Job ID = 1292353 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,184,450 reads read : 18,184,450 reads written : 18,184,450 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: 00:04:40 18184450 reads; of these: 18184450 (100.00%) were unpaired; of these: 1329593 (7.31%) aligned 0 times 13803224 (75.91%) aligned exactly 1 time 3051633 (16.78%) aligned >1 times 92.69% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 5274772 / 16854857 = 0.3130 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 18:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.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 18:05:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:05:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.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 18:05:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:05:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.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 18:05:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:05:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:05:37: 1000000 INFO @ Sun, 02 Jun 2019 18:05:38: 1000000 INFO @ Sun, 02 Jun 2019 18:05:39: 1000000 INFO @ Sun, 02 Jun 2019 18:05:44: 2000000 INFO @ Sun, 02 Jun 2019 18:05:46: 2000000 INFO @ Sun, 02 Jun 2019 18:05:49: 2000000 INFO @ Sun, 02 Jun 2019 18:05:52: 3000000 INFO @ Sun, 02 Jun 2019 18:05:54: 3000000 INFO @ Sun, 02 Jun 2019 18:05:59: 3000000 INFO @ Sun, 02 Jun 2019 18:05:59: 4000000 INFO @ Sun, 02 Jun 2019 18:06:03: 4000000 INFO @ Sun, 02 Jun 2019 18:06:07: 5000000 INFO @ Sun, 02 Jun 2019 18:06:09: 4000000 INFO @ Sun, 02 Jun 2019 18:06:11: 5000000 INFO @ Sun, 02 Jun 2019 18:06:14: 6000000 INFO @ Sun, 02 Jun 2019 18:06:19: 5000000 INFO @ Sun, 02 Jun 2019 18:06:19: 6000000 INFO @ Sun, 02 Jun 2019 18:06:22: 7000000 INFO @ Sun, 02 Jun 2019 18:06:27: 7000000 INFO @ Sun, 02 Jun 2019 18:06:29: 6000000 INFO @ Sun, 02 Jun 2019 18:06:29: 8000000 INFO @ Sun, 02 Jun 2019 18:06:35: 8000000 INFO @ Sun, 02 Jun 2019 18:06:37: 9000000 INFO @ Sun, 02 Jun 2019 18:06:39: 7000000 INFO @ Sun, 02 Jun 2019 18:06:44: 9000000 INFO @ Sun, 02 Jun 2019 18:06:45: 10000000 INFO @ Sun, 02 Jun 2019 18:06:48: 8000000 INFO @ Sun, 02 Jun 2019 18:06:52: 10000000 INFO @ Sun, 02 Jun 2019 18:06:54: 11000000 INFO @ Sun, 02 Jun 2019 18:06:58: 9000000 INFO @ Sun, 02 Jun 2019 18:06:59: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:06:59: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:06:59: #1 total tags in treatment: 11580085 INFO @ Sun, 02 Jun 2019 18:06:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:06:59: #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 18:06:59: #1 tags after filtering in treatment: 11580085 INFO @ Sun, 02 Jun 2019 18:06:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:06:59: #1 finished! INFO @ Sun, 02 Jun 2019 18:06:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:06:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:07:00: #2 number of paired peaks: 335 WARNING @ Sun, 02 Jun 2019 18:07:00: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 02 Jun 2019 18:07:00: start model_add_line... INFO @ Sun, 02 Jun 2019 18:07:00: start X-correlation... INFO @ Sun, 02 Jun 2019 18:07:00: end of X-cor INFO @ Sun, 02 Jun 2019 18:07:00: #2 finished! INFO @ Sun, 02 Jun 2019 18:07:00: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 18:07:00: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 02 Jun 2019 18:07:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.05_model.r WARNING @ Sun, 02 Jun 2019 18:07:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:07:00: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 02 Jun 2019 18:07:00: #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 18:07:00: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:07:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:07:00: 11000000 INFO @ Sun, 02 Jun 2019 18:07:05: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:07:05: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:07:05: #1 total tags in treatment: 11580085 INFO @ Sun, 02 Jun 2019 18:07:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:07:05: #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 18:07:05: #1 tags after filtering in treatment: 11580085 INFO @ Sun, 02 Jun 2019 18:07:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:07:05: #1 finished! INFO @ Sun, 02 Jun 2019 18:07:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:07:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:07:06: #2 number of paired peaks: 335 WARNING @ Sun, 02 Jun 2019 18:07:06: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 02 Jun 2019 18:07:06: start model_add_line... INFO @ Sun, 02 Jun 2019 18:07:06: start X-correlation... INFO @ Sun, 02 Jun 2019 18:07:06: end of X-cor INFO @ Sun, 02 Jun 2019 18:07:06: #2 finished! INFO @ Sun, 02 Jun 2019 18:07:06: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 18:07:06: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 02 Jun 2019 18:07:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.10_model.r WARNING @ Sun, 02 Jun 2019 18:07:06: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:07:06: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 02 Jun 2019 18:07:06: #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 18:07:06: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:07:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:07:08: 10000000 INFO @ Sun, 02 Jun 2019 18:07:17: 11000000 INFO @ Sun, 02 Jun 2019 18:07:23: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 18:07:23: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 18:07:23: #1 total tags in treatment: 11580085 INFO @ Sun, 02 Jun 2019 18:07:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:07:23: #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 18:07:23: #1 tags after filtering in treatment: 11580085 INFO @ Sun, 02 Jun 2019 18:07:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:07:23: #1 finished! INFO @ Sun, 02 Jun 2019 18:07:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:07:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:07:24: #2 number of paired peaks: 335 WARNING @ Sun, 02 Jun 2019 18:07:24: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 02 Jun 2019 18:07:24: start model_add_line... INFO @ Sun, 02 Jun 2019 18:07:24: start X-correlation... INFO @ Sun, 02 Jun 2019 18:07:24: end of X-cor INFO @ Sun, 02 Jun 2019 18:07:24: #2 finished! INFO @ Sun, 02 Jun 2019 18:07:24: #2 predicted fragment length is 53 bps INFO @ Sun, 02 Jun 2019 18:07:24: #2 alternative fragment length(s) may be 2,53 bps INFO @ Sun, 02 Jun 2019 18:07:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.20_model.r WARNING @ Sun, 02 Jun 2019 18:07:24: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:07:24: #2 You may need to consider one of the other alternative d(s): 2,53 WARNING @ Sun, 02 Jun 2019 18:07:24: #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 18:07:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:07:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:07:30: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:07:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:07:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:07:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:07:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.05_summits.bed INFO @ Sun, 02 Jun 2019 18:07:45: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (666 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:07:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:07:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:07:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.10_summits.bed INFO @ Sun, 02 Jun 2019 18:07:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (434 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:07:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:08:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:08:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:08:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX373266/SRX373266.20_summits.bed INFO @ Sun, 02 Jun 2019 18:08:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (178 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。