Job ID = 2590235 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,679,048 reads read : 32,679,048 reads written : 32,679,048 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: 00:07:07 32679048 reads; of these: 32679048 (100.00%) were unpaired; of these: 20156595 (61.68%) aligned 0 times 10447958 (31.97%) aligned exactly 1 time 2074495 (6.35%) aligned >1 times 38.32% overall alignment rate Time searching: 00:07:07 Overall time: 00:07:07 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] 915545 / 12522453 = 0.0731 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 20:46:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.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 20:46:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:46:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.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 20:46:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:46:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:46:08: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.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 20:46:08: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:46:08: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:46:15: 1000000 INFO @ Mon, 12 Aug 2019 20:46:17: 1000000 INFO @ Mon, 12 Aug 2019 20:46:18: 1000000 INFO @ Mon, 12 Aug 2019 20:46:23: 2000000 INFO @ Mon, 12 Aug 2019 20:46:26: 2000000 INFO @ Mon, 12 Aug 2019 20:46:27: 2000000 INFO @ Mon, 12 Aug 2019 20:46:31: 3000000 INFO @ Mon, 12 Aug 2019 20:46:34: 3000000 INFO @ Mon, 12 Aug 2019 20:46:35: 3000000 INFO @ Mon, 12 Aug 2019 20:46:39: 4000000 INFO @ Mon, 12 Aug 2019 20:46:43: 4000000 INFO @ Mon, 12 Aug 2019 20:46:44: 4000000 INFO @ Mon, 12 Aug 2019 20:46:47: 5000000 INFO @ Mon, 12 Aug 2019 20:46:52: 5000000 INFO @ Mon, 12 Aug 2019 20:46:53: 5000000 INFO @ Mon, 12 Aug 2019 20:46:55: 6000000 INFO @ Mon, 12 Aug 2019 20:47:01: 6000000 INFO @ Mon, 12 Aug 2019 20:47:02: 6000000 INFO @ Mon, 12 Aug 2019 20:47:03: 7000000 INFO @ Mon, 12 Aug 2019 20:47:11: 7000000 INFO @ Mon, 12 Aug 2019 20:47:11: 8000000 INFO @ Mon, 12 Aug 2019 20:47:11: 7000000 INFO @ Mon, 12 Aug 2019 20:47:20: 9000000 INFO @ Mon, 12 Aug 2019 20:47:20: 8000000 INFO @ Mon, 12 Aug 2019 20:47:21: 8000000 INFO @ Mon, 12 Aug 2019 20:47:28: 10000000 INFO @ Mon, 12 Aug 2019 20:47:29: 9000000 INFO @ Mon, 12 Aug 2019 20:47:30: 9000000 INFO @ Mon, 12 Aug 2019 20:47:36: 11000000 INFO @ Mon, 12 Aug 2019 20:47:38: 10000000 INFO @ Mon, 12 Aug 2019 20:47:39: 10000000 INFO @ Mon, 12 Aug 2019 20:47:41: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:47:41: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:47:41: #1 total tags in treatment: 11606908 INFO @ Mon, 12 Aug 2019 20:47:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:47:41: #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 20:47:41: #1 tags after filtering in treatment: 11606908 INFO @ Mon, 12 Aug 2019 20:47:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:47:41: #1 finished! INFO @ Mon, 12 Aug 2019 20:47:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:47:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:47:42: #2 number of paired peaks: 308 WARNING @ Mon, 12 Aug 2019 20:47:42: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Mon, 12 Aug 2019 20:47:42: start model_add_line... INFO @ Mon, 12 Aug 2019 20:47:42: start X-correlation... INFO @ Mon, 12 Aug 2019 20:47:42: end of X-cor INFO @ Mon, 12 Aug 2019 20:47:42: #2 finished! INFO @ Mon, 12 Aug 2019 20:47:42: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 20:47:42: #2 alternative fragment length(s) may be 3,71 bps INFO @ Mon, 12 Aug 2019 20:47:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.05_model.r WARNING @ Mon, 12 Aug 2019 20:47:42: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:47:42: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Mon, 12 Aug 2019 20:47:42: #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 20:47:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:47:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:47:47: 11000000 INFO @ Mon, 12 Aug 2019 20:47:48: 11000000 INFO @ Mon, 12 Aug 2019 20:47:52: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:47:52: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:47:52: #1 total tags in treatment: 11606908 INFO @ Mon, 12 Aug 2019 20:47:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:47:52: #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 20:47:52: #1 tags after filtering in treatment: 11606908 INFO @ Mon, 12 Aug 2019 20:47:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:47:52: #1 finished! INFO @ Mon, 12 Aug 2019 20:47:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:47:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:47:53: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:47:53: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:47:53: #1 total tags in treatment: 11606908 INFO @ Mon, 12 Aug 2019 20:47:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:47:53: #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 20:47:53: #1 tags after filtering in treatment: 11606908 INFO @ Mon, 12 Aug 2019 20:47:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:47:53: #1 finished! INFO @ Mon, 12 Aug 2019 20:47:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:47:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:47:53: #2 number of paired peaks: 308 WARNING @ Mon, 12 Aug 2019 20:47:53: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Mon, 12 Aug 2019 20:47:53: start model_add_line... INFO @ Mon, 12 Aug 2019 20:47:53: start X-correlation... INFO @ Mon, 12 Aug 2019 20:47:54: end of X-cor INFO @ Mon, 12 Aug 2019 20:47:54: #2 finished! INFO @ Mon, 12 Aug 2019 20:47:54: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 20:47:54: #2 alternative fragment length(s) may be 3,71 bps INFO @ Mon, 12 Aug 2019 20:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.10_model.r WARNING @ Mon, 12 Aug 2019 20:47:54: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:47:54: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Mon, 12 Aug 2019 20:47:54: #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 20:47:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:47:54: #2 number of paired peaks: 308 WARNING @ Mon, 12 Aug 2019 20:47:54: Fewer paired peaks (308) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 308 pairs to build model! INFO @ Mon, 12 Aug 2019 20:47:54: start model_add_line... INFO @ Mon, 12 Aug 2019 20:47:54: start X-correlation... INFO @ Mon, 12 Aug 2019 20:47:54: end of X-cor INFO @ Mon, 12 Aug 2019 20:47:54: #2 finished! INFO @ Mon, 12 Aug 2019 20:47:54: #2 predicted fragment length is 71 bps INFO @ Mon, 12 Aug 2019 20:47:54: #2 alternative fragment length(s) may be 3,71 bps INFO @ Mon, 12 Aug 2019 20:47:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.20_model.r WARNING @ Mon, 12 Aug 2019 20:47:54: #2 Since the d (71) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:47:54: #2 You may need to consider one of the other alternative d(s): 3,71 WARNING @ Mon, 12 Aug 2019 20:47:54: #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 20:47:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:47:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:48:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:48:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:48:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:48:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:48:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:48:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.05_summits.bed INFO @ Mon, 12 Aug 2019 20:48:27: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (542 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:48:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:48:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:48:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.10_summits.bed INFO @ Mon, 12 Aug 2019 20:48:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (415 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:48:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:48:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:48:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985669/SRX5985669.20_summits.bed INFO @ Mon, 12 Aug 2019 20:48:39: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (235 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。