Job ID = 4178576 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,626,481 reads read : 61,252,962 reads written : 30,626,481 reads 0-length : 30,626,481 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: 00:12:12 30626481 reads; of these: 30626481 (100.00%) were unpaired; of these: 4384277 (14.32%) aligned 0 times 19415140 (63.39%) aligned exactly 1 time 6827064 (22.29%) aligned >1 times 85.68% overall alignment rate Time searching: 00:12:13 Overall time: 00:12:13 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 12 files... [bam_rmdupse_core] 13283928 / 26242204 = 0.5062 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:36:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.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 @ Thu, 05 Dec 2019 13:36:10: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:36:10: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:36:20: 1000000 INFO @ Thu, 05 Dec 2019 13:36:30: 2000000 INFO @ Thu, 05 Dec 2019 13:36:39: 3000000 INFO @ Thu, 05 Dec 2019 13:36:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.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 @ Thu, 05 Dec 2019 13:36:40: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:36:40: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:36:48: 4000000 INFO @ Thu, 05 Dec 2019 13:36:49: 1000000 INFO @ Thu, 05 Dec 2019 13:36:56: 5000000 INFO @ Thu, 05 Dec 2019 13:36:58: 2000000 INFO @ Thu, 05 Dec 2019 13:37:05: 6000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:37:07: 3000000 INFO @ Thu, 05 Dec 2019 13:37:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.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 @ Thu, 05 Dec 2019 13:37:11: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:37:11: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:37:15: 7000000 INFO @ Thu, 05 Dec 2019 13:37:16: 4000000 INFO @ Thu, 05 Dec 2019 13:37:19: 1000000 INFO @ Thu, 05 Dec 2019 13:37:24: 8000000 INFO @ Thu, 05 Dec 2019 13:37:24: 5000000 INFO @ Thu, 05 Dec 2019 13:37:29: 2000000 INFO @ Thu, 05 Dec 2019 13:37:33: 9000000 INFO @ Thu, 05 Dec 2019 13:37:33: 6000000 INFO @ Thu, 05 Dec 2019 13:37:38: 3000000 INFO @ Thu, 05 Dec 2019 13:37:42: 10000000 INFO @ Thu, 05 Dec 2019 13:37:42: 7000000 INFO @ Thu, 05 Dec 2019 13:37:48: 4000000 INFO @ Thu, 05 Dec 2019 13:37:51: 8000000 INFO @ Thu, 05 Dec 2019 13:37:52: 11000000 INFO @ Thu, 05 Dec 2019 13:37:58: 5000000 INFO @ Thu, 05 Dec 2019 13:38:01: 9000000 INFO @ Thu, 05 Dec 2019 13:38:02: 12000000 INFO @ Thu, 05 Dec 2019 13:38:07: 6000000 INFO @ Thu, 05 Dec 2019 13:38:12: 10000000 INFO @ Thu, 05 Dec 2019 13:38:12: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:38:12: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:38:12: #1 total tags in treatment: 12958276 INFO @ Thu, 05 Dec 2019 13:38:12: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:38:12: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:38:13: #1 tags after filtering in treatment: 12958276 INFO @ Thu, 05 Dec 2019 13:38:13: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:38:13: #1 finished! INFO @ Thu, 05 Dec 2019 13:38:13: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:38:13: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:38:14: #2 number of paired peaks: 382 WARNING @ Thu, 05 Dec 2019 13:38:14: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Thu, 05 Dec 2019 13:38:14: start model_add_line... INFO @ Thu, 05 Dec 2019 13:38:14: start X-correlation... INFO @ Thu, 05 Dec 2019 13:38:14: end of X-cor INFO @ Thu, 05 Dec 2019 13:38:14: #2 finished! INFO @ Thu, 05 Dec 2019 13:38:14: #2 predicted fragment length is 52 bps INFO @ Thu, 05 Dec 2019 13:38:14: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 05 Dec 2019 13:38:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.05_model.r WARNING @ Thu, 05 Dec 2019 13:38:14: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:38:14: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 05 Dec 2019 13:38:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:38:14: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:38:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:38:16: 7000000 INFO @ Thu, 05 Dec 2019 13:38:22: 11000000 INFO @ Thu, 05 Dec 2019 13:38:25: 8000000 INFO @ Thu, 05 Dec 2019 13:38:31: 12000000 INFO @ Thu, 05 Dec 2019 13:38:35: 9000000 INFO @ Thu, 05 Dec 2019 13:38:40: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:38:40: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:38:40: #1 total tags in treatment: 12958276 INFO @ Thu, 05 Dec 2019 13:38:40: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:38:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:38:41: #1 tags after filtering in treatment: 12958276 INFO @ Thu, 05 Dec 2019 13:38:41: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:38:41: #1 finished! INFO @ Thu, 05 Dec 2019 13:38:41: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:38:41: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:38:42: #2 number of paired peaks: 382 WARNING @ Thu, 05 Dec 2019 13:38:42: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Thu, 05 Dec 2019 13:38:42: start model_add_line... INFO @ Thu, 05 Dec 2019 13:38:42: start X-correlation... INFO @ Thu, 05 Dec 2019 13:38:42: end of X-cor INFO @ Thu, 05 Dec 2019 13:38:42: #2 finished! INFO @ Thu, 05 Dec 2019 13:38:42: #2 predicted fragment length is 52 bps INFO @ Thu, 05 Dec 2019 13:38:42: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 05 Dec 2019 13:38:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.10_model.r WARNING @ Thu, 05 Dec 2019 13:38:42: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:38:42: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 05 Dec 2019 13:38:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:38:42: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:38:43: 10000000 INFO @ Thu, 05 Dec 2019 13:38:53: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:38:53: 11000000 INFO @ Thu, 05 Dec 2019 13:39:03: 12000000 INFO @ Thu, 05 Dec 2019 13:39:15: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:39:15: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:39:15: #1 total tags in treatment: 12958276 INFO @ Thu, 05 Dec 2019 13:39:15: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:39:15: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.05_summits.bed INFO @ Thu, 05 Dec 2019 13:39:15: Done! INFO @ Thu, 05 Dec 2019 13:39:15: #1 tags after filtering in treatment: 12958276 INFO @ Thu, 05 Dec 2019 13:39:15: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:39:15: #1 finished! INFO @ Thu, 05 Dec 2019 13:39:15: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:39:15: #2 looking for paired plus/minus strand peaks... pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (1763 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:39:16: #2 number of paired peaks: 382 WARNING @ Thu, 05 Dec 2019 13:39:16: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Thu, 05 Dec 2019 13:39:16: start model_add_line... INFO @ Thu, 05 Dec 2019 13:39:16: start X-correlation... INFO @ Thu, 05 Dec 2019 13:39:16: end of X-cor INFO @ Thu, 05 Dec 2019 13:39:16: #2 finished! INFO @ Thu, 05 Dec 2019 13:39:16: #2 predicted fragment length is 52 bps INFO @ Thu, 05 Dec 2019 13:39:16: #2 alternative fragment length(s) may be 52 bps INFO @ Thu, 05 Dec 2019 13:39:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.20_model.r WARNING @ Thu, 05 Dec 2019 13:39:16: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:39:16: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Thu, 05 Dec 2019 13:39:16: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:39:16: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:39:16: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:39:21: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:39:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:39:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:39:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.10_summits.bed INFO @ Thu, 05 Dec 2019 13:39:39: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1369 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:39:53: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:40:12: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:40:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:40:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5827841/SRX5827841.20_summits.bed INFO @ Thu, 05 Dec 2019 13:40:12: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (989 records, 4 fields): 27 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。