Job ID = 1291693 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,457,393 reads read : 25,457,393 reads written : 25,457,393 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: 00:05:33 25457393 reads; of these: 25457393 (100.00%) were unpaired; of these: 5623352 (22.09%) aligned 0 times 17804107 (69.94%) aligned exactly 1 time 2029934 (7.97%) aligned >1 times 77.91% overall alignment rate Time searching: 00:05:33 Overall time: 00:05:33 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] 5466369 / 19834041 = 0.2756 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 16:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.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 16:28:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:28:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.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 16:28:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:28:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:28:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.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 16:28:39: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:28:39: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:28:46: 1000000 INFO @ Sun, 02 Jun 2019 16:28:47: 1000000 INFO @ Sun, 02 Jun 2019 16:28:48: 1000000 INFO @ Sun, 02 Jun 2019 16:28:53: 2000000 INFO @ Sun, 02 Jun 2019 16:28:54: 2000000 INFO @ Sun, 02 Jun 2019 16:28:56: 2000000 INFO @ Sun, 02 Jun 2019 16:29:00: 3000000 INFO @ Sun, 02 Jun 2019 16:29:02: 3000000 INFO @ Sun, 02 Jun 2019 16:29:05: 3000000 INFO @ Sun, 02 Jun 2019 16:29:07: 4000000 INFO @ Sun, 02 Jun 2019 16:29:09: 4000000 INFO @ Sun, 02 Jun 2019 16:29:13: 5000000 INFO @ Sun, 02 Jun 2019 16:29:14: 4000000 INFO @ Sun, 02 Jun 2019 16:29:17: 5000000 INFO @ Sun, 02 Jun 2019 16:29:20: 6000000 INFO @ Sun, 02 Jun 2019 16:29:22: 5000000 INFO @ Sun, 02 Jun 2019 16:29:24: 6000000 INFO @ Sun, 02 Jun 2019 16:29:27: 7000000 INFO @ Sun, 02 Jun 2019 16:29:31: 6000000 INFO @ Sun, 02 Jun 2019 16:29:32: 7000000 INFO @ Sun, 02 Jun 2019 16:29:34: 8000000 INFO @ Sun, 02 Jun 2019 16:29:39: 7000000 INFO @ Sun, 02 Jun 2019 16:29:40: 8000000 INFO @ Sun, 02 Jun 2019 16:29:41: 9000000 INFO @ Sun, 02 Jun 2019 16:29:47: 9000000 INFO @ Sun, 02 Jun 2019 16:29:48: 10000000 INFO @ Sun, 02 Jun 2019 16:29:48: 8000000 INFO @ Sun, 02 Jun 2019 16:29:54: 11000000 INFO @ Sun, 02 Jun 2019 16:29:54: 10000000 INFO @ Sun, 02 Jun 2019 16:29:56: 9000000 INFO @ Sun, 02 Jun 2019 16:30:01: 12000000 INFO @ Sun, 02 Jun 2019 16:30:02: 11000000 INFO @ Sun, 02 Jun 2019 16:30:04: 10000000 INFO @ Sun, 02 Jun 2019 16:30:08: 13000000 INFO @ Sun, 02 Jun 2019 16:30:09: 12000000 INFO @ Sun, 02 Jun 2019 16:30:13: 11000000 INFO @ Sun, 02 Jun 2019 16:30:15: 14000000 INFO @ Sun, 02 Jun 2019 16:30:17: 13000000 INFO @ Sun, 02 Jun 2019 16:30:17: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:30:17: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:30:17: #1 total tags in treatment: 14367672 INFO @ Sun, 02 Jun 2019 16:30:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:30:17: #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 16:30:17: #1 tags after filtering in treatment: 14367672 INFO @ Sun, 02 Jun 2019 16:30:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:30:17: #1 finished! INFO @ Sun, 02 Jun 2019 16:30:17: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:30:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:30:19: #2 number of paired peaks: 836 WARNING @ Sun, 02 Jun 2019 16:30:19: Fewer paired peaks (836) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 836 pairs to build model! INFO @ Sun, 02 Jun 2019 16:30:19: start model_add_line... INFO @ Sun, 02 Jun 2019 16:30:19: start X-correlation... INFO @ Sun, 02 Jun 2019 16:30:19: end of X-cor INFO @ Sun, 02 Jun 2019 16:30:19: #2 finished! INFO @ Sun, 02 Jun 2019 16:30:19: #2 predicted fragment length is 164 bps INFO @ Sun, 02 Jun 2019 16:30:19: #2 alternative fragment length(s) may be 4,164 bps INFO @ Sun, 02 Jun 2019 16:30:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.20_model.r