Job ID = 2590319 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: 00:09:04 18127616 reads; of these: 18127616 (100.00%) were unpaired; of these: 720389 (3.97%) aligned 0 times 10742654 (59.26%) aligned exactly 1 time 6664573 (36.76%) aligned >1 times 96.03% overall alignment rate Time searching: 00:09:04 Overall time: 00:09:04 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] 3065691 / 17407227 = 0.1761 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 21:01:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.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 21:01:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:01:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:01:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.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 21:01:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:01:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:01:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.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 21:01:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 21:01:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 21:01:56: 1000000 INFO @ Mon, 12 Aug 2019 21:01:56: 1000000 INFO @ Mon, 12 Aug 2019 21:01:57: 1000000 INFO @ Mon, 12 Aug 2019 21:02:04: 2000000 INFO @ Mon, 12 Aug 2019 21:02:04: 2000000 INFO @ Mon, 12 Aug 2019 21:02:04: 2000000 INFO @ Mon, 12 Aug 2019 21:02:11: 3000000 INFO @ Mon, 12 Aug 2019 21:02:12: 3000000 INFO @ Mon, 12 Aug 2019 21:02:12: 3000000 INFO @ Mon, 12 Aug 2019 21:02:18: 4000000 INFO @ Mon, 12 Aug 2019 21:02:19: 4000000 INFO @ Mon, 12 Aug 2019 21:02:19: 4000000 INFO @ Mon, 12 Aug 2019 21:02:25: 5000000 INFO @ Mon, 12 Aug 2019 21:02:25: 5000000 INFO @ Mon, 12 Aug 2019 21:02:26: 5000000 INFO @ Mon, 12 Aug 2019 21:02:32: 6000000 INFO @ Mon, 12 Aug 2019 21:02:32: 6000000 INFO @ Mon, 12 Aug 2019 21:02:34: 6000000 INFO @ Mon, 12 Aug 2019 21:02:39: 7000000 INFO @ Mon, 12 Aug 2019 21:02:39: 7000000 INFO @ Mon, 12 Aug 2019 21:02:41: 7000000 INFO @ Mon, 12 Aug 2019 21:02:45: 8000000 INFO @ Mon, 12 Aug 2019 21:02:46: 8000000 INFO @ Mon, 12 Aug 2019 21:02:49: 8000000 INFO @ Mon, 12 Aug 2019 21:02:52: 9000000 INFO @ Mon, 12 Aug 2019 21:02:53: 9000000 INFO @ Mon, 12 Aug 2019 21:02:56: 9000000 INFO @ Mon, 12 Aug 2019 21:02:59: 10000000 INFO @ Mon, 12 Aug 2019 21:03:00: 10000000 INFO @ Mon, 12 Aug 2019 21:03:03: 10000000 INFO @ Mon, 12 Aug 2019 21:03:06: 11000000 INFO @ Mon, 12 Aug 2019 21:03:07: 11000000 INFO @ Mon, 12 Aug 2019 21:03:14: 11000000 INFO @ Mon, 12 Aug 2019 21:03:16: 12000000 INFO @ Mon, 12 Aug 2019 21:03:18: 12000000 INFO @ Mon, 12 Aug 2019 21:03:21: 12000000 INFO @ Mon, 12 Aug 2019 21:03:23: 13000000 INFO @ Mon, 12 Aug 2019 21:03:25: 13000000 INFO @ Mon, 12 Aug 2019 21:03:29: 13000000 INFO @ Mon, 12 Aug 2019 21:03:30: 14000000 INFO @ Mon, 12 Aug 2019 21:03:32: 14000000 INFO @ Mon, 12 Aug 2019 21:03:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:03:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:03:33: #1 total tags in treatment: 14341536 INFO @ Mon, 12 Aug 2019 21:03:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:03:33: #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 21:03:33: #1 tags after filtering in treatment: 14341536 INFO @ Mon, 12 Aug 2019 21:03:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:03:33: #1 finished! INFO @ Mon, 12 Aug 2019 21:03:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:03:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:34: #2 number of paired peaks: 788 WARNING @ Mon, 12 Aug 2019 21:03:34: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Mon, 12 Aug 2019 21:03:34: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:34: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:34: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:34: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:34: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 21:03:34: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 12 Aug 2019 21:03:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.20_model.r WARNING @ Mon, 12 Aug 2019 21:03:34: #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 21:03:34: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 12 Aug 2019 21:03:34: #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 21:03:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:03:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:03:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:03:35: #1 total tags in treatment: 14341536 INFO @ Mon, 12 Aug 2019 21:03:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:03:35: #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 21:03:35: #1 tags after filtering in treatment: 14341536 INFO @ Mon, 12 Aug 2019 21:03:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:03:35: #1 finished! INFO @ Mon, 12 Aug 2019 21:03:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:03:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:36: 14000000 INFO @ Mon, 12 Aug 2019 21:03:36: #2 number of paired peaks: 788 WARNING @ Mon, 12 Aug 2019 21:03:36: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Mon, 12 Aug 2019 21:03:36: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:36: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:36: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:36: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:36: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 21:03:36: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 12 Aug 2019 21:03:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.10_model.r WARNING @ Mon, 12 Aug 2019 21:03:36: #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 21:03:36: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 12 Aug 2019 21:03:36: #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 21:03:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:03:39: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 21:03:39: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 21:03:39: #1 total tags in treatment: 14341536 INFO @ Mon, 12 Aug 2019 21:03:39: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 21:03:39: #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 21:03:39: #1 tags after filtering in treatment: 14341536 INFO @ Mon, 12 Aug 2019 21:03:39: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 21:03:39: #1 finished! INFO @ Mon, 12 Aug 2019 21:03:39: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 21:03:39: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 21:03:40: #2 number of paired peaks: 788 WARNING @ Mon, 12 Aug 2019 21:03:40: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Mon, 12 Aug 2019 21:03:40: start model_add_line... INFO @ Mon, 12 Aug 2019 21:03:40: start X-correlation... INFO @ Mon, 12 Aug 2019 21:03:40: end of X-cor INFO @ Mon, 12 Aug 2019 21:03:40: #2 finished! INFO @ Mon, 12 Aug 2019 21:03:40: #2 predicted fragment length is 45 bps INFO @ Mon, 12 Aug 2019 21:03:40: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 12 Aug 2019 21:03:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.05_model.r WARNING @ Mon, 12 Aug 2019 21:03:40: #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 21:03:40: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 12 Aug 2019 21:03:40: #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 21:03:40: #3 Call peaks... INFO @ Mon, 12 Aug 2019 21:03:40: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 21:04:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:04:15: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:04:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 21:04:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.20_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.20_summits.bed INFO @ Mon, 12 Aug 2019 21:04:33: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1651 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:04:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.10_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.10_summits.bed INFO @ Mon, 12 Aug 2019 21:04:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2684 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 21:04:38: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.05_peaks.xls INFO @ Mon, 12 Aug 2019 21:04:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 21:04:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331425/SRX331425.05_summits.bed INFO @ Mon, 12 Aug 2019 21:04:38: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3363 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。