Job ID = 1290652 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,147,180 reads read : 11,147,180 reads written : 11,147,180 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: 00:03:09 11147180 reads; of these: 11147180 (100.00%) were unpaired; of these: 192378 (1.73%) aligned 0 times 8676798 (77.84%) aligned exactly 1 time 2278004 (20.44%) aligned >1 times 98.27% overall alignment rate Time searching: 00:03:09 Overall time: 00:03:09 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] 2859644 / 10954802 = 0.2610 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 @ Sat, 01 Jun 2019 21:51:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.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 @ Sat, 01 Jun 2019 21:51:21: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:21: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.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 @ Sat, 01 Jun 2019 21:51:22: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:22: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.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 @ Sat, 01 Jun 2019 21:51:22: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:22: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:31: 1000000 INFO @ Sat, 01 Jun 2019 21:51:31: 1000000 INFO @ Sat, 01 Jun 2019 21:51:31: 1000000 INFO @ Sat, 01 Jun 2019 21:51:40: 2000000 INFO @ Sat, 01 Jun 2019 21:51:40: 2000000 INFO @ Sat, 01 Jun 2019 21:51:40: 2000000 INFO @ Sat, 01 Jun 2019 21:51:49: 3000000 INFO @ Sat, 01 Jun 2019 21:51:49: 3000000 INFO @ Sat, 01 Jun 2019 21:51:49: 3000000 INFO @ Sat, 01 Jun 2019 21:51:57: 4000000 INFO @ Sat, 01 Jun 2019 21:51:58: 4000000 INFO @ Sat, 01 Jun 2019 21:51:58: 4000000 INFO @ Sat, 01 Jun 2019 21:52:06: 5000000 INFO @ Sat, 01 Jun 2019 21:52:07: 5000000 INFO @ Sat, 01 Jun 2019 21:52:07: 5000000 INFO @ Sat, 01 Jun 2019 21:52:15: 6000000 INFO @ Sat, 01 Jun 2019 21:52:16: 6000000 INFO @ Sat, 01 Jun 2019 21:52:16: 6000000 INFO @ Sat, 01 Jun 2019 21:52:23: 7000000 INFO @ Sat, 01 Jun 2019 21:52:25: 7000000 INFO @ Sat, 01 Jun 2019 21:52:25: 7000000 INFO @ Sat, 01 Jun 2019 21:52:32: 8000000 INFO @ Sat, 01 Jun 2019 21:52:33: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:52:33: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:52:33: #1 total tags in treatment: 8095158 INFO @ Sat, 01 Jun 2019 21:52:33: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:33: #1 tags after filtering in treatment: 8095158 INFO @ Sat, 01 Jun 2019 21:52:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:33: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:33: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:34: #2 number of paired peaks: 290 WARNING @ Sat, 01 Jun 2019 21:52:34: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:34: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:34: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:34: 8000000 INFO @ Sat, 01 Jun 2019 21:52:34: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:34: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:34: #2 predicted fragment length is 44 bps INFO @ Sat, 01 Jun 2019 21:52:34: #2 alternative fragment length(s) may be 2,44,518,568,578,590 bps INFO @ Sat, 01 Jun 2019 21:52:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.20_model.r WARNING @ Sat, 01 Jun 2019 21:52:34: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:34: #2 You may need to consider one of the other alternative d(s): 2,44,518,568,578,590 WARNING @ Sat, 01 Jun 2019 21:52:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:52:34: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:34: 8000000 INFO @ Sat, 01 Jun 2019 21:52:35: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:52:35: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:52:35: #1 total tags in treatment: 8095158 INFO @ Sat, 01 Jun 2019 21:52:35: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:35: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:52:35: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:52:35: #1 total tags in treatment: 8095158 INFO @ Sat, 01 Jun 2019 21:52:35: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:35: #1 tags after filtering in treatment: 8095158 INFO @ Sat, 01 Jun 2019 21:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:35: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:35: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:35: #1 tags after filtering in treatment: 8095158 INFO @ Sat, 01 Jun 2019 21:52:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:35: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:35: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:36: #2 number of paired peaks: 290 WARNING @ Sat, 01 Jun 2019 21:52:36: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:36: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:36: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:36: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:36: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:36: #2 predicted fragment length is 44 bps INFO @ Sat, 01 Jun 2019 21:52:36: #2 alternative fragment length(s) may be 2,44,518,568,578,590 bps INFO @ Sat, 01 Jun 2019 21:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.05_model.r WARNING @ Sat, 01 Jun 2019 21:52:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:36: #2 You may need to consider one of the other alternative d(s): 2,44,518,568,578,590 WARNING @ Sat, 01 Jun 2019 21:52:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:52:36: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:36: #2 number of paired peaks: 290 WARNING @ Sat, 01 Jun 2019 21:52:36: Fewer paired peaks (290) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 290 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:36: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:36: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:36: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:36: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:36: #2 predicted fragment length is 44 bps INFO @ Sat, 01 Jun 2019 21:52:36: #2 alternative fragment length(s) may be 2,44,518,568,578,590 bps INFO @ Sat, 01 Jun 2019 21:52:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.10_model.r WARNING @ Sat, 01 Jun 2019 21:52:36: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:36: #2 You may need to consider one of the other alternative d(s): 2,44,518,568,578,590 WARNING @ Sat, 01 Jun 2019 21:52:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:52:36: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:56: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:57: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:57: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.20_summits.bed INFO @ Sat, 01 Jun 2019 21:53:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.05_summits.bed INFO @ Sat, 01 Jun 2019 21:53:08: Done! INFO @ Sat, 01 Jun 2019 21:53:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4200531/SRX4200531.10_summits.bed INFO @ Sat, 01 Jun 2019 21:53:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (414 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (185 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。