Job ID = 1291815 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,761,013 reads read : 13,761,013 reads written : 13,761,013 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: 00:03:52 13761013 reads; of these: 13761013 (100.00%) were unpaired; of these: 720055 (5.23%) aligned 0 times 10797897 (78.47%) aligned exactly 1 time 2243061 (16.30%) aligned >1 times 94.77% overall alignment rate Time searching: 00:03:52 Overall time: 00:03:52 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] 1092317 / 13040958 = 0.0838 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 16:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.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 16:45:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:45:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.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 16:45:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:45:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:45:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.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 16:45:34: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:45:34: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:45:42: 1000000 INFO @ Sun, 02 Jun 2019 16:45:43: 1000000 INFO @ Sun, 02 Jun 2019 16:45:43: 1000000 INFO @ Sun, 02 Jun 2019 16:45:49: 2000000 INFO @ Sun, 02 Jun 2019 16:45:51: 2000000 INFO @ Sun, 02 Jun 2019 16:45:52: 2000000 INFO @ Sun, 02 Jun 2019 16:45:56: 3000000 INFO @ Sun, 02 Jun 2019 16:46:00: 3000000 INFO @ Sun, 02 Jun 2019 16:46:00: 3000000 INFO @ Sun, 02 Jun 2019 16:46:03: 4000000 INFO @ Sun, 02 Jun 2019 16:46:08: 4000000 INFO @ Sun, 02 Jun 2019 16:46:09: 4000000 INFO @ Sun, 02 Jun 2019 16:46:11: 5000000 INFO @ Sun, 02 Jun 2019 16:46:16: 5000000 INFO @ Sun, 02 Jun 2019 16:46:17: 5000000 INFO @ Sun, 02 Jun 2019 16:46:18: 6000000 INFO @ Sun, 02 Jun 2019 16:46:24: 6000000 INFO @ Sun, 02 Jun 2019 16:46:25: 6000000 INFO @ Sun, 02 Jun 2019 16:46:25: 7000000 INFO @ Sun, 02 Jun 2019 16:46:32: 7000000 INFO @ Sun, 02 Jun 2019 16:46:33: 8000000 INFO @ Sun, 02 Jun 2019 16:46:34: 7000000 INFO @ Sun, 02 Jun 2019 16:46:40: 9000000 INFO @ Sun, 02 Jun 2019 16:46:40: 8000000 INFO @ Sun, 02 Jun 2019 16:46:42: 8000000 INFO @ Sun, 02 Jun 2019 16:46:47: 10000000 INFO @ Sun, 02 Jun 2019 16:46:48: 9000000 INFO @ Sun, 02 Jun 2019 16:46:50: 9000000 INFO @ Sun, 02 Jun 2019 16:46:54: 11000000 INFO @ Sun, 02 Jun 2019 16:46:56: 10000000 INFO @ Sun, 02 Jun 2019 16:46:58: 10000000 INFO @ Sun, 02 Jun 2019 16:47:02: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:47:02: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:47:02: #1 total tags in treatment: 11948641 INFO @ Sun, 02 Jun 2019 16:47:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:02: #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 16:47:02: #1 tags after filtering in treatment: 11948641 INFO @ Sun, 02 Jun 2019 16:47:02: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:02: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:02: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:02: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:03: #2 number of paired peaks: 313 WARNING @ Sun, 02 Jun 2019 16:47:03: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:03: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:03: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:03: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:03: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:03: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 16:47:03: #2 alternative fragment length(s) may be 2,44 bps INFO @ Sun, 02 Jun 2019 16:47:03: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.20_model.r WARNING @ Sun, 02 Jun 2019 16:47:03: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:47:03: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Sun, 02 Jun 2019 16:47:03: #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 16:47:03: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:03: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:04: 11000000 INFO @ Sun, 02 Jun 2019 16:47:06: 11000000 INFO @ Sun, 02 Jun 2019 16:47:12: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:47:12: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:47:12: #1 total tags in treatment: 11948641 INFO @ Sun, 02 Jun 2019 16:47:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:12: #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 16:47:12: #1 tags after filtering in treatment: 11948641 INFO @ Sun, 02 Jun 2019 16:47:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:12: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:13: #2 number of paired peaks: 313 WARNING @ Sun, 02 Jun 2019 16:47:13: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:13: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:13: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:13: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:13: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:13: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 16:47:13: #2 alternative fragment length(s) may be 2,44 bps INFO @ Sun, 02 Jun 2019 16:47:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.05_model.r WARNING @ Sun, 02 Jun 2019 16:47:13: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:47:13: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Sun, 02 Jun 2019 16:47:13: #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 16:47:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:14: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 16:47:14: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 16:47:14: #1 total tags in treatment: 11948641 INFO @ Sun, 02 Jun 2019 16:47:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:47:14: #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 16:47:14: #1 tags after filtering in treatment: 11948641 INFO @ Sun, 02 Jun 2019 16:47:14: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:47:14: #1 finished! INFO @ Sun, 02 Jun 2019 16:47:14: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:47:14: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:47:16: #2 number of paired peaks: 313 WARNING @ Sun, 02 Jun 2019 16:47:16: Fewer paired peaks (313) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 313 pairs to build model! INFO @ Sun, 02 Jun 2019 16:47:16: start model_add_line... INFO @ Sun, 02 Jun 2019 16:47:16: start X-correlation... INFO @ Sun, 02 Jun 2019 16:47:16: end of X-cor INFO @ Sun, 02 Jun 2019 16:47:16: #2 finished! INFO @ Sun, 02 Jun 2019 16:47:16: #2 predicted fragment length is 44 bps INFO @ Sun, 02 Jun 2019 16:47:16: #2 alternative fragment length(s) may be 2,44 bps INFO @ Sun, 02 Jun 2019 16:47:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.10_model.r WARNING @ Sun, 02 Jun 2019 16:47:16: #2 Since the d (44) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 16:47:16: #2 You may need to consider one of the other alternative d(s): 2,44 WARNING @ Sun, 02 Jun 2019 16:47:16: #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 16:47:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:47:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:47:34: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:47: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:47:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:47:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:47:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.20_summits.bed INFO @ Sun, 02 Jun 2019 16:47:50: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.05_summits.bed INFO @ Sun, 02 Jun 2019 16:48:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (679 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:48:04: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:48:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:48:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257656/SRX257656.10_summits.bed INFO @ Sun, 02 Jun 2019 16:48:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (421 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。