Job ID = 1291526 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,039,671 reads read : 11,039,671 reads written : 11,039,671 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: 00:02:39 11039671 reads; of these: 11039671 (100.00%) were unpaired; of these: 568111 (5.15%) aligned 0 times 8158802 (73.90%) aligned exactly 1 time 2312758 (20.95%) aligned >1 times 94.85% overall alignment rate Time searching: 00:02:39 Overall time: 00:02:39 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_rmdupse_core] 2667758 / 10471560 = 0.2548 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 15:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.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 15:59:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 15:59:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 15:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.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 15:59:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 15:59:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 15:59:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.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 15:59:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 15:59:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 15:59:44: 1000000 INFO @ Sun, 02 Jun 2019 15:59:45: 1000000 INFO @ Sun, 02 Jun 2019 15:59:45: 1000000 INFO @ Sun, 02 Jun 2019 15:59:51: 2000000 INFO @ Sun, 02 Jun 2019 15:59:52: 2000000 INFO @ Sun, 02 Jun 2019 15:59:52: 2000000 INFO @ Sun, 02 Jun 2019 15:59:58: 3000000 INFO @ Sun, 02 Jun 2019 15:59:59: 3000000 INFO @ Sun, 02 Jun 2019 16:00:00: 3000000 INFO @ Sun, 02 Jun 2019 16:00:04: 4000000 INFO @ Sun, 02 Jun 2019 16:00:06: 4000000 INFO @ Sun, 02 Jun 2019 16:00:07: 4000000 INFO @ Sun, 02 Jun 2019 16:00:11: 5000000 INFO @ Sun, 02 Jun 2019 16:00:13: 5000000 INFO @ Sun, 02 Jun 2019 16:00:14: 5000000 INFO @ Sun, 02 Jun 2019 16:00:18: 6000000 INFO @ Sun, 02 Jun 2019 16:00:20: 6000000 INFO @ Sun, 02 Jun 2019 16:00:22: 6000000 INFO @ Sun, 02 Jun 2019 16:00:25: 7000000 INFO @ Sun, 02 Jun 2019 16:00:27: 7000000 INFO @ Sun, 02 Jun 2019 16:00:30: 7000000 INFO @ Sun, 02 Jun 2019 16:00:31: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:00:31: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:00:31: #1 total tags in treatment: 7803802 INFO @ Sun, 02 Jun 2019 16:00:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:00:31: #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 16:00:31: #1 tags after filtering in treatment: 7803802 INFO @ Sun, 02 Jun 2019 16:00:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:00:31: #1 finished! INFO @ Sun, 02 Jun 2019 16:00:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:00:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:00:32: #2 number of paired peaks: 273 WARNING @ Sun, 02 Jun 2019 16:00:32: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Sun, 02 Jun 2019 16:00:32: start model_add_line... INFO @ Sun, 02 Jun 2019 16:00:32: start X-correlation... INFO @ Sun, 02 Jun 2019 16:00:32: end of X-cor INFO @ Sun, 02 Jun 2019 16:00:32: #2 finished! INFO @ Sun, 02 Jun 2019 16:00:32: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 16:00:32: #2 alternative fragment length(s) may be 0,39,97,118,135,173,200,269,355,377,500,534,549 bps INFO @ Sun, 02 Jun 2019 16:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.10_model.r WARNING @ Sun, 02 Jun 2019 16:00:32: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:00:32: #2 You may need to consider one of the other alternative d(s): 0,39,97,118,135,173,200,269,355,377,500,534,549 WARNING @ Sun, 02 Jun 2019 16:00:32: #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 16:00:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:00:32: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:00:32: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:00:32: #1 total tags in treatment: 7803802 INFO @ Sun, 02 Jun 2019 16:00:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:00:32: #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 16:00:33: #1 tags after filtering in treatment: 7803802 INFO @ Sun, 02 Jun 2019 16:00:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:00:33: #1 finished! INFO @ Sun, 02 Jun 2019 16:00:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:00:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:00:33: #2 number of paired peaks: 273 WARNING @ Sun, 02 Jun 2019 16:00:33: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Sun, 02 Jun 2019 16:00:33: start model_add_line... INFO @ Sun, 02 Jun 2019 16:00:33: start X-correlation... INFO @ Sun, 02 Jun 2019 16:00:33: end of X-cor INFO @ Sun, 02 Jun 2019 16:00:33: #2 finished! INFO @ Sun, 02 Jun 2019 16:00:33: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 16:00:33: #2 alternative fragment length(s) may be 0,39,97,118,135,173,200,269,355,377,500,534,549 bps INFO @ Sun, 02 Jun 2019 16:00:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.20_model.r WARNING @ Sun, 02 Jun 2019 16:00:33: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:00:33: #2 You may need to consider one of the other alternative d(s): 0,39,97,118,135,173,200,269,355,377,500,534,549 WARNING @ Sun, 02 Jun 2019 16:00:33: #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 16:00:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:00:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:00:36: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 16:00:36: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 16:00:36: #1 total tags in treatment: 7803802 INFO @ Sun, 02 Jun 2019 16:00:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:00:36: #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 16:00:36: #1 tags after filtering in treatment: 7803802 INFO @ Sun, 02 Jun 2019 16:00:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:00:36: #1 finished! INFO @ Sun, 02 Jun 2019 16:00:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:00:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:00:37: #2 number of paired peaks: 273 WARNING @ Sun, 02 Jun 2019 16:00:37: Fewer paired peaks (273) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 273 pairs to build model! INFO @ Sun, 02 Jun 2019 16:00:37: start model_add_line... INFO @ Sun, 02 Jun 2019 16:00:37: start X-correlation... INFO @ Sun, 02 Jun 2019 16:00:37: end of X-cor INFO @ Sun, 02 Jun 2019 16:00:37: #2 finished! INFO @ Sun, 02 Jun 2019 16:00:37: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 16:00:37: #2 alternative fragment length(s) may be 0,39,97,118,135,173,200,269,355,377,500,534,549 bps INFO @ Sun, 02 Jun 2019 16:00:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.05_model.r WARNING @ Sun, 02 Jun 2019 16:00:37: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:00:37: #2 You may need to consider one of the other alternative d(s): 0,39,97,118,135,173,200,269,355,377,500,534,549 WARNING @ Sun, 02 Jun 2019 16:00:37: #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 16:00:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:00:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:00:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:00:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:00:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:01:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:01:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:01:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.10_summits.bed INFO @ Sun, 02 Jun 2019 16:01:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (76 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:01:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:01:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:01:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.20_summits.bed INFO @ Sun, 02 Jun 2019 16:01:04: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (12 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:01:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:01:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:01:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX113604/SRX113604.05_summits.bed INFO @ Sun, 02 Jun 2019 16:01:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (257 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。