Job ID = 1292860 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,854,814 reads read : 18,854,814 reads written : 18,854,814 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: 00:04:08 18854814 reads; of these: 18854814 (100.00%) were unpaired; of these: 289140 (1.53%) aligned 0 times 14953762 (79.31%) aligned exactly 1 time 3611912 (19.16%) aligned >1 times 98.47% overall alignment rate Time searching: 00:04:08 Overall time: 00:04:08 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] 3521983 / 18565674 = 0.1897 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 21:05:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.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 21:05:42: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:05:42: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:05:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.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 21:05:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:05:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:05:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.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 21:05:43: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:05:43: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:05:49: 1000000 INFO @ Sun, 02 Jun 2019 21:05:50: 1000000 INFO @ Sun, 02 Jun 2019 21:05:51: 1000000 INFO @ Sun, 02 Jun 2019 21:05:56: 2000000 INFO @ Sun, 02 Jun 2019 21:05:57: 2000000 INFO @ Sun, 02 Jun 2019 21:05:59: 2000000 INFO @ Sun, 02 Jun 2019 21:06:02: 3000000 INFO @ Sun, 02 Jun 2019 21:06:05: 3000000 INFO @ Sun, 02 Jun 2019 21:06:07: 3000000 INFO @ Sun, 02 Jun 2019 21:06:09: 4000000 INFO @ Sun, 02 Jun 2019 21:06:12: 4000000 INFO @ Sun, 02 Jun 2019 21:06:15: 4000000 INFO @ Sun, 02 Jun 2019 21:06:15: 5000000 INFO @ Sun, 02 Jun 2019 21:06:19: 5000000 INFO @ Sun, 02 Jun 2019 21:06:22: 6000000 INFO @ Sun, 02 Jun 2019 21:06:23: 5000000 INFO @ Sun, 02 Jun 2019 21:06:26: 6000000 INFO @ Sun, 02 Jun 2019 21:06:28: 7000000 INFO @ Sun, 02 Jun 2019 21:06:31: 6000000 INFO @ Sun, 02 Jun 2019 21:06:33: 7000000 INFO @ Sun, 02 Jun 2019 21:06:35: 8000000 INFO @ Sun, 02 Jun 2019 21:06:39: 7000000 INFO @ Sun, 02 Jun 2019 21:06:41: 8000000 INFO @ Sun, 02 Jun 2019 21:06:41: 9000000 INFO @ Sun, 02 Jun 2019 21:06:47: 8000000 INFO @ Sun, 02 Jun 2019 21:06:48: 10000000 INFO @ Sun, 02 Jun 2019 21:06:48: 9000000 INFO @ Sun, 02 Jun 2019 21:06:54: 11000000 INFO @ Sun, 02 Jun 2019 21:06:55: 10000000 INFO @ Sun, 02 Jun 2019 21:06:56: 9000000 INFO @ Sun, 02 Jun 2019 21:07:01: 12000000 INFO @ Sun, 02 Jun 2019 21:07:02: 11000000 INFO @ Sun, 02 Jun 2019 21:07:04: 10000000 INFO @ Sun, 02 Jun 2019 21:07:07: 13000000 INFO @ Sun, 02 Jun 2019 21:07:10: 12000000 INFO @ Sun, 02 Jun 2019 21:07:12: 11000000 INFO @ Sun, 02 Jun 2019 21:07:14: 14000000 INFO @ Sun, 02 Jun 2019 21:07:17: 13000000 INFO @ Sun, 02 Jun 2019 21:07:20: 15000000 INFO @ Sun, 02 Jun 2019 21:07:20: 12000000 INFO @ Sun, 02 Jun 2019 21:07:20: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:07:20: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:07:20: #1 total tags in treatment: 15043691 INFO @ Sun, 02 Jun 2019 21:07:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:07:20: #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 21:07:21: #1 tags after filtering in treatment: 15043691 INFO @ Sun, 02 Jun 2019 21:07:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:07:21: #1 finished! INFO @ Sun, 02 Jun 2019 21:07:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:07:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:07:22: #2 number of paired peaks: 431 WARNING @ Sun, 02 Jun 2019 21:07:22: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sun, 02 Jun 2019 21:07:22: start model_add_line... INFO @ Sun, 02 Jun 2019 21:07:22: start X-correlation... INFO @ Sun, 02 Jun 2019 21:07:22: end of X-cor INFO @ Sun, 02 Jun 2019 21:07:22: #2 finished! INFO @ Sun, 02 Jun 2019 21:07:22: #2 predicted fragment length is 59 bps INFO @ Sun, 02 Jun 2019 21:07:22: #2 alternative fragment length(s) may be 2,59,598 bps INFO @ Sun, 02 Jun 2019 21:07:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.10_model.r WARNING @ Sun, 02 Jun 2019 21:07:22: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:07:22: #2 You may need to consider one of the other alternative d(s): 2,59,598 WARNING @ Sun, 02 Jun 2019 21:07:22: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:07:22: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:07:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:07:24: 14000000 INFO @ Sun, 02 Jun 2019 21:07:28: 13000000 INFO @ Sun, 02 Jun 2019 21:07:31: 15000000 INFO @ Sun, 02 Jun 2019 21:07:31: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:07:31: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:07:31: #1 total tags in treatment: 15043691 INFO @ Sun, 02 Jun 2019 21:07:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:07:31: #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 21:07:32: #1 tags after filtering in treatment: 15043691 INFO @ Sun, 02 Jun 2019 21:07:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:07:32: #1 finished! INFO @ Sun, 02 Jun 2019 21:07:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:07:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:07:33: #2 number of paired peaks: 431 WARNING @ Sun, 02 Jun 2019 21:07:33: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sun, 02 Jun 2019 21:07:33: start model_add_line... INFO @ Sun, 02 Jun 2019 21:07:33: start X-correlation... INFO @ Sun, 02 Jun 2019 21:07:33: end of X-cor INFO @ Sun, 02 Jun 2019 21:07:33: #2 finished! INFO @ Sun, 02 Jun 2019 21:07:33: #2 predicted fragment length is 59 bps INFO @ Sun, 02 Jun 2019 21:07:33: #2 alternative fragment length(s) may be 2,59,598 bps INFO @ Sun, 02 Jun 2019 21:07:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.20_model.r WARNING @ Sun, 02 Jun 2019 21:07:33: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:07:33: #2 You may need to consider one of the other alternative d(s): 2,59,598 WARNING @ Sun, 02 Jun 2019 21:07:33: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:07:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:07:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:07:35: 14000000 INFO @ Sun, 02 Jun 2019 21:07:43: 15000000 INFO @ Sun, 02 Jun 2019 21:07:43: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:07:43: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:07:43: #1 total tags in treatment: 15043691 INFO @ Sun, 02 Jun 2019 21:07:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:07:43: #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 21:07:44: #1 tags after filtering in treatment: 15043691 INFO @ Sun, 02 Jun 2019 21:07:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:07:44: #1 finished! INFO @ Sun, 02 Jun 2019 21:07:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:07:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:07:45: #2 number of paired peaks: 431 WARNING @ Sun, 02 Jun 2019 21:07:45: Fewer paired peaks (431) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 431 pairs to build model! INFO @ Sun, 02 Jun 2019 21:07:45: start model_add_line... INFO @ Sun, 02 Jun 2019 21:07:45: start X-correlation... INFO @ Sun, 02 Jun 2019 21:07:45: end of X-cor INFO @ Sun, 02 Jun 2019 21:07:45: #2 finished! INFO @ Sun, 02 Jun 2019 21:07:45: #2 predicted fragment length is 59 bps INFO @ Sun, 02 Jun 2019 21:07:45: #2 alternative fragment length(s) may be 2,59,598 bps INFO @ Sun, 02 Jun 2019 21:07:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.05_model.r WARNING @ Sun, 02 Jun 2019 21:07:45: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:07:45: #2 You may need to consider one of the other alternative d(s): 2,59,598 WARNING @ Sun, 02 Jun 2019 21:07:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 21:07:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:07:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:08:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:08:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:08:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:08:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:08:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.10_summits.bed INFO @ Sun, 02 Jun 2019 21:08:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1375 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:08:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:08:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:08:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:08:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.20_summits.bed INFO @ Sun, 02 Jun 2019 21:08:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (367 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:08:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:08:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:08:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495086/SRX495086.05_summits.bed INFO @ Sun, 02 Jun 2019 21:08:42: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5755 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。