Job ID = 2589219 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,220,063 reads read : 4,220,063 reads written : 4,220,063 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR163973.sra.cache’: 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: 00:00:43 4220063 reads; of these: 4220063 (100.00%) were unpaired; of these: 1201130 (28.46%) aligned 0 times 2673860 (63.36%) aligned exactly 1 time 345073 (8.18%) aligned >1 times 71.54% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 223636 / 3018933 = 0.0741 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 17:11:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.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 17:11:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:11:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.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 17:11:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:11:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:11:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.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 17:11:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:11:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:11:42: 1000000 INFO @ Mon, 12 Aug 2019 17:11:43: 1000000 INFO @ Mon, 12 Aug 2019 17:11:44: 1000000 INFO @ Mon, 12 Aug 2019 17:11:51: 2000000 INFO @ Mon, 12 Aug 2019 17:11:52: 2000000 INFO @ Mon, 12 Aug 2019 17:11:53: 2000000 INFO @ Mon, 12 Aug 2019 17:11:58: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:11:58: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:11:58: #1 total tags in treatment: 2795297 INFO @ Mon, 12 Aug 2019 17:11:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:11:58: #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 17:11:58: #1 tags after filtering in treatment: 2795297 INFO @ Mon, 12 Aug 2019 17:11:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:11:58: #1 finished! INFO @ Mon, 12 Aug 2019 17:11:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:11:58: #2 number of paired peaks: 161 WARNING @ Mon, 12 Aug 2019 17:11:58: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 12 Aug 2019 17:11:58: start model_add_line... INFO @ Mon, 12 Aug 2019 17:11:58: start X-correlation... INFO @ Mon, 12 Aug 2019 17:11:58: end of X-cor INFO @ Mon, 12 Aug 2019 17:11:58: #2 finished! INFO @ Mon, 12 Aug 2019 17:11:58: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 17:11:58: #2 alternative fragment length(s) may be 4,46,59,163,214,300,461,478,504,511,571,592 bps INFO @ Mon, 12 Aug 2019 17:11:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.05_model.r WARNING @ Mon, 12 Aug 2019 17:11:58: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:11:58: #2 You may need to consider one of the other alternative d(s): 4,46,59,163,214,300,461,478,504,511,571,592 WARNING @ Mon, 12 Aug 2019 17:11:58: #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 17:11:58: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:11:58: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:11:59: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:11:59: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:11:59: #1 total tags in treatment: 2795297 INFO @ Mon, 12 Aug 2019 17:11:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:11:59: #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 17:11:59: #1 tags after filtering in treatment: 2795297 INFO @ Mon, 12 Aug 2019 17:11:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:11:59: #1 finished! INFO @ Mon, 12 Aug 2019 17:11:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:11:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:11:59: #2 number of paired peaks: 161 WARNING @ Mon, 12 Aug 2019 17:11:59: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 12 Aug 2019 17:11:59: start model_add_line... INFO @ Mon, 12 Aug 2019 17:11:59: start X-correlation... INFO @ Mon, 12 Aug 2019 17:11:59: end of X-cor INFO @ Mon, 12 Aug 2019 17:11:59: #2 finished! INFO @ Mon, 12 Aug 2019 17:11:59: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 17:11:59: #2 alternative fragment length(s) may be 4,46,59,163,214,300,461,478,504,511,571,592 bps INFO @ Mon, 12 Aug 2019 17:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.10_model.r WARNING @ Mon, 12 Aug 2019 17:11:59: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:11:59: #2 You may need to consider one of the other alternative d(s): 4,46,59,163,214,300,461,478,504,511,571,592 WARNING @ Mon, 12 Aug 2019 17:11:59: #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 17:11:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:11:59: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:11:59: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:11:59: #1 total tags in treatment: 2795297 INFO @ Mon, 12 Aug 2019 17:11:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:11:59: #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 17:12:00: #1 tags after filtering in treatment: 2795297 INFO @ Mon, 12 Aug 2019 17:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:12:00: #1 finished! INFO @ Mon, 12 Aug 2019 17:12:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:12:00: #2 number of paired peaks: 161 WARNING @ Mon, 12 Aug 2019 17:12:00: Fewer paired peaks (161) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 161 pairs to build model! INFO @ Mon, 12 Aug 2019 17:12:00: start model_add_line... INFO @ Mon, 12 Aug 2019 17:12:00: start X-correlation... INFO @ Mon, 12 Aug 2019 17:12:00: end of X-cor INFO @ Mon, 12 Aug 2019 17:12:00: #2 finished! INFO @ Mon, 12 Aug 2019 17:12:00: #2 predicted fragment length is 59 bps INFO @ Mon, 12 Aug 2019 17:12:00: #2 alternative fragment length(s) may be 4,46,59,163,214,300,461,478,504,511,571,592 bps INFO @ Mon, 12 Aug 2019 17:12:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.20_model.r WARNING @ Mon, 12 Aug 2019 17:12:00: #2 Since the d (59) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:12:00: #2 You may need to consider one of the other alternative d(s): 4,46,59,163,214,300,461,478,504,511,571,592 WARNING @ Mon, 12 Aug 2019 17:12:00: #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 17:12:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:12:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:12:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:12:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:12:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:12:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:12:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:12:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.05_summits.bed INFO @ Mon, 12 Aug 2019 17:12:11: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (106 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:12:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:12:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:12:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.10_summits.bed INFO @ Mon, 12 Aug 2019 17:12:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:12:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:12:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:12:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX054207/SRX054207.20_summits.bed INFO @ Mon, 12 Aug 2019 17:12:13: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (8 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。