22:13:02: #2 finished! INFO @ Sun, 02 Jun 2019 22:13:02: #2 predicted fragment length is 179 bps INFO @ Sun, 02 Jun 2019 22:13:02: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 02 Jun 2019 22:13:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.05_model.r INFO @ Sun, 02 Jun 2019 22:13:02: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:13:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:13:03: 2000000 INFO @ Sun, 02 Jun 2019 22:13:04: 2000000 INFO @ Sun, 02 Jun 2019 22:13:04: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:13:04: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:13:04: #1 total tags in treatment: 2223914 INFO @ Sun, 02 Jun 2019 22:13:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:13:04: #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 22:13:04: #1 tags after filtering in treatment: 2223914 INFO @ Sun, 02 Jun 2019 22:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:13:04: #1 finished! INFO @ Sun, 02 Jun 2019 22:13:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:13:05: #2 number of paired peaks: 5308 INFO @ Sun, 02 Jun 2019 22:13:05: start model_add_line... INFO @ Sun, 02 Jun 2019 22:13:05: start X-correlation... INFO @ Sun, 02 Jun 2019 22:13:05: end of X-cor INFO @ Sun, 02 Jun 2019 22:13:05: #2 finished! INFO @ Sun, 02 Jun 2019 22:13:05: #2 predicted fragment length is 179 bps INFO @ Sun, 02 Jun 2019 22:13:05: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 02 Jun 2019 22:13:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.20_model.r INFO @ Sun, 02 Jun 2019 22:13:05: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:13:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:13:06: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:13:06: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:13:06: #1 total tags in treatment: 2223914 INFO @ Sun, 02 Jun 2019 22:13:06: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:13:06: #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 22:13:06: #1 tags after filtering in treatment: 2223914 INFO @ Sun, 02 Jun 2019 22:13:06: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:13:06: #1 finished! INFO @ Sun, 02 Jun 2019 22:13:06: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:13:06: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:13:07: #2 number of paired peaks: 5308 INFO @ Sun, 02 Jun 2019 22:13:07: start model_add_line... INFO @ Sun, 02 Jun 2019 22:13:07: start X-correlation... INFO @ Sun, 02 Jun 2019 22:13:07: end of X-cor INFO @ Sun, 02 Jun 2019 22:13:07: #2 finished! INFO @ Sun, 02 Jun 2019 22:13:07: #2 predicted fragment length is 179 bps INFO @ Sun, 02 Jun 2019 22:13:07: #2 alternative fragment length(s) may be 179 bps INFO @ Sun, 02 Jun 2019 22:13:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.10_model.r INFO @ Sun, 02 Jun 2019 22:13:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:13:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:13:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:13:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:13:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:13:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.05_summits.bed INFO @ Sun, 02 Jun 2019 22:13:13: Done! INFO @ Sun, 02 Jun 2019 22:13:13: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4854 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:13:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:13:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:13:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:13:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.20_summits.bed INFO @ Sun, 02 Jun 2019 22:13:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2983 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 22:13:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:13:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:13:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402738/SRX5402738.10_summits.bed INFO @ Sun, 02 Jun 2019 22:13:19: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3835 records, 4 fields): 7 millis CompletedMACS2peakCalling BigWig に変換しました。