Job ID = 1293173 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,679,782 reads read : 20,679,782 reads written : 20,679,782 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: 00:04:20 20679782 reads; of these: 20679782 (100.00%) were unpaired; of these: 2349545 (11.36%) aligned 0 times 17126118 (82.82%) aligned exactly 1 time 1204119 (5.82%) aligned >1 times 88.64% overall alignment rate Time searching: 00:04:20 Overall time: 00:04:20 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] 13147078 / 18330237 = 0.7172 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 22:25:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.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 22:25:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:25:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:25:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.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 22:25:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:25:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:25:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.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 22:25:49: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:25:49: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:25:57: 1000000 INFO @ Sun, 02 Jun 2019 22:25:59: 1000000 INFO @ Sun, 02 Jun 2019 22:26:00: 1000000 INFO @ Sun, 02 Jun 2019 22:26:04: 2000000 INFO @ Sun, 02 Jun 2019 22:26:08: 2000000 INFO @ Sun, 02 Jun 2019 22:26:10: 2000000 INFO @ Sun, 02 Jun 2019 22:26:11: 3000000 INFO @ Sun, 02 Jun 2019 22:26:18: 3000000 INFO @ Sun, 02 Jun 2019 22:26:19: 4000000 INFO @ Sun, 02 Jun 2019 22:26:19: 3000000 INFO @ Sun, 02 Jun 2019 22:26:26: 5000000 INFO @ Sun, 02 Jun 2019 22:26:27: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:27: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:27: #1 total tags in treatment: 5183159 INFO @ Sun, 02 Jun 2019 22:26:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:27: #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 22:26:27: #1 tags after filtering in treatment: 5183159 INFO @ Sun, 02 Jun 2019 22:26:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:27: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:27: 4000000 INFO @ Sun, 02 Jun 2019 22:26:28: #2 number of paired peaks: 7009 INFO @ Sun, 02 Jun 2019 22:26:28: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:29: 4000000 INFO @ Sun, 02 Jun 2019 22:26:29: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:29: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:29: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:29: #2 predicted fragment length is 171 bps INFO @ Sun, 02 Jun 2019 22:26:29: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 02 Jun 2019 22:26:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.20_model.r INFO @ Sun, 02 Jun 2019 22:26:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:37: 5000000 INFO @ Sun, 02 Jun 2019 22:26:38: 5000000 INFO @ Sun, 02 Jun 2019 22:26:39: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:39: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:39: #1 total tags in treatment: 5183159 INFO @ Sun, 02 Jun 2019 22:26:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:39: #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 22:26:39: #1 tags after filtering in treatment: 5183159 INFO @ Sun, 02 Jun 2019 22:26:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:39: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:40: #1 total tags in treatment: 5183159 INFO @ Sun, 02 Jun 2019 22:26:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:40: #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 22:26:40: #1 tags after filtering in treatment: 5183159 INFO @ Sun, 02 Jun 2019 22:26:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:40: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:40: #2 number of paired peaks: 7009 INFO @ Sun, 02 Jun 2019 22:26:40: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:41: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:41: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:41: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:41: #2 predicted fragment length is 171 bps INFO @ Sun, 02 Jun 2019 22:26:41: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 02 Jun 2019 22:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.05_model.r INFO @ Sun, 02 Jun 2019 22:26:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:41: #2 number of paired peaks: 7009 INFO @ Sun, 02 Jun 2019 22:26:41: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:41: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:41: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:41: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:41: #2 predicted fragment length is 171 bps INFO @ Sun, 02 Jun 2019 22:26:41: #2 alternative fragment length(s) may be 171 bps INFO @ Sun, 02 Jun 2019 22:26:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.10_model.r INFO @ Sun, 02 Jun 2019 22:26:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:49: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 22:26:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:26:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:26:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.20_summits.bed INFO @ Sun, 02 Jun 2019 22:26:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (4407 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:27:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:27:01: #3 Call peaks for each chromosome... BigWig に変換しました。 INFO @ Sun, 02 Jun 2019 22:27:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.10_summits.bed INFO @ Sun, 02 Jun 2019 22:27:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (5318 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:27:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402737/SRX5402737.05_summits.bed INFO @ Sun, 02 Jun 2019 22:27:09: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (6313 records, 4 fields): 15 millis CompletedMACS2peakCalling