Job ID = 1293168 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,980,982 reads read : 13,961,964 reads written : 6,980,982 reads 0-length : 6,980,982 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: 00:01:31 6980982 reads; of these: 6980982 (100.00%) were unpaired; of these: 452698 (6.48%) aligned 0 times 5746588 (82.32%) aligned exactly 1 time 781696 (11.20%) aligned >1 times 93.52% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 1903003 / 6528284 = 0.2915 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 22:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.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 22:10:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:10:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.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 22:10:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.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 22:10:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:10:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:10:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:10:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:11:02: 1000000 INFO @ Sun, 02 Jun 2019 22:11:02: 1000000 INFO @ Sun, 02 Jun 2019 22:11:02: 1000000 INFO @ Sun, 02 Jun 2019 22:11:11: 2000000 INFO @ Sun, 02 Jun 2019 22:11:11: 2000000 INFO @ Sun, 02 Jun 2019 22:11:11: 2000000 INFO @ Sun, 02 Jun 2019 22:11:20: 3000000 INFO @ Sun, 02 Jun 2019 22:11:20: 3000000 INFO @ Sun, 02 Jun 2019 22:11:20: 3000000 INFO @ Sun, 02 Jun 2019 22:11:28: 4000000 INFO @ Sun, 02 Jun 2019 22:11:29: 4000000 INFO @ Sun, 02 Jun 2019 22:11:29: 4000000 INFO @ Sun, 02 Jun 2019 22:11:34: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:11:34: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:11:34: #1 total tags in treatment: 4625281 INFO @ Sun, 02 Jun 2019 22:11:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:11:34: #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 22:11:34: #1 tags after filtering in treatment: 4625281 INFO @ Sun, 02 Jun 2019 22:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:11:34: #1 finished! INFO @ Sun, 02 Jun 2019 22:11:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:11:34: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:11:34: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:11:34: #1 total tags in treatment: 4625281 INFO @ Sun, 02 Jun 2019 22:11:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:11:34: #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 22:11:34: #1 tags after filtering in treatment: 4625281 INFO @ Sun, 02 Jun 2019 22:11:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:11:34: #1 finished! INFO @ Sun, 02 Jun 2019 22:11:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:11:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:11:35: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:11:35: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:11:35: #1 total tags in treatment: 4625281 INFO @ Sun, 02 Jun 2019 22:11:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:11:35: #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 22:11:35: #1 tags after filtering in treatment: 4625281 INFO @ Sun, 02 Jun 2019 22:11:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:11:35: #1 finished! INFO @ Sun, 02 Jun 2019 22:11:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:11:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:11:35: #2 number of paired peaks: 4438 INFO @ Sun, 02 Jun 2019 22:11:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:11:35: start X-correlation... INFO @ Sun, 02 Jun 2019 22:11:35: #2 number of paired peaks: 4438 INFO @ Sun, 02 Jun 2019 22:11:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:11:35: end of X-cor INFO @ Sun, 02 Jun 2019 22:11:35: #2 finished! INFO @ Sun, 02 Jun 2019 22:11:35: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 22:11:35: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 02 Jun 2019 22:11:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.10_model.r INFO @ Sun, 02 Jun 2019 22:11:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:11:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:11:35: start X-correlation... INFO @ Sun, 02 Jun 2019 22:11:35: end of X-cor INFO @ Sun, 02 Jun 2019 22:11:35: #2 finished! INFO @ Sun, 02 Jun 2019 22:11:35: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 22:11:35: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 02 Jun 2019 22:11:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.20_model.r INFO @ Sun, 02 Jun 2019 22:11:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:11:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:11:35: #2 number of paired peaks: 4438 INFO @ Sun, 02 Jun 2019 22:11:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:11:35: start X-correlation... INFO @ Sun, 02 Jun 2019 22:11:35: end of X-cor INFO @ Sun, 02 Jun 2019 22:11:35: #2 finished! INFO @ Sun, 02 Jun 2019 22:11:35: #2 predicted fragment length is 160 bps INFO @ Sun, 02 Jun 2019 22:11:35: #2 alternative fragment length(s) may be 160 bps INFO @ Sun, 02 Jun 2019 22:11:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.05_model.r INFO @ Sun, 02 Jun 2019 22:11:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:11:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:11:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:11:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:11:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:11:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:11:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:11:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.20_summits.bed INFO @ Sun, 02 Jun 2019 22:11:57: Done! INFO @ Sun, 02 Jun 2019 22:11:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:11:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:11:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.10_summits.bed INFO @ Sun, 02 Jun 2019 22:11:57: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (3916 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4822 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:11:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:11:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:11:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402733/SRX5402733.05_summits.bed INFO @ Sun, 02 Jun 2019 22:11:58: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5614 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。