Job ID = 2589658 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,095,968 reads read : 7,095,968 reads written : 7,095,968 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:18 7095968 reads; of these: 7095968 (100.00%) were unpaired; of these: 922414 (13.00%) aligned 0 times 5237358 (73.81%) aligned exactly 1 time 936196 (13.19%) aligned >1 times 87.00% overall alignment rate Time searching: 00:01:18 Overall time: 00:01:18 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] 581828 / 6173554 = 0.0942 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 @ Mon, 12 Aug 2019 18:15:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.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 @ Mon, 12 Aug 2019 18:15:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:15:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:15:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.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 @ Mon, 12 Aug 2019 18:15:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:15:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:15:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.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 @ Mon, 12 Aug 2019 18:15:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:15:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:15:23: 1000000 INFO @ Mon, 12 Aug 2019 18:15:24: 1000000 INFO @ Mon, 12 Aug 2019 18:15:30: 1000000 INFO @ Mon, 12 Aug 2019 18:15:31: 2000000 INFO @ Mon, 12 Aug 2019 18:15:36: 2000000 INFO @ Mon, 12 Aug 2019 18:15:38: 3000000 INFO @ Mon, 12 Aug 2019 18:15:41: 2000000 INFO @ Mon, 12 Aug 2019 18:15:45: 4000000 INFO @ Mon, 12 Aug 2019 18:15:47: 3000000 INFO @ Mon, 12 Aug 2019 18:15:52: 5000000 INFO @ Mon, 12 Aug 2019 18:15:52: 3000000 INFO @ Mon, 12 Aug 2019 18:15:56: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:15:56: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:15:56: #1 total tags in treatment: 5591726 INFO @ Mon, 12 Aug 2019 18:15:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:15:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:15:56: #1 tags after filtering in treatment: 5591726 INFO @ Mon, 12 Aug 2019 18:15:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:15:56: #1 finished! INFO @ Mon, 12 Aug 2019 18:15:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:15:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:15:56: #2 number of paired peaks: 390 WARNING @ Mon, 12 Aug 2019 18:15:56: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Mon, 12 Aug 2019 18:15:56: start model_add_line... INFO @ Mon, 12 Aug 2019 18:15:56: start X-correlation... INFO @ Mon, 12 Aug 2019 18:15:56: end of X-cor INFO @ Mon, 12 Aug 2019 18:15:56: #2 finished! INFO @ Mon, 12 Aug 2019 18:15:56: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:15:56: #2 alternative fragment length(s) may be 2,30,570,596 bps INFO @ Mon, 12 Aug 2019 18:15:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.10_model.r WARNING @ Mon, 12 Aug 2019 18:15:57: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:15:57: #2 You may need to consider one of the other alternative d(s): 2,30,570,596 WARNING @ Mon, 12 Aug 2019 18:15:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:15:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:15:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:15:57: 4000000 INFO @ Mon, 12 Aug 2019 18:16:02: 4000000 INFO @ Mon, 12 Aug 2019 18:16:07: 5000000 INFO @ Mon, 12 Aug 2019 18:16:11: 5000000 INFO @ Mon, 12 Aug 2019 18:16:12: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:16:12: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:16:12: #1 total tags in treatment: 5591726 INFO @ Mon, 12 Aug 2019 18:16:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:16:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:16:12: #1 tags after filtering in treatment: 5591726 INFO @ Mon, 12 Aug 2019 18:16:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:16:12: #1 finished! INFO @ Mon, 12 Aug 2019 18:16:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:16:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:16:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:16:13: #2 number of paired peaks: 390 WARNING @ Mon, 12 Aug 2019 18:16:13: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Mon, 12 Aug 2019 18:16:13: start model_add_line... INFO @ Mon, 12 Aug 2019 18:16:13: start X-correlation... INFO @ Mon, 12 Aug 2019 18:16:13: end of X-cor INFO @ Mon, 12 Aug 2019 18:16:13: #2 finished! INFO @ Mon, 12 Aug 2019 18:16:13: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:16:13: #2 alternative fragment length(s) may be 2,30,570,596 bps INFO @ Mon, 12 Aug 2019 18:16:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.05_model.r WARNING @ Mon, 12 Aug 2019 18:16:13: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:16:13: #2 You may need to consider one of the other alternative d(s): 2,30,570,596 WARNING @ Mon, 12 Aug 2019 18:16:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:16:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:16:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:16:16: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:16:16: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:16:16: #1 total tags in treatment: 5591726 INFO @ Mon, 12 Aug 2019 18:16:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:16:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:16:16: #1 tags after filtering in treatment: 5591726 INFO @ Mon, 12 Aug 2019 18:16:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:16:16: #1 finished! INFO @ Mon, 12 Aug 2019 18:16:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:16:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:16:16: #2 number of paired peaks: 390 WARNING @ Mon, 12 Aug 2019 18:16:16: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Mon, 12 Aug 2019 18:16:16: start model_add_line... INFO @ Mon, 12 Aug 2019 18:16:16: start X-correlation... INFO @ Mon, 12 Aug 2019 18:16:16: end of X-cor INFO @ Mon, 12 Aug 2019 18:16:16: #2 finished! INFO @ Mon, 12 Aug 2019 18:16:16: #2 predicted fragment length is 30 bps INFO @ Mon, 12 Aug 2019 18:16:16: #2 alternative fragment length(s) may be 2,30,570,596 bps INFO @ Mon, 12 Aug 2019 18:16:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.20_model.r WARNING @ Mon, 12 Aug 2019 18:16:16: #2 Since the d (30) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:16:16: #2 You may need to consider one of the other alternative d(s): 2,30,570,596 WARNING @ Mon, 12 Aug 2019 18:16:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 18:16:16: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:16:16: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:16:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:16:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:16:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.10_summits.bed INFO @ Mon, 12 Aug 2019 18:16:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (198 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:16:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:16:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:16:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:16:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:16:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.05_summits.bed INFO @ Mon, 12 Aug 2019 18:16:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:16:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:16:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:16:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277102/SRX277102.20_summits.bed INFO @ Mon, 12 Aug 2019 18:16:40: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (53 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。