Job ID = 1291812 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,930,018 reads read : 18,930,018 reads written : 18,930,018 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: 00:03:23 18930018 reads; of these: 18930018 (100.00%) were unpaired; of these: 2656042 (14.03%) aligned 0 times 13795638 (72.88%) aligned exactly 1 time 2478338 (13.09%) aligned >1 times 85.97% overall alignment rate Time searching: 00:03:23 Overall time: 00:03:23 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] 5323332 / 16273976 = 0.3271 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 16:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.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 16:45:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:45:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.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 16:45:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:45:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:45:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.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 16:45:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:45:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:46:04: 1000000 INFO @ Sun, 02 Jun 2019 16:46:04: 1000000 INFO @ Sun, 02 Jun 2019 16:46:04: 1000000 INFO @ Sun, 02 Jun 2019 16:46:13: 2000000 INFO @ Sun, 02 Jun 2019 16:46:13: 2000000 INFO @ Sun, 02 Jun 2019 16:46:14: 2000000 INFO @ Sun, 02 Jun 2019 16:46:22: 3000000 INFO @ Sun, 02 Jun 2019 16:46:22: 3000000 INFO @ Sun, 02 Jun 2019 16:46:23: 3000000 INFO @ Sun, 02 Jun 2019 16:46:31: 4000000 INFO @ Sun, 02 Jun 2019 16:46:31: 4000000 INFO @ Sun, 02 Jun 2019 16:46:32: 4000000 INFO @ Sun, 02 Jun 2019 16:46:40: 5000000 INFO @ Sun, 02 Jun 2019 16:46:40: 5000000 INFO @ Sun, 02 Jun 2019 16:46:42: 5000000 INFO @ Sun, 02 Jun 2019 16:46:49: 6000000 INFO @ Sun, 02 Jun 2019 16:46:50: 6000000 INFO @ Sun, 02 Jun 2019 16:46:52: 6000000 INFO @ Sun, 02 Jun 2019 16:46:58: 7000000 INFO @ Sun, 02 Jun 2019 16:46:59: 7000000 INFO @ Sun, 02 Jun 2019 16:47:01: 7000000 INFO @ Sun, 02 Jun 2019 16:47:07: 8000000 INFO @ Sun, 02 Jun 2019 16:47:08: 8000000 INFO @ Sun, 02 Jun 2019 16:47:10: 8000000 INFO @ Sun, 02 Jun 2019 16:47:16: 9000000 INFO @ Sun, 02 Jun 2019 16:47:17: 9000000 INFO @ Sun, 02 Jun 2019 16:47:19: 9000000 INFO @ Sun, 02 Jun 2019 16:47:25: 10000000 INFO @ Sun, 02 Jun 2019 16:47:26: 10000000 INFO @ Sun, 02 Jun 2019 16:47:29: 10000000 INFO @ Sun, 02 Jun 2019 16:47:34: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:47:34: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:47:34: #1 total tags in treatment: 10950644 INFO @ Sun, 02 Jun 2019 16:47:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:34: #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 16:47:34: #1 tags after filtering in treatment: 10950644 INFO @ Sun, 02 Jun 2019 16:47:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:34: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:35: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:47:35: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:47:35: #1 total tags in treatment: 10950644 INFO @ Sun, 02 Jun 2019 16:47:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:35: #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 16:47:35: #1 tags after filtering in treatment: 10950644 INFO @ Sun, 02 Jun 2019 16:47:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:35: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:35: #2 number of paired peaks: 721 WARNING @ Sun, 02 Jun 2019 16:47:35: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:35: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:35: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:35: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:35: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:35: #2 predicted fragment length is 217 bps INFO @ Sun, 02 Jun 2019 16:47:35: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 02 Jun 2019 16:47:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.20_model.r INFO @ Sun, 02 Jun 2019 16:47:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:36: #2 number of paired peaks: 721 WARNING @ Sun, 02 Jun 2019 16:47:36: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:36: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:36: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:36: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:36: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:36: #2 predicted fragment length is 217 bps INFO @ Sun, 02 Jun 2019 16:47:36: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 02 Jun 2019 16:47:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.10_model.r INFO @ Sun, 02 Jun 2019 16:47:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:38: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:47:38: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:47:38: #1 total tags in treatment: 10950644 INFO @ Sun, 02 Jun 2019 16:47:38: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:38: #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 16:47:39: #1 tags after filtering in treatment: 10950644 INFO @ Sun, 02 Jun 2019 16:47:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:39: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:40: #2 number of paired peaks: 721 WARNING @ Sun, 02 Jun 2019 16:47:40: Fewer paired peaks (721) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 721 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:40: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:40: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:40: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:40: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:40: #2 predicted fragment length is 217 bps INFO @ Sun, 02 Jun 2019 16:47:40: #2 alternative fragment length(s) may be 217 bps INFO @ Sun, 02 Jun 2019 16:47:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.05_model.r INFO @ Sun, 02 Jun 2019 16:47:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:48:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:48:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.20_summits.bed INFO @ Sun, 02 Jun 2019 16:48:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (976 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.10_summits.bed INFO @ Sun, 02 Jun 2019 16:48:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1797 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257654/SRX257654.05_summits.bed INFO @ Sun, 02 Jun 2019 16:48:31: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3194 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。