Job ID = 1293192 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,026,804 reads read : 25,026,804 reads written : 25,026,804 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: 00:08:02 25026804 reads; of these: 25026804 (100.00%) were unpaired; of these: 4239925 (16.94%) aligned 0 times 10917911 (43.62%) aligned exactly 1 time 9868968 (39.43%) aligned >1 times 83.06% overall alignment rate Time searching: 00:08:02 Overall time: 00:08:02 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] 9697595 / 20786879 = 0.4665 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 22:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.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 22:33:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:33:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.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 22:33:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:33:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:33:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.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 22:33:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:33:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:33:45: 1000000 INFO @ Sun, 02 Jun 2019 22:33:48: 1000000 INFO @ Sun, 02 Jun 2019 22:33:48: 1000000 INFO @ Sun, 02 Jun 2019 22:33:52: 2000000 INFO @ Sun, 02 Jun 2019 22:33:59: 2000000 INFO @ Sun, 02 Jun 2019 22:33:59: 2000000 INFO @ Sun, 02 Jun 2019 22:33:59: 3000000 INFO @ Sun, 02 Jun 2019 22:34:06: 4000000 INFO @ Sun, 02 Jun 2019 22:34:09: 3000000 INFO @ Sun, 02 Jun 2019 22:34:09: 3000000 INFO @ Sun, 02 Jun 2019 22:34:14: 5000000 INFO @ Sun, 02 Jun 2019 22:34:19: 4000000 INFO @ Sun, 02 Jun 2019 22:34:19: 4000000 INFO @ Sun, 02 Jun 2019 22:34:21: 6000000 INFO @ Sun, 02 Jun 2019 22:34:28: 7000000 INFO @ Sun, 02 Jun 2019 22:34:29: 5000000 INFO @ Sun, 02 Jun 2019 22:34:29: 5000000 INFO @ Sun, 02 Jun 2019 22:34:36: 8000000 INFO @ Sun, 02 Jun 2019 22:34:39: 6000000 INFO @ Sun, 02 Jun 2019 22:34:40: 6000000 INFO @ Sun, 02 Jun 2019 22:34:43: 9000000 INFO @ Sun, 02 Jun 2019 22:34:49: 7000000 INFO @ Sun, 02 Jun 2019 22:34:51: 7000000 INFO @ Sun, 02 Jun 2019 22:34:51: 10000000 INFO @ Sun, 02 Jun 2019 22:34:58: 11000000 INFO @ Sun, 02 Jun 2019 22:34:59: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:34:59: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:34:59: #1 total tags in treatment: 11089284 INFO @ Sun, 02 Jun 2019 22:34:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:34:59: #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 22:34:59: 8000000 INFO @ Sun, 02 Jun 2019 22:34:59: #1 tags after filtering in treatment: 11089284 INFO @ Sun, 02 Jun 2019 22:34:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:34:59: #1 finished! INFO @ Sun, 02 Jun 2019 22:34:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:34:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:35:01: #2 number of paired peaks: 3504 INFO @ Sun, 02 Jun 2019 22:35:01: start model_add_line... INFO @ Sun, 02 Jun 2019 22:35:01: 8000000 INFO @ Sun, 02 Jun 2019 22:35:01: start X-correlation... INFO @ Sun, 02 Jun 2019 22:35:01: end of X-cor INFO @ Sun, 02 Jun 2019 22:35:01: #2 finished! INFO @ Sun, 02 Jun 2019 22:35:01: #2 predicted fragment length is 109 bps INFO @ Sun, 02 Jun 2019 22:35:01: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 02 Jun 2019 22:35:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.20_model.r INFO @ Sun, 02 Jun 2019 22:35:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:35:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:35:09: 9000000 INFO @ Sun, 02 Jun 2019 22:35:12: 9000000 INFO @ Sun, 02 Jun 2019 22:35:20: 10000000 INFO @ Sun, 02 Jun 2019 22:35:24: 10000000 INFO @ Sun, 02 Jun 2019 22:35:31: 11000000 INFO @ Sun, 02 Jun 2019 22:35:31: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:35:31: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:35:31: #1 total tags in treatment: 11089284 INFO @ Sun, 02 Jun 2019 22:35:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:35:31: #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 22:35:32: #1 tags after filtering in treatment: 11089284 INFO @ Sun, 02 Jun 2019 22:35:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:35:32: #1 finished! INFO @ Sun, 02 Jun 2019 22:35:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:35:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:35:33: #2 number of paired peaks: 3504 INFO @ Sun, 02 Jun 2019 22:35:33: start model_add_line... INFO @ Sun, 02 Jun 2019 22:35:33: start X-correlation... INFO @ Sun, 02 Jun 2019 22:35:33: end of X-cor INFO @ Sun, 02 Jun 2019 22:35:33: #2 finished! INFO @ Sun, 02 Jun 2019 22:35:33: #2 predicted fragment length is 109 bps INFO @ Sun, 02 Jun 2019 22:35:33: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 02 Jun 2019 22:35:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.05_model.r INFO @ Sun, 02 Jun 2019 22:35:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:35:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:35:35: 11000000 INFO @ Sun, 02 Jun 2019 22:35:36: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:35:36: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:35:36: #1 total tags in treatment: 11089284 INFO @ Sun, 02 Jun 2019 22:35:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:35:36: #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 22:35:36: #1 tags after filtering in treatment: 11089284 INFO @ Sun, 02 Jun 2019 22:35:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:35:36: #1 finished! INFO @ Sun, 02 Jun 2019 22:35:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:35:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:35:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:35:37: #2 number of paired peaks: 3504 INFO @ Sun, 02 Jun 2019 22:35:37: start model_add_line... INFO @ Sun, 02 Jun 2019 22:35:38: start X-correlation... INFO @ Sun, 02 Jun 2019 22:35:38: end of X-cor INFO @ Sun, 02 Jun 2019 22:35:38: #2 finished! INFO @ Sun, 02 Jun 2019 22:35:38: #2 predicted fragment length is 109 bps INFO @ Sun, 02 Jun 2019 22:35:38: #2 alternative fragment length(s) may be 109 bps INFO @ Sun, 02 Jun 2019 22:35:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.10_model.r INFO @ Sun, 02 Jun 2019 22:35:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:35:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:35:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:35:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:35:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.20_summits.bed INFO @ Sun, 02 Jun 2019 22:35:50: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3698 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:36:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:36:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:36:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:36:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:36:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.05_summits.bed INFO @ Sun, 02 Jun 2019 22:36:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (9425 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:36:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:36:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:36:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402749/SRX5402749.10_summits.bed INFO @ Sun, 02 Jun 2019 22:36:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6667 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。