Job ID = 1293212 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,972,064 reads read : 24,972,064 reads written : 24,972,064 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: 00:05:14 24972064 reads; of these: 24972064 (100.00%) were unpaired; of these: 6747556 (27.02%) aligned 0 times 14657713 (58.70%) aligned exactly 1 time 3566795 (14.28%) aligned >1 times 72.98% overall alignment rate Time searching: 00:05:14 Overall time: 00:05:14 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] 6171883 / 18224508 = 0.3387 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 22:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.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 22:35:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:35:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.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 22:35:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:35:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:35:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.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 22:35:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:35:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:35:33: 1000000 INFO @ Sun, 02 Jun 2019 22:35:33: 1000000 INFO @ Sun, 02 Jun 2019 22:35:34: 1000000 INFO @ Sun, 02 Jun 2019 22:35:41: 2000000 INFO @ Sun, 02 Jun 2019 22:35:41: 2000000 INFO @ Sun, 02 Jun 2019 22:35:43: 2000000 INFO @ Sun, 02 Jun 2019 22:35:49: 3000000 INFO @ Sun, 02 Jun 2019 22:35:49: 3000000 INFO @ Sun, 02 Jun 2019 22:35:52: 3000000 INFO @ Sun, 02 Jun 2019 22:35:57: 4000000 INFO @ Sun, 02 Jun 2019 22:35:57: 4000000 INFO @ Sun, 02 Jun 2019 22:36:01: 4000000 INFO @ Sun, 02 Jun 2019 22:36:04: 5000000 INFO @ Sun, 02 Jun 2019 22:36:05: 5000000 INFO @ Sun, 02 Jun 2019 22:36:10: 5000000 INFO @ Sun, 02 Jun 2019 22:36:12: 6000000 INFO @ Sun, 02 Jun 2019 22:36:13: 6000000 INFO @ Sun, 02 Jun 2019 22:36:19: 6000000 INFO @ Sun, 02 Jun 2019 22:36:19: 7000000 INFO @ Sun, 02 Jun 2019 22:36:21: 7000000 INFO @ Sun, 02 Jun 2019 22:36:27: 8000000 INFO @ Sun, 02 Jun 2019 22:36:28: 7000000 INFO @ Sun, 02 Jun 2019 22:36:29: 8000000 INFO @ Sun, 02 Jun 2019 22:36:35: 9000000 INFO @ Sun, 02 Jun 2019 22:36:37: 9000000 INFO @ Sun, 02 Jun 2019 22:36:37: 8000000 INFO @ Sun, 02 Jun 2019 22:36:42: 10000000 INFO @ Sun, 02 Jun 2019 22:36:44: 10000000 INFO @ Sun, 02 Jun 2019 22:36:45: 9000000 INFO @ Sun, 02 Jun 2019 22:36:50: 11000000 INFO @ Sun, 02 Jun 2019 22:36:52: 11000000 INFO @ Sun, 02 Jun 2019 22:36:54: 10000000 INFO @ Sun, 02 Jun 2019 22:36:57: 12000000 INFO @ Sun, 02 Jun 2019 22:36:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:36:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:36:58: #1 total tags in treatment: 12052625 INFO @ Sun, 02 Jun 2019 22:36:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:36:58: #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 22:36:58: #1 tags after filtering in treatment: 12052625 INFO @ Sun, 02 Jun 2019 22:36:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:36:58: #1 finished! INFO @ Sun, 02 Jun 2019 22:36:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:36:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:36:59: #2 number of paired peaks: 399 WARNING @ Sun, 02 Jun 2019 22:36:59: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Sun, 02 Jun 2019 22:36:59: start model_add_line... INFO @ Sun, 02 Jun 2019 22:36:59: 12000000 INFO @ Sun, 02 Jun 2019 22:36:59: start X-correlation... INFO @ Sun, 02 Jun 2019 22:36:59: end of X-cor INFO @ Sun, 02 Jun 2019 22:36:59: #2 finished! INFO @ Sun, 02 Jun 2019 22:36:59: #2 predicted fragment length is 43 bps INFO @ Sun, 02 Jun 2019 22:36:59: #2 alternative fragment length(s) may be 1,43,568 bps INFO @ Sun, 02 Jun 2019 22:36:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.20_model.r WARNING @ Sun, 02 Jun 2019 22:36:59: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:36:59: #2 You may need to consider one of the other alternative d(s): 1,43,568 WARNING @ Sun, 02 Jun 2019 22:36:59: #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 22:36:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:36:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:37:00: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:37:00: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:37:00: #1 total tags in treatment: 12052625 INFO @ Sun, 02 Jun 2019 22:37:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:37:00: #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 22:37:00: #1 tags after filtering in treatment: 12052625 INFO @ Sun, 02 Jun 2019 22:37:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:37:00: #1 finished! INFO @ Sun, 02 Jun 2019 22:37:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:37:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:37:01: #2 number of paired peaks: 399 WARNING @ Sun, 02 Jun 2019 22:37:01: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Sun, 02 Jun 2019 22:37:01: start model_add_line... INFO @ Sun, 02 Jun 2019 22:37:01: start X-correlation... INFO @ Sun, 02 Jun 2019 22:37:01: end of X-cor INFO @ Sun, 02 Jun 2019 22:37:01: #2 finished! INFO @ Sun, 02 Jun 2019 22:37:01: #2 predicted fragment length is 43 bps INFO @ Sun, 02 Jun 2019 22:37:01: #2 alternative fragment length(s) may be 1,43,568 bps INFO @ Sun, 02 Jun 2019 22:37:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.10_model.r WARNING @ Sun, 02 Jun 2019 22:37:01: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:37:01: #2 You may need to consider one of the other alternative d(s): 1,43,568 WARNING @ Sun, 02 Jun 2019 22:37:01: #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 22:37:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:37:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:37:03: 11000000 INFO @ Sun, 02 Jun 2019 22:37:11: 12000000 INFO @ Sun, 02 Jun 2019 22:37:12: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:37:12: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:37:12: #1 total tags in treatment: 12052625 INFO @ Sun, 02 Jun 2019 22:37:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:37:12: #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 22:37:12: #1 tags after filtering in treatment: 12052625 INFO @ Sun, 02 Jun 2019 22:37:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:37:12: #1 finished! INFO @ Sun, 02 Jun 2019 22:37:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:37:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:37:13: #2 number of paired peaks: 399 WARNING @ Sun, 02 Jun 2019 22:37:13: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Sun, 02 Jun 2019 22:37:13: start model_add_line... INFO @ Sun, 02 Jun 2019 22:37:13: start X-correlation... INFO @ Sun, 02 Jun 2019 22:37:13: end of X-cor INFO @ Sun, 02 Jun 2019 22:37:13: #2 finished! INFO @ Sun, 02 Jun 2019 22:37:13: #2 predicted fragment length is 43 bps INFO @ Sun, 02 Jun 2019 22:37:13: #2 alternative fragment length(s) may be 1,43,568 bps INFO @ Sun, 02 Jun 2019 22:37:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.05_model.r WARNING @ Sun, 02 Jun 2019 22:37:13: #2 Since the d (43) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:37:13: #2 You may need to consider one of the other alternative d(s): 1,43,568 WARNING @ Sun, 02 Jun 2019 22:37:13: #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 22:37:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:37:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:37:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:37:32: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:37:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:37:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:37:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:37:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.20_summits.bed INFO @ Sun, 02 Jun 2019 22:37:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (190 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:37:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:37:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:37:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.10_summits.bed INFO @ Sun, 02 Jun 2019 22:37:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (513 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:38:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:38:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:38:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402762/SRX5402762.05_summits.bed INFO @ Sun, 02 Jun 2019 22:38:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (811 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。