Job ID = 1290651 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,867,984 reads read : 10,867,984 reads written : 10,867,984 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: 00:02:50 10867984 reads; of these: 10867984 (100.00%) were unpaired; of these: 475182 (4.37%) aligned 0 times 8415394 (77.43%) aligned exactly 1 time 1977408 (18.19%) aligned >1 times 95.63% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 1009079 / 10392802 = 0.0971 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 21:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.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 21:51:10: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:10: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.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 21:51:10: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:10: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.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 21:51:10: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:10: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:18: 1000000 INFO @ Sat, 01 Jun 2019 21:51:18: 1000000 INFO @ Sat, 01 Jun 2019 21:51:19: 1000000 INFO @ Sat, 01 Jun 2019 21:51:27: 2000000 INFO @ Sat, 01 Jun 2019 21:51:29: 2000000 INFO @ Sat, 01 Jun 2019 21:51:30: 2000000 INFO @ Sat, 01 Jun 2019 21:51:34: 3000000 INFO @ Sat, 01 Jun 2019 21:51:39: 3000000 INFO @ Sat, 01 Jun 2019 21:51:41: 3000000 INFO @ Sat, 01 Jun 2019 21:51:42: 4000000 INFO @ Sat, 01 Jun 2019 21:51:50: 5000000 INFO @ Sat, 01 Jun 2019 21:51:50: 4000000 INFO @ Sat, 01 Jun 2019 21:51:51: 4000000 INFO @ Sat, 01 Jun 2019 21:51:57: 6000000 INFO @ Sat, 01 Jun 2019 21:52:01: 5000000 INFO @ Sat, 01 Jun 2019 21:52:02: 5000000 INFO @ Sat, 01 Jun 2019 21:52:05: 7000000 INFO @ Sat, 01 Jun 2019 21:52:11: 6000000 INFO @ Sat, 01 Jun 2019 21:52:12: 8000000 INFO @ Sat, 01 Jun 2019 21:52:13: 6000000 INFO @ Sat, 01 Jun 2019 21:52:20: 9000000 INFO @ Sat, 01 Jun 2019 21:52:21: 7000000 INFO @ Sat, 01 Jun 2019 21:52:23: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:23: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:23: #1 total tags in treatment: 9383723 INFO @ Sat, 01 Jun 2019 21:52:23: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:23: #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 21:52:23: #1 tags after filtering in treatment: 9383723 INFO @ Sat, 01 Jun 2019 21:52:23: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:23: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:23: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:23: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:23: 7000000 INFO @ Sat, 01 Jun 2019 21:52:24: #2 number of paired peaks: 420 WARNING @ Sat, 01 Jun 2019 21:52:24: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:24: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:24: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:24: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:24: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:24: #2 predicted fragment length is 57 bps INFO @ Sat, 01 Jun 2019 21:52:24: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 01 Jun 2019 21:52:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.20_model.r WARNING @ Sat, 01 Jun 2019 21:52:24: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:24: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 01 Jun 2019 21:52:24: #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 21:52:24: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:32: 8000000 INFO @ Sat, 01 Jun 2019 21:52:33: 8000000 INFO @ Sat, 01 Jun 2019 21:52:42: 9000000 INFO @ Sat, 01 Jun 2019 21:52:43: 9000000 INFO @ Sat, 01 Jun 2019 21:52:46: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:46: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:46: #1 total tags in treatment: 9383723 INFO @ Sat, 01 Jun 2019 21:52:46: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:46: #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 21:52:46: #1 tags after filtering in treatment: 9383723 INFO @ Sat, 01 Jun 2019 21:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:46: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:46: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:47: #2 number of paired peaks: 420 WARNING @ Sat, 01 Jun 2019 21:52:47: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:47: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:47: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:47: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:47: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:47: #2 predicted fragment length is 57 bps INFO @ Sat, 01 Jun 2019 21:52:47: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 01 Jun 2019 21:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.10_model.r WARNING @ Sat, 01 Jun 2019 21:52:47: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:47: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 01 Jun 2019 21:52:47: #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 21:52:47: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:47: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:47: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:47: #1 total tags in treatment: 9383723 INFO @ Sat, 01 Jun 2019 21:52:47: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:47: #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 21:52:47: #1 tags after filtering in treatment: 9383723 INFO @ Sat, 01 Jun 2019 21:52:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:47: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:47: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:48: #2 number of paired peaks: 420 WARNING @ Sat, 01 Jun 2019 21:52:48: Fewer paired peaks (420) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 420 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:48: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:48: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:48: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:48: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:48: #2 predicted fragment length is 57 bps INFO @ Sat, 01 Jun 2019 21:52:48: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 01 Jun 2019 21:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.05_model.r WARNING @ Sat, 01 Jun 2019 21:52:48: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:48: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 01 Jun 2019 21:52:48: #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 21:52:48: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:49: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.20_summits.bed INFO @ Sat, 01 Jun 2019 21:53:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (181 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:13: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:14: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.10_summits.bed INFO @ Sat, 01 Jun 2019 21:53:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (447 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX982085/SRX982085.05_summits.bed INFO @ Sat, 01 Jun 2019 21:53:27: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1155 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。