INFO @ Sun, 02 Jun 2019 16:30:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:30:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:30:21: 12000000 INFO @ Sun, 02 Jun 2019 16:30:24: 14000000 INFO @ Sun, 02 Jun 2019 16:30:27: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:30:27: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:30:27: #1 total tags in treatment: 14367672 INFO @ Sun, 02 Jun 2019 16:30:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:30:27: #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 16:30:27: #1 tags after filtering in treatment: 14367672 INFO @ Sun, 02 Jun 2019 16:30:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:30:27: #1 finished! INFO @ Sun, 02 Jun 2019 16:30:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:30:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:30:28: #2 number of paired peaks: 836 WARNING @ Sun, 02 Jun 2019 16:30:28: Fewer paired peaks (836) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 836 pairs to build model! INFO @ Sun, 02 Jun 2019 16:30:28: start model_add_line... INFO @ Sun, 02 Jun 2019 16:30:28: start X-correlation... INFO @ Sun, 02 Jun 2019 16:30:28: end of X-cor INFO @ Sun, 02 Jun 2019 16:30:28: #2 finished! INFO @ Sun, 02 Jun 2019 16:30:28: #2 predicted fragment length is 164 bps INFO @ Sun, 02 Jun 2019 16:30:28: #2 alternative fragment length(s) may be 4,164 bps INFO @ Sun, 02 Jun 2019 16:30:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.05_model.r INFO @ Sun, 02 Jun 2019 16:30:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:30:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:30:30: 13000000 INFO @ Sun, 02 Jun 2019 16:30:38: 14000000 INFO @ Sun, 02 Jun 2019 16:30:41: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:30:41: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:30:41: #1 total tags in treatment: 14367672 INFO @ Sun, 02 Jun 2019 16:30:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:30:41: #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 16:30:42: #1 tags after filtering in treatment: 14367672 INFO @ Sun, 02 Jun 2019 16:30:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:30:42: #1 finished! INFO @ Sun, 02 Jun 2019 16:30:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:30:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:30:43: #2 number of paired peaks: 836 WARNING @ Sun, 02 Jun 2019 16:30:43: Fewer paired peaks (836) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 836 pairs to build model! INFO @ Sun, 02 Jun 2019 16:30:43: start model_add_line... INFO @ Sun, 02 Jun 2019 16:30:43: start X-correlation... INFO @ Sun, 02 Jun 2019 16:30:43: end of X-cor INFO @ Sun, 02 Jun 2019 16:30:43: #2 finished! INFO @ Sun, 02 Jun 2019 16:30:43: #2 predicted fragment length is 164 bps INFO @ Sun, 02 Jun 2019 16:30:43: #2 alternative fragment length(s) may be 4,164 bps INFO @ Sun, 02 Jun 2019 16:30:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.10_model.r INFO @ Sun, 02 Jun 2019 16:30:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:30:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:31:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:31:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:31:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.20_summits.bed INFO @ Sun, 02 Jun 2019 16:31:20: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1688 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:31:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:31:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.05_summits.bed INFO @ Sun, 02 Jun 2019 16:31:30: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5943 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:31:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:31:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:31:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX216764/SRX216764.10_summits.bed INFO @ Sun, 02 Jun 2019 16:31:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3584 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。