Job ID = 1292482 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 38,123,596 reads read : 38,123,596 reads written : 38,123,596 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: 00:09:53 38123596 reads; of these: 38123596 (100.00%) were unpaired; of these: 1263482 (3.31%) aligned 0 times 30407738 (79.76%) aligned exactly 1 time 6452376 (16.92%) aligned >1 times 96.69% overall alignment rate Time searching: 00:09:53 Overall time: 00:09:53 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 16 files... [bam_rmdupse_core] 18267419 / 36860114 = 0.4956 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 19:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.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 19:26:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:26:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.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 19:26:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:26:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:26:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.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 19:26:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:26:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:27:01: 1000000 INFO @ Sun, 02 Jun 2019 19:27:01: 1000000 INFO @ Sun, 02 Jun 2019 19:27:01: 1000000 INFO @ Sun, 02 Jun 2019 19:27:07: 2000000 INFO @ Sun, 02 Jun 2019 19:27:08: 2000000 INFO @ Sun, 02 Jun 2019 19:27:08: 2000000 INFO @ Sun, 02 Jun 2019 19:27:14: 3000000 INFO @ Sun, 02 Jun 2019 19:27:14: 3000000 INFO @ Sun, 02 Jun 2019 19:27:16: 3000000 INFO @ Sun, 02 Jun 2019 19:27:21: 4000000 INFO @ Sun, 02 Jun 2019 19:27:21: 4000000 INFO @ Sun, 02 Jun 2019 19:27:23: 4000000 INFO @ Sun, 02 Jun 2019 19:27:27: 5000000 INFO @ Sun, 02 Jun 2019 19:27:27: 5000000 INFO @ Sun, 02 Jun 2019 19:27:31: 5000000 INFO @ Sun, 02 Jun 2019 19:27:34: 6000000 INFO @ Sun, 02 Jun 2019 19:27:34: 6000000 INFO @ Sun, 02 Jun 2019 19:27:38: 6000000 INFO @ Sun, 02 Jun 2019 19:27:40: 7000000 INFO @ Sun, 02 Jun 2019 19:27:40: 7000000 INFO @ Sun, 02 Jun 2019 19:27:45: 7000000 INFO @ Sun, 02 Jun 2019 19:27:47: 8000000 INFO @ Sun, 02 Jun 2019 19:27:47: 8000000 INFO @ Sun, 02 Jun 2019 19:27:52: 8000000 INFO @ Sun, 02 Jun 2019 19:27:54: 9000000 INFO @ Sun, 02 Jun 2019 19:27:54: 9000000 INFO @ Sun, 02 Jun 2019 19:28:00: 9000000 INFO @ Sun, 02 Jun 2019 19:28:01: 10000000 INFO @ Sun, 02 Jun 2019 19:28:01: 10000000 INFO @ Sun, 02 Jun 2019 19:28:07: 10000000 INFO @ Sun, 02 Jun 2019 19:28:08: 11000000 INFO @ Sun, 02 Jun 2019 19:28:08: 11000000 INFO @ Sun, 02 Jun 2019 19:28:14: 11000000 INFO @ Sun, 02 Jun 2019 19:28:15: 12000000 INFO @ Sun, 02 Jun 2019 19:28:15: 12000000 INFO @ Sun, 02 Jun 2019 19:28:21: 12000000 INFO @ Sun, 02 Jun 2019 19:28:21: 13000000 INFO @ Sun, 02 Jun 2019 19:28:21: 13000000 INFO @ Sun, 02 Jun 2019 19:28:28: 13000000 INFO @ Sun, 02 Jun 2019 19:28:28: 14000000 INFO @ Sun, 02 Jun 2019 19:28:28: 14000000 INFO @ Sun, 02 Jun 2019 19:28:34: 14000000 INFO @ Sun, 02 Jun 2019 19:28:35: 15000000 INFO @ Sun, 02 Jun 2019 19:28:35: 15000000 INFO @ Sun, 02 Jun 2019 19:28:41: 16000000 INFO @ Sun, 02 Jun 2019 19:28:41: 16000000 INFO @ Sun, 02 Jun 2019 19:28:42: 15000000 INFO @ Sun, 02 Jun 2019 19:28:48: 17000000 INFO @ Sun, 02 Jun 2019 19:28:48: 17000000 INFO @ Sun, 02 Jun 2019 19:28:49: 16000000 INFO @ Sun, 02 Jun 2019 19:28:54: 18000000 INFO @ Sun, 02 Jun 2019 19:28:54: 18000000 INFO @ Sun, 02 Jun 2019 19:28:56: 17000000 INFO @ Sun, 02 Jun 2019 19:28:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:28:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:28:58: #1 total tags in treatment: 18592695 INFO @ Sun, 02 Jun 2019 19:28:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:28:58: #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 19:28:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:28:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:28:58: #1 total tags in treatment: 18592695 INFO @ Sun, 02 Jun 2019 19:28:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:28:58: #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 19:28:59: #1 tags after filtering in treatment: 18592695 INFO @ Sun, 02 Jun 2019 19:28:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:28:59: #1 finished! INFO @ Sun, 02 Jun 2019 19:28:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:28:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:28:59: #1 tags after filtering in treatment: 18592695 INFO @ Sun, 02 Jun 2019 19:28:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:28:59: #1 finished! INFO @ Sun, 02 Jun 2019 19:28:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:28:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:29:00: #2 number of paired