Job ID = 2590303 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,127,616 reads read : 18,127,616 reads written : 18,127,616 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: 00:09:02 18127616 reads; of these: 18127616 (100.00%) were unpaired; of these: 720392 (3.97%) aligned 0 times 10742673 (59.26%) aligned exactly 1 time 6664551 (36.76%) aligned >1 times 96.03% overall alignment rate Time searching: 00:09:02 Overall time: 00:09:02 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3066646 / 17407224 = 0.1762 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 20:55:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.bam'] # control file = None # effective genome size = 1.20e+08 # 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 20:55:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:55:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:55:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.bam'] # control file = None # effective genome size = 1.20e+08 # 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 20:55:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:55:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:55:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.bam'] # control file = None # effective genome size = 1.20e+08 # 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 20:55:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:55:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:55:09: 1000000 INFO @ Mon, 12 Aug 2019 20:55:11: 1000000 INFO @ Mon, 12 Aug 2019 20:55:13: 1000000 INFO @ Mon, 12 Aug 2019 20:55:16: 2000000 INFO @ Mon, 12 Aug 2019 20:55:21: 2000000 INFO @ Mon, 12 Aug 2019 20:55:23: 2000000 INFO @ Mon, 12 Aug 2019 20:55:24: 3000000 INFO @ Mon, 12 Aug 2019 20:55:30: 3000000 INFO @ Mon, 12 Aug 2019 20:55:31: 4000000 INFO @ Mon, 12 Aug 2019 20:55:32: 3000000 INFO @ Mon, 12 Aug 2019 20:55:39: 4000000 INFO @ Mon, 12 Aug 2019 20:55:40: 5000000 INFO @ Mon, 12 Aug 2019 20:55:41: 4000000 INFO @ Mon, 12 Aug 2019 20:55:47: 6000000 INFO @ Mon, 12 Aug 2019 20:55:48: 5000000 INFO @ Mon, 12 Aug 2019 20:55:51: 5000000 INFO @ Mon, 12 Aug 2019 20:55:55: 7000000 INFO @ Mon, 12 Aug 2019 20:55:57: 6000000 INFO @ Mon, 12 Aug 2019 20:56:01: 6000000 INFO @ Mon, 12 Aug 2019 20:56:03: 8000000 INFO @ Mon, 12 Aug 2019 20:56:07: 7000000 INFO @ Mon, 12 Aug 2019 20:56:10: 9000000 INFO @ Mon, 12 Aug 2019 20:56:11: 7000000 INFO @ Mon, 12 Aug 2019 20:56:16: 8000000 INFO @ Mon, 12 Aug 2019 20:56:18: 10000000 INFO @ Mon, 12 Aug 2019 20:56:20: 8000000 INFO @ Mon, 12 Aug 2019 20:56:25: 11000000 INFO @ Mon, 12 Aug 2019 20:56:26: 9000000 INFO @ Mon, 12 Aug 2019 20:56:30: 9000000 INFO @ Mon, 12 Aug 2019 20:56:32: 12000000 INFO @ Mon, 12 Aug 2019 20:56:35: 10000000 INFO @ Mon, 12 Aug 2019 20:56:40: 13000000 INFO @ Mon, 12 Aug 2019 20:56:40: 10000000 INFO @ Mon, 12 Aug 2019 20:56:44: 11000000 INFO @ Mon, 12 Aug 2019 20:56:47: 14000000 INFO @ Mon, 12 Aug 2019 20:56:49: 11000000 INFO @ Mon, 12 Aug 2019 20:56:50: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:56:50: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:56:50: #1 total tags in treatment: 14340578 INFO @ Mon, 12 Aug 2019 20:56:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:56:50: #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 20:56:50: #1 tags after filtering in treatment: 14340578 INFO @ Mon, 12 Aug 2019 20:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:56:50: #1 finished! INFO @ Mon, 12 Aug 2019 20:56:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:56:51: #2 number of paired peaks: 789 WARNING @ Mon, 12 Aug 2019 20:56:51: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Mon, 12 Aug 2019 20:56:51: start model_add_line... INFO @ Mon, 12 Aug 2019 20:56:52: start X-correlation... INFO @ Mon, 12 Aug 2019 20:56:52: end of X-cor INFO @ Mon, 12 Aug 2019 20:56:52: #2 finished! INFO @ Mon, 12 Aug 2019 20:56:52: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 20:56:52: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 12 Aug 2019 20:56:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.10_model.r WARNING @ Mon, 12 Aug 2019 20:56:52: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:56:52: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 12 Aug 2019 20:56:52: #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 20:56:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:56:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:56:52: 12000000 INFO @ Mon, 12 Aug 2019 20:56:58: 