Job ID = 1291792 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,950,927 reads read : 35,901,854 reads written : 17,950,927 reads 0-length : 17,950,927 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: 00:05:40 17950927 reads; of these: 17950927 (100.00%) were unpaired; of these: 6211245 (34.60%) aligned 0 times 9416573 (52.46%) aligned exactly 1 time 2323109 (12.94%) aligned >1 times 65.40% overall alignment rate Time searching: 00:05:40 Overall time: 00:05:40 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 8 files... [bam_rmdupse_core] 4445081 / 11739682 = 0.3786 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 16:43:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.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 16:43:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:43:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:43:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.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 16:43:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:43:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:43:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.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 16:43:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:43:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:43:51: 1000000 INFO @ Sun, 02 Jun 2019 16:43:53: 1000000 INFO @ Sun, 02 Jun 2019 16:43:54: 1000000 INFO @ Sun, 02 Jun 2019 16:43:58: 2000000 INFO @ Sun, 02 Jun 2019 16:44:01: 2000000 INFO @ Sun, 02 Jun 2019 16:44:04: 2000000 INFO @ Sun, 02 Jun 2019 16:44:05: 3000000 INFO @ Sun, 02 Jun 2019 16:44:10: 3000000 INFO @ Sun, 02 Jun 2019 16:44:12: 4000000 INFO @ Sun, 02 Jun 2019 16:44:13: 3000000 INFO @ Sun, 02 Jun 2019 16:44:19: 4000000 INFO @ Sun, 02 Jun 2019 16:44:19: 5000000 INFO @ Sun, 02 Jun 2019 16:44:23: 4000000 INFO @ Sun, 02 Jun 2019 16:44:26: 6000000 INFO @ Sun, 02 Jun 2019 16:44:27: 5000000 INFO @ Sun, 02 Jun 2019 16:44:32: 5000000 INFO @ Sun, 02 Jun 2019 16:44:32: 7000000 INFO @ Sun, 02 Jun 2019 16:44:34: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:44:34: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:44:34: #1 total tags in treatment: 7294601 INFO @ Sun, 02 Jun 2019 16:44:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:44:34: #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 16:44:35: #1 tags after filtering in treatment: 7294601 INFO @ Sun, 02 Jun 2019 16:44:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:44:35: #1 finished! INFO @ Sun, 02 Jun 2019 16:44:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:44:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:44:35: #2 number of paired peaks: 1061 INFO @ Sun, 02 Jun 2019 16:44:35: start model_add_line... INFO @ Sun, 02 Jun 2019 16:44:35: start X-correlation... INFO @ Sun, 02 Jun 2019 16:44:35: 6000000 INFO @ Sun, 02 Jun 2019 16:44:35: end of X-cor INFO @ Sun, 02 Jun 2019 16:44:35: #2 finished! INFO @ Sun, 02 Jun 2019 16:44:35: #2 predicted fragment length is 181 bps INFO @ Sun, 02 Jun 2019 16:44:35: #2 alternative fragment length(s) may be 4,181 bps INFO @ Sun, 02 Jun 2019 16:44:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.05_model.r INFO @ Sun, 02 Jun 2019 16:44:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:44:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:44:41: 6000000 INFO @ Sun, 02 Jun 2019 16:44:44: 7000000 INFO @ Sun, 02 Jun 2019 16:44:46: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:44:46: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:44:46: #1 total tags in treatment: 7294601 INFO @ Sun, 02 Jun 2019 16:44:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:44:46: #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 16:44:46: #1 tags after filtering in treatment: 7294601 INFO @ Sun, 02 Jun 2019 16:44:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:44:46: #1 finished! INFO @ Sun, 02 Jun 2019 16:44:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:44:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:44:47: #2 number of paired peaks: 1061 INFO @ Sun, 02 Jun 2019 16:44:47: start model_add_line... INFO @ Sun, 02 Jun 2019 16:44:47: start X-correlation... INFO @ Sun, 02 Jun 2019 16:44:47: end of X-cor INFO @ Sun, 02 Jun 2019 16:44:47: #2 finished! INFO @ Sun, 02 Jun 2019 16:44:47: #2 predicted fragment length is 181 bps INFO @ Sun, 02 Jun 2019 16:44:47: #2 alternative fragment length(s) may be 4,181 bps INFO @ Sun, 02 Jun 2019 16:44:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.10_model.r INFO @ Sun, 02 Jun 2019 16:44:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:44:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:44:49: 7000000 INFO @ Sun, 02 Jun 2019 16:44:52: #1 tag size is determined as 75 bps INFO @ Sun, 02 Jun 2019 16:44:52: #1 tag size = 75 INFO @ Sun, 02 Jun 2019 16:44:52: #1 total tags in treatment: 7294601 INFO @ Sun, 02 Jun 2019 16:44:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:44:52: #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 16:44:52: #1 tags after filtering in treatment: 7294601 INFO @ Sun, 02 Jun 2019 16:44:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:44:52: #1 finished! INFO @ Sun, 02 Jun 2019 16:44:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:44:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:44:53: #2 number of paired peaks: 1061 INFO @ Sun, 02 Jun 2019 16:44:53: start model_add_line... INFO @ Sun, 02 Jun 2019 16:44:53: start X-correlation... INFO @ Sun, 02 Jun 2019 16:44:53: end of X-cor INFO @ Sun, 02 Jun 2019 16:44:53: #2 finished! INFO @ Sun, 02 Jun 2019 16:44:53: #2 predicted fragment length is 181 bps INFO @ Sun, 02 Jun 2019 16:44:53: #2 alternative fragment length(s) may be 4,181 bps INFO @ Sun, 02 Jun 2019 16:44:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.20_model.r INFO @ Sun, 02 Jun 2019 16:44:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:44:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:44:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:45:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:45:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:45:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.05_summits.bed INFO @ Sun, 02 Jun 2019 16:45:10: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1393 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:45:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:45:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:45:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:45:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:45:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.10_summits.bed INFO @ Sun, 02 Jun 2019 16:45:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (945 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:45:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:45:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:45:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX2543060/SRX2543060.20_summits.bed INFO @ Sun, 02 Jun 2019 16:45:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (572 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。