Job ID = 2590817 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 32,830,552 reads read : 65,661,104 reads written : 32,830,552 reads 0-length : 32,830,552 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: 00:15:07 32830552 reads; of these: 32830552 (100.00%) were unpaired; of these: 1875480 (5.71%) aligned 0 times 21511180 (65.52%) aligned exactly 1 time 9443892 (28.77%) aligned >1 times 94.29% overall alignment rate Time searching: 00:15:07 Overall time: 00:15:07 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 16 files... [bam_rmdupse_core] 15689684 / 30955072 = 0.5069 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 23:47:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.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 23:47:22: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:47:22: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:47:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.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 23:47:23: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:47:23: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:47:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.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 23:47:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:47:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:47:30: 1000000 INFO @ Mon, 12 Aug 2019 23:47:31: 1000000 INFO @ Mon, 12 Aug 2019 23:47:32: 1000000 INFO @ Mon, 12 Aug 2019 23:47:38: 2000000 INFO @ Mon, 12 Aug 2019 23:47:39: 2000000 INFO @ Mon, 12 Aug 2019 23:47:41: 2000000 INFO @ Mon, 12 Aug 2019 23:47:46: 3000000 INFO @ Mon, 12 Aug 2019 23:47:47: 3000000 INFO @ Mon, 12 Aug 2019 23:47:49: 3000000 INFO @ Mon, 12 Aug 2019 23:47:55: 4000000 INFO @ Mon, 12 Aug 2019 23:47:56: 4000000 INFO @ Mon, 12 Aug 2019 23:47:57: 4000000 INFO @ Mon, 12 Aug 2019 23:48:03: 5000000 INFO @ Mon, 12 Aug 2019 23:48:04: 5000000 INFO @ Mon, 12 Aug 2019 23:48:05: 5000000 INFO @ Mon, 12 Aug 2019 23:48:11: 6000000 INFO @ Mon, 12 Aug 2019 23:48:12: 6000000 INFO @ Mon, 12 Aug 2019 23:48:13: 6000000 INFO @ Mon, 12 Aug 2019 23:48:20: 7000000 INFO @ Mon, 12 Aug 2019 23:48:21: 7000000 INFO @ Mon, 12 Aug 2019 23:48:23: 7000000 INFO @ Mon, 12 Aug 2019 23:48:29: 8000000 INFO @ Mon, 12 Aug 2019 23:48:29: 8000000 INFO @ Mon, 12 Aug 2019 23:48:31: 8000000 INFO @ Mon, 12 Aug 2019 23:48:37: 9000000 INFO @ Mon, 12 Aug 2019 23:48:38: 9000000 INFO @ Mon, 12 Aug 2019 23:48:39: 9000000 INFO @ Mon, 12 Aug 2019 23:48:46: 10000000 INFO @ Mon, 12 Aug 2019 23:48:46: 10000000 INFO @ Mon, 12 Aug 2019 23:48:48: 10000000 INFO @ Mon, 12 Aug 2019 23:48:54: 11000000 INFO @ Mon, 12 Aug 2019 23:48:54: 11000000 INFO @ Mon, 12 Aug 2019 23:48:56: 11000000 INFO @ Mon, 12 Aug 2019 23:49:02: 12000000 INFO @ Mon, 12 Aug 2019 23:49:03: 12000000 INFO @ Mon, 12 Aug 2019 23:49:04: 12000000 INFO @ Mon, 12 Aug 2019 23:49:11: 13000000 INFO @ Mon, 12 Aug 2019 23:49:11: 13000000 INFO @ Mon, 12 Aug 2019 23:49:13: 13000000 INFO @ Mon, 12 Aug 2019 23:49:19: 14000000 INFO @ Mon, 12 Aug 2019 23:49:19: 14000000 INFO @ Mon, 12 Aug 2019 23:49:21: 14000000 INFO @ Mon, 12 Aug 2019 23:49:27: 15000000 INFO @ Mon, 12 Aug 2019 23:49:28: 15000000 INFO @ Mon, 12 Aug 2019 23:49:29: 15000000 INFO @ Mon, 12 Aug 2019 23:49:29: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:49:29: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:49:29: #1 total tags in treatment: 15265388 INFO @ Mon, 12 Aug 2019 23:49:29: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:49:29: #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 23:49:30: #1 tags after filtering in treatment: 15265388 INFO @ Mon, 12 Aug 2019 23:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:49:30: #1 finished! INFO @ Mon, 12 Aug 2019 23:49:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:49:30: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:49:30: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:49:30: #1 total tags in treatment: 15265388 INFO @ Mon, 12 Aug 2019 23:49:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:49:30: #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 23:49:30: #1 tags after filtering in treatment: 15265388 INFO @ Mon, 12 Aug 2019 23:49:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:49:30: #1 finished! INFO @ Mon, 12 Aug 2019 23:49:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:49:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:49:31: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:49:31: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:49:31: #1 total tags in treatment: 15265388 INFO @ Mon, 12 Aug 2019 23:49:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:49:31: #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 23:49:31: #2 number of paired peaks: 822 WARNING @ Mon, 12 Aug 2019 23:49:31: Fewer paired peaks (822) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 822 pairs to build model! INFO @ Mon, 12 Aug 2019 23:49:31: start model_add_line... INFO @ Mon, 12 Aug 2019 23:49:31: start X-correlation... INFO @ Mon, 12 Aug 2019 23:49:31: end of X-cor INFO @ Mon, 12 Aug 2019 23:49:31: #2 finished! INFO @ Mon, 12 Aug 2019 23:49:31: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 23:49:31: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 12 Aug 2019 23:49:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.05_model.r WARNING @ Mon, 12 Aug 2019 23:49:31: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:49:31: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 12 Aug 2019 23:49:31: #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 23:49:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:49:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:49:31: #1 tags after filtering in treatment: 15265388 INFO @ Mon, 12 Aug 2019 23:49:31: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:49:31: #1 finished! INFO @ Mon, 12 Aug 2019 23:49:31: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:49:31: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:49:32: #2