peaks: 260 WARNING @ Sun, 02 Jun 2019 19:29:00: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sun, 02 Jun 2019 19:29:00: start model_add_line... INFO @ Sun, 02 Jun 2019 19:29:00: #2 number of paired peaks: 260 WARNING @ Sun, 02 Jun 2019 19:29:00: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sun, 02 Jun 2019 19:29:00: start model_add_line... INFO @ Sun, 02 Jun 2019 19:29:00: start X-correlation... INFO @ Sun, 02 Jun 2019 19:29:00: end of X-cor INFO @ Sun, 02 Jun 2019 19:29:00: #2 finished! INFO @ Sun, 02 Jun 2019 19:29:00: #2 predicted fragment length is 46 bps INFO @ Sun, 02 Jun 2019 19:29:00: #2 alternative fragment length(s) may be 1,46 bps INFO @ Sun, 02 Jun 2019 19:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.05_model.r WARNING @ Sun, 02 Jun 2019 19:29:00: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:29:00: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Sun, 02 Jun 2019 19:29:00: #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 19:29:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:29:00: start X-correlation... INFO @ Sun, 02 Jun 2019 19:29:00: end of X-cor INFO @ Sun, 02 Jun 2019 19:29:00: #2 finished! INFO @ Sun, 02 Jun 2019 19:29:00: #2 predicted fragment length is 46 bps INFO @ Sun, 02 Jun 2019 19:29:00: #2 alternative fragment length(s) may be 1,46 bps INFO @ Sun, 02 Jun 2019 19:29:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.10_model.r WARNING @ Sun, 02 Jun 2019 19:29:00: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:29:00: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Sun, 02 Jun 2019 19:29:00: #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 19:29:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:29:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:29:03: 18000000 INFO @ Sun, 02 Jun 2019 19:29:07: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:29:07: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:29:07: #1 total tags in treatment: 18592695 INFO @ Sun, 02 Jun 2019 19:29:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:29:07: #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 19:29:07: #1 tags after filtering in treatment: 18592695 INFO @ Sun, 02 Jun 2019 19:29:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:29:07: #1 finished! INFO @ Sun, 02 Jun 2019 19:29:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:29:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:29:09: #2 number of paired peaks: 260 WARNING @ Sun, 02 Jun 2019 19:29:09: Fewer paired peaks (260) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 260 pairs to build model! INFO @ Sun, 02 Jun 2019 19:29:09: start model_add_line... INFO @ Sun, 02 Jun 2019 19:29:09: start X-correlation... INFO @ Sun, 02 Jun 2019 19:29:09: end of X-cor INFO @ Sun, 02 Jun 2019 19:29:09: #2 finished! INFO @ Sun, 02 Jun 2019 19:29:09: #2 predicted fragment length is 46 bps INFO @ Sun, 02 Jun 2019 19:29:09: #2 alternative fragment length(s) may be 1,46 bps INFO @ Sun, 02 Jun 2019 19:29:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.20_model.r WARNING @ Sun, 02 Jun 2019 19:29:09: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:29:09: #2 You may need to consider one of the other alternative d(s): 1,46 WARNING @ Sun, 02 Jun 2019 19:29:09: #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 19:29:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:29:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:29:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:29:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:29:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:30:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:30:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:30:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.10_summits.bed INFO @ Sun, 02 Jun 2019 19:30:06: Done! INFO @ Sun, 02 Jun 2019 19:30:06: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:30:06: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:30:06: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.05_summits.bed INFO @ Sun, 02 Jun 2019 19:30:06: Done! pass1 - making usageList (6 chroms)pass1 - making usageList (6 chroms): 2 millis : 2 millis pass2 - checking and writing primary data (580 records, 4 fields): 4 millis pass2 - checking and writing primary data (1577 records, 4 fields): 7 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:30:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:30:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:30:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466469/SRX466469.20_summits.bed INFO @ Sun, 02 Jun 2019 19:30:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (192 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。