Job ID = 1293109 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,022,245 reads read : 26,022,245 reads written : 26,022,245 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: 00:04:23 26022245 reads; of these: 26022245 (100.00%) were unpaired; of these: 4979128 (19.13%) aligned 0 times 17208817 (66.13%) aligned exactly 1 time 3834300 (14.73%) aligned >1 times 80.87% overall alignment rate Time searching: 00:04:23 Overall time: 00:04:23 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] 3725108 / 21043117 = 0.1770 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 22:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.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 22:05:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:05:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.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 22:05:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:05:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.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 22:05:57: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:05:57: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:06:04: 1000000 INFO @ Sun, 02 Jun 2019 22:06:05: 1000000 INFO @ Sun, 02 Jun 2019 22:06:06: 1000000 INFO @ Sun, 02 Jun 2019 22:06:12: 2000000 INFO @ Sun, 02 Jun 2019 22:06:13: 2000000 INFO @ Sun, 02 Jun 2019 22:06:15: 2000000 INFO @ Sun, 02 Jun 2019 22:06:19: 3000000 INFO @ Sun, 02 Jun 2019 22:06:21: 3000000 INFO @ Sun, 02 Jun 2019 22:06:24: 3000000 INFO @ Sun, 02 Jun 2019 22:06:26: 4000000 INFO @ Sun, 02 Jun 2019 22:06:29: 4000000 INFO @ Sun, 02 Jun 2019 22:06:33: 4000000 INFO @ Sun, 02 Jun 2019 22:06:33: 5000000 INFO @ Sun, 02 Jun 2019 22:06:37: 5000000 INFO @ Sun, 02 Jun 2019 22:06:40: 6000000 INFO @ Sun, 02 Jun 2019 22:06:42: 5000000 INFO @ Sun, 02 Jun 2019 22:06:45: 6000000 INFO @ Sun, 02 Jun 2019 22:06:47: 7000000 INFO @ Sun, 02 Jun 2019 22:06:51: 6000000 INFO @ Sun, 02 Jun 2019 22:06:52: 7000000 INFO @ Sun, 02 Jun 2019 22:06:55: 8000000 INFO @ Sun, 02 Jun 2019 22:06:59: 7000000 INFO @ Sun, 02 Jun 2019 22:07:00: 8000000 INFO @ Sun, 02 Jun 2019 22:07:02: 9000000 INFO @ Sun, 02 Jun 2019 22:07:08: 9000000 INFO @ Sun, 02 Jun 2019 22:07:08: 8000000 INFO @ Sun, 02 Jun 2019 22:07:09: 10000000 INFO @ Sun, 02 Jun 2019 22:07:16: 10000000 INFO @ Sun, 02 Jun 2019 22:07:17: 11000000 INFO @ Sun, 02 Jun 2019 22:07:17: 9000000 INFO @ Sun, 02 Jun 2019 22:07:24: 11000000 INFO @ Sun, 02 Jun 2019 22:07:24: 12000000 INFO @ Sun, 02 Jun 2019 22:07:26: 10000000 INFO @ Sun, 02 Jun 2019 22:07:32: 12000000 INFO @ Sun, 02 Jun 2019 22:07:32: 13000000 INFO @ Sun, 02 Jun 2019 22:07:34: 11000000 INFO @ Sun, 02 Jun 2019 22:07:39: 14000000 INFO @ Sun, 02 Jun 2019 22:07:40: 13000000 INFO @ Sun, 02 Jun 2019 22:07:42: 12000000 INFO @ Sun, 02 Jun 2019 22:07:47: 15000000 INFO @ Sun, 02 Jun 2019 22:07:47: 14000000 INFO @ Sun, 02 Jun 2019 22:07:50: 13000000 INFO @ Sun, 02 Jun 2019 22:07:54: 16000000 INFO @ Sun, 02 Jun 2019 22:07:55: 15000000 INFO @ Sun, 02 Jun 2019 22:07:58: 14000000 INFO @ Sun, 02 Jun 2019 22:08:01: 17000000 INFO @ Sun, 02 Jun 2019 22:08:02: 16000000 INFO @ Sun, 02 Jun 2019 22:08:04: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:08:04: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:08:04: #1 total tags in treatment: 17318009 INFO @ Sun, 02 Jun 2019 22:08:04: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:08:04: #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 22:08:04: #1 tags after filtering in treatment: 17318009 INFO @ Sun, 02 Jun 2019 22:08:04: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:08:04: #1 finished! INFO @ Sun, 02 Jun 2019 22:08:04: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:08:04: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:08:06: #2 number of paired peaks: 373 WARNING @ Sun, 02 Jun 2019 22:08:06: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Sun, 02 Jun 2019 22:08:06: start model_add_line... INFO @ Sun, 02 Jun 2019 22:08:06: start X-correlation... INFO @ Sun, 02 Jun 2019 22:08:06: end of X-cor INFO @ Sun, 02 Jun 2019 22:08:06: #2 finished! INFO @ Sun, 02 Jun 2019 22:08:06: #2 predicted fragment length is 120 bps INFO @ Sun, 02 Jun 2019 22:08:06: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 02 Jun 2019 22:08:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.20_model.r INFO @ Sun, 02 Jun 2019 22:08:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:08:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:08:07: 15000000 INFO @ Sun, 02 Jun 2019 22:08:10: 17000000 INFO @ Sun, 02 Jun 2019 22:08:12: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:08:12: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:08:12: #1 total tags in treatment: 17318009 INFO @ Sun, 02 Jun 2019 22:08:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:08:12: #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 22:08:13: #1 tags after filtering in treatment: 17318009 INFO @ Sun, 02 Jun 2019 22:08:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:08:13: #1 finished! INFO @ Sun, 02 Jun 2019 22:08:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:08:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:08:14: #2 number of paired peaks: 373 WARNING @ Sun, 02 Jun 2019 22:08:14: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Sun, 02 Jun 2019 22:08:14: start model_add_line... INFO @ Sun, 02 Jun 2019 22:08:14: start X-correlation... INFO @ Sun, 02 Jun 2019 22:08:14: end of X-cor INFO @ Sun, 02 Jun 2019 22:08:14: #2 finished! INFO @ Sun, 02 Jun 2019 22:08:14: #2 predicted fragment length is 120 bps INFO @ Sun, 02 Jun 2019 22:08:14: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 02 Jun 2019 22:08:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.10_model.r INFO @ Sun, 02 Jun 2019 22:08:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:08:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:08:15: 16000000 INFO @ Sun, 02 Jun 2019 22:08:22: 17000000 INFO @ Sun, 02 Jun 2019 22:08:25: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:08:25: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:08:25: #1 total tags in treatment: 17318009 INFO @ Sun, 02 Jun 2019 22:08:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:08:25: #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 22:08:25: #1 tags after filtering in treatment: 17318009 INFO @ Sun, 02 Jun 2019 22:08:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:08:25: #1 finished! INFO @ Sun, 02 Jun 2019 22:08:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:08:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:08:27: #2 number of paired peaks: 373 WARNING @ Sun, 02 Jun 2019 22:08:27: Fewer paired peaks (373) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 373 pairs to build model! INFO @ Sun, 02 Jun 2019 22:08:27: start model_add_line... INFO @ Sun, 02 Jun 2019 22:08:27: start X-correlation... INFO @ Sun, 02 Jun 2019 22:08:27: end of X-cor INFO @ Sun, 02 Jun 2019 22:08:27: #2 finished! INFO @ Sun, 02 Jun 2019 22:08:27: #2 predicted fragment length is 120 bps INFO @ Sun, 02 Jun 2019 22:08:27: #2 alternative fragment length(s) may be 120 bps INFO @ Sun, 02 Jun 2019 22:08:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.05_model.r INFO @ Sun, 02 Jun 2019 22:08:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:08:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:08:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:08:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:09:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:09:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:09:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.20_summits.bed INFO @ Sun, 02 Jun 2019 22:09:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1377 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:09:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:09:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:09:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:09:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.10_summits.bed INFO @ Sun, 02 Jun 2019 22:09:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2030 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:09:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:09:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:09:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529221/SRX529221.05_summits.bed INFO @ Sun, 02 Jun 2019 22:09:31: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (2958 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。