Job ID = 2590805 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,993,989 reads read : 43,987,978 reads written : 21,993,989 reads 0-length : 21,993,989 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: 00:10:13 21993989 reads; of these: 21993989 (100.00%) were unpaired; of these: 1390658 (6.32%) aligned 0 times 14281580 (64.93%) aligned exactly 1 time 6321751 (28.74%) aligned >1 times 93.68% overall alignment rate Time searching: 00:10:13 Overall time: 00:10:13 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] 8698328 / 20603331 = 0.4222 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 23:34:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.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 23:34:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.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 23:34:41: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:41: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.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 23:34:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:34:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:34:48: 1000000 INFO @ Mon, 12 Aug 2019 23:34:48: 1000000 INFO @ Mon, 12 Aug 2019 23:34:52: 1000000 INFO @ Mon, 12 Aug 2019 23:34:55: 2000000 INFO @ Mon, 12 Aug 2019 23:34:56: 2000000 INFO @ Mon, 12 Aug 2019 23:35:02: 2000000 INFO @ Mon, 12 Aug 2019 23:35:03: 3000000 INFO @ Mon, 12 Aug 2019 23:35:03: 3000000 INFO @ Mon, 12 Aug 2019 23:35:10: 4000000 INFO @ Mon, 12 Aug 2019 23:35:11: 4000000 INFO @ Mon, 12 Aug 2019 23:35:11: 3000000 INFO @ Mon, 12 Aug 2019 23:35:17: 5000000 INFO @ Mon, 12 Aug 2019 23:35:19: 5000000 INFO @ Mon, 12 Aug 2019 23:35:20: 4000000 INFO @ Mon, 12 Aug 2019 23:35:24: 6000000 INFO @ Mon, 12 Aug 2019 23:35:26: 6000000 INFO @ Mon, 12 Aug 2019 23:35:29: 5000000 INFO @ Mon, 12 Aug 2019 23:35:30: 7000000 INFO @ Mon, 12 Aug 2019 23:35:34: 7000000 INFO @ Mon, 12 Aug 2019 23:35:37: 8000000 INFO @ Mon, 12 Aug 2019 23:35:37: 6000000 INFO @ Mon, 12 Aug 2019 23:35:41: 8000000 INFO @ Mon, 12 Aug 2019 23:35:44: 9000000 INFO @ Mon, 12 Aug 2019 23:35:47: 7000000 INFO @ Mon, 12 Aug 2019 23:35:49: 9000000 INFO @ Mon, 12 Aug 2019 23:35:51: 10000000 INFO @ Mon, 12 Aug 2019 23:35:56: 8000000 INFO @ Mon, 12 Aug 2019 23:35:56: 10000000 INFO @ Mon, 12 Aug 2019 23:35:58: 11000000 INFO @ Mon, 12 Aug 2019 23:36:04: 11000000 INFO @ Mon, 12 Aug 2019 23:36:04: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:36:04: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:36:04: #1 total tags in treatment: 11905003 INFO @ Mon, 12 Aug 2019 23:36:04: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:36:04: #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 23:36:04: #1 tags after filtering in treatment: 11905003 INFO @ Mon, 12 Aug 2019 23:36:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:36:04: #1 finished! INFO @ Mon, 12 Aug 2019 23:36:04: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:36:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:36:05: 9000000 INFO @ Mon, 12 Aug 2019 23:36:06: #2 number of paired peaks: 799 WARNING @ Mon, 12 Aug 2019 23:36:06: Fewer paired peaks (799) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 799 pairs to build model! INFO @ Mon, 12 Aug 2019 23:36:06: start model_add_line... INFO @ Mon, 12 Aug 2019 23:36:06: start X-correlation... INFO @ Mon, 12 Aug 2019 23:36:06: end of X-cor INFO @ Mon, 12 Aug 2019 23:36:06: #2 finished! INFO @ Mon, 12 Aug 2019 23:36:06: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 23:36:06: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 12 Aug 2019 23:36:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.10_model.r WARNING @ Mon, 12 Aug 2019 23:36:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:36:06: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 12 Aug 2019 23:36:06: #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 23:36:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:36:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:36:10: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:36:10: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:36:10: #1 total tags in treatment: 11905003 INFO @ Mon, 12 Aug 2019 23:36:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:36:10: #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 23:36:11: #1 tags after filtering in treatment: 11905003 INFO @ Mon, 12 Aug 2019 23:36:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:36:11: #1 finished! INFO @ Mon, 12 Aug 2019 23:36:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:36:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:36:12: #2 number of paired peaks: 799 WARNING @ Mon, 12 Aug 2019 23:36:12: Fewer paired peaks (799) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 799 pairs to build model! INFO @ Mon, 12 Aug 2019 23:36:12: start model_add_line... INFO @ Mon, 12 Aug 2019 23:36:12: start X-correlation... INFO @ Mon, 12 Aug 2019 23:36:12: end of X-cor INFO @ Mon, 12 Aug 2019 23:36:12: #2 finished! INFO @ Mon, 12 Aug 2019 23:36:12: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 23:36:12: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 12 Aug 2019 23:36:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.05_model.r WARNING @ Mon, 12 Aug 2019 23:36:12: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:36:12: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 12 Aug 2019 23:36:12: #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 23:36:12: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:36:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:36:14: 10000000 INFO @ Mon, 12 Aug 2019 23:36:24: 11000000 INFO @ Mon, 12 Aug 2019 23:36:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:36:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:36:32: #1 total tags in treatment: 11905003 INFO @ Mon, 12 Aug 2019 23:36:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:36:32: #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 23:36:32: #1 tags after filtering in treatment: 11905003 INFO @ Mon, 12 Aug 2019 23:36:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:36:32: #1 finished! INFO @ Mon, 12 Aug 2019 23:36:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:36:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:36:33: #2 number of paired peaks: 799 WARNING @ Mon, 12 Aug 2019 23:36:33: Fewer paired peaks (799) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 799 pairs to build model! INFO @ Mon, 12 Aug 2019 23:36:33: start model_add_line... INFO @ Mon, 12 Aug 2019 23:36:33: start X-correlation... INFO @ Mon, 12 Aug 2019 23:36:33: end of X-cor INFO @ Mon, 12 Aug 2019 23:36:33: #2 finished! INFO @ Mon, 12 Aug 2019 23:36:33: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 23:36:33: #2 alternative fragment length(s) may be 50 bps INFO @ Mon, 12 Aug 2019 23:36:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.20_model.r WARNING @ Mon, 12 Aug 2019 23:36:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:36:33: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Mon, 12 Aug 2019 23:36:33: #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 23:36:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:36:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:36:39: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:36:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:36:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:36:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:36:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.10_summits.bed INFO @ Mon, 12 Aug 2019 23:36:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2874 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:37:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:37:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:37:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.05_summits.bed INFO @ Mon, 12 Aug 2019 23:37:02: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4007 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:37:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:37:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:37:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:37:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011047/SRX5011047.20_summits.bed INFO @ Mon, 12 Aug 2019 23:37:24: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1281 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。