Job ID = 1293158 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,857,285 reads read : 23,857,285 reads written : 23,857,285 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: 00:05:32 23857285 reads; of these: 23857285 (100.00%) were unpaired; of these: 2659132 (11.15%) aligned 0 times 18262851 (76.55%) aligned exactly 1 time 2935302 (12.30%) aligned >1 times 88.85% overall alignment rate Time searching: 00:05:32 Overall time: 00:05:32 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] 7655197 / 21198153 = 0.3611 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 22:24:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.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 22:24:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:24:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:24:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.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 22:24:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:24:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:24:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.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 22:24:27: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:24:27: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:24:35: 1000000 INFO @ Sun, 02 Jun 2019 22:24:35: 1000000 INFO @ Sun, 02 Jun 2019 22:24:35: 1000000 INFO @ Sun, 02 Jun 2019 22:24:43: 2000000 INFO @ Sun, 02 Jun 2019 22:24:44: 2000000 INFO @ Sun, 02 Jun 2019 22:24:44: 2000000 INFO @ Sun, 02 Jun 2019 22:24:51: 3000000 INFO @ Sun, 02 Jun 2019 22:24:52: 3000000 INFO @ Sun, 02 Jun 2019 22:24:52: 3000000 INFO @ Sun, 02 Jun 2019 22:24:59: 4000000 INFO @ Sun, 02 Jun 2019 22:25:01: 4000000 INFO @ Sun, 02 Jun 2019 22:25:01: 4000000 INFO @ Sun, 02 Jun 2019 22:25:06: 5000000 INFO @ Sun, 02 Jun 2019 22:25:09: 5000000 INFO @ Sun, 02 Jun 2019 22:25:09: 5000000 INFO @ Sun, 02 Jun 2019 22:25:14: 6000000 INFO @ Sun, 02 Jun 2019 22:25:18: 6000000 INFO @ Sun, 02 Jun 2019 22:25:18: 6000000 INFO @ Sun, 02 Jun 2019 22:25:22: 7000000 INFO @ Sun, 02 Jun 2019 22:25:26: 7000000 INFO @ Sun, 02 Jun 2019 22:25:27: 7000000 INFO @ Sun, 02 Jun 2019 22:25:29: 8000000 INFO @ Sun, 02 Jun 2019 22:25:34: 8000000 INFO @ Sun, 02 Jun 2019 22:25:35: 8000000 INFO @ Sun, 02 Jun 2019 22:25:37: 9000000 INFO @ Sun, 02 Jun 2019 22:25:42: 9000000 INFO @ Sun, 02 Jun 2019 22:25:42: 9000000 INFO @ Sun, 02 Jun 2019 22:25:44: 10000000 INFO @ Sun, 02 Jun 2019 22:25:49: 10000000 INFO @ Sun, 02 Jun 2019 22:25:50: 10000000 INFO @ Sun, 02 Jun 2019 22:25:52: 11000000 INFO @ Sun, 02 Jun 2019 22:25:57: 11000000 INFO @ Sun, 02 Jun 2019 22:25:58: 11000000 INFO @ Sun, 02 Jun 2019 22:26:00: 12000000 INFO @ Sun, 02 Jun 2019 22:26:06: 12000000 INFO @ Sun, 02 Jun 2019 22:26:06: 12000000 INFO @ Sun, 02 Jun 2019 22:26:07: 13000000 INFO @ Sun, 02 Jun 2019 22:26:12: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:12: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:12: #1 total tags in treatment: 13542956 INFO @ Sun, 02 Jun 2019 22:26:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:12: #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 22:26:12: #1 tags after filtering in treatment: 13542956 INFO @ Sun, 02 Jun 2019 22:26:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:12: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:14: #2 number of paired peaks: 2568 INFO @ Sun, 02 Jun 2019 22:26:14: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:14: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:14: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:14: #2 predicted fragment length is 186 bps INFO @ Sun, 02 Jun 2019 22:26:14: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 02 Jun 2019 22:26:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.20_model.r INFO @ Sun, 02 Jun 2019 22:26:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:14: 13000000 INFO @ Sun, 02 Jun 2019 22:26:15: 13000000 INFO @ Sun, 02 Jun 2019 22:26:19: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:19: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:19: #1 total tags in treatment: 13542956 INFO @ Sun, 02 Jun 2019 22:26:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:19: #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 22:26:19: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:26:19: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:26:19: #1 total tags in treatment: 13542956 INFO @ Sun, 02 Jun 2019 22:26:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:26:19: #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 22:26:19: #1 tags after filtering in treatment: 13542956 INFO @ Sun, 02 Jun 2019 22:26:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:19: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:20: #1 tags after filtering in treatment: 13542956 INFO @ Sun, 02 Jun 2019 22:26:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:26:20: #1 finished! INFO @ Sun, 02 Jun 2019 22:26:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:26:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:26:21: #2 number of paired peaks: 2568 INFO @ Sun, 02 Jun 2019 22:26:21: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:21: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:21: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:21: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:21: #2 predicted fragment length is 186 bps INFO @ Sun, 02 Jun 2019 22:26:21: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 02 Jun 2019 22:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.05_model.r INFO @ Sun, 02 Jun 2019 22:26:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:21: #2 number of paired peaks: 2568 INFO @ Sun, 02 Jun 2019 22:26:21: start model_add_line... INFO @ Sun, 02 Jun 2019 22:26:21: start X-correlation... INFO @ Sun, 02 Jun 2019 22:26:21: end of X-cor INFO @ Sun, 02 Jun 2019 22:26:21: #2 finished! INFO @ Sun, 02 Jun 2019 22:26:21: #2 predicted fragment length is 186 bps INFO @ Sun, 02 Jun 2019 22:26:21: #2 alternative fragment length(s) may be 186 bps INFO @ Sun, 02 Jun 2019 22:26:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.10_model.r INFO @ Sun, 02 Jun 2019 22:26:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:26:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:27:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:27:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:27:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.20_summits.bed INFO @ Sun, 02 Jun 2019 22:27:14: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3616 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:27:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:27:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.05_summits.bed INFO @ Sun, 02 Jun 2019 22:27:22: Done! INFO @ Sun, 02 Jun 2019 22:27:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:27:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402724/SRX5402724.10_summits.bed INFO @ Sun, 02 Jun 2019 22:27:22: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (5260 records, 4 fields): 9 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4365 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。