12000000 INFO @ Mon, 12 Aug 2019 20:57:01: 13000000 INFO @ Mon, 12 Aug 2019 20:57:06: 13000000 INFO @ Mon, 12 Aug 2019 20:57:09: 14000000 INFO @ Mon, 12 Aug 2019 20:57:12: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:57:12: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:57:12: #1 total tags in treatment: 14340578 INFO @ Mon, 12 Aug 2019 20:57:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:57:12: #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 20:57:13: #1 tags after filtering in treatment: 14340578 INFO @ Mon, 12 Aug 2019 20:57:13: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:57:13: #1 finished! INFO @ Mon, 12 Aug 2019 20:57:13: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:57:13: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:57:14: 14000000 INFO @ Mon, 12 Aug 2019 20:57:14: #2 number of paired peaks: 789 WARNING @ Mon, 12 Aug 2019 20:57:14: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Mon, 12 Aug 2019 20:57:14: start model_add_line... INFO @ Mon, 12 Aug 2019 20:57:14: start X-correlation... INFO @ Mon, 12 Aug 2019 20:57:14: end of X-cor INFO @ Mon, 12 Aug 2019 20:57:14: #2 finished! INFO @ Mon, 12 Aug 2019 20:57:14: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 20:57:14: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 12 Aug 2019 20:57:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.05_model.r WARNING @ Mon, 12 Aug 2019 20:57:14: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:57:14: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 12 Aug 2019 20:57:14: #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 20:57:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:57:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:57:16: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:57:16: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:57:16: #1 total tags in treatment: 14340578 INFO @ Mon, 12 Aug 2019 20:57:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:57:16: #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 20:57:17: #1 tags after filtering in treatment: 14340578 INFO @ Mon, 12 Aug 2019 20:57:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:57:17: #1 finished! INFO @ Mon, 12 Aug 2019 20:57:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:57:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:57:18: #2 number of paired peaks: 789 WARNING @ Mon, 12 Aug 2019 20:57:18: Fewer paired peaks (789) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 789 pairs to build model! INFO @ Mon, 12 Aug 2019 20:57:18: start model_add_line... INFO @ Mon, 12 Aug 2019 20:57:18: start X-correlation... INFO @ Mon, 12 Aug 2019 20:57:18: end of X-cor INFO @ Mon, 12 Aug 2019 20:57:18: #2 finished! INFO @ Mon, 12 Aug 2019 20:57:18: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 20:57:18: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 12 Aug 2019 20:57:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.20_model.r WARNING @ Mon, 12 Aug 2019 20:57:18: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:57:18: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 12 Aug 2019 20:57:18: #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 20:57:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:57:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:57:30: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:57:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:57:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:57:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.10_summits.bed INFO @ Mon, 12 Aug 2019 20:57:49: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2646 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:57:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:57:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:58:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:58:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:58:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.05_summits.bed INFO @ Mon, 12 Aug 2019 20:58:12: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3372 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:58:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:58:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:58:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318798/SRX318798.20_summits.bed INFO @ Mon, 12 Aug 2019 20:58:17: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1624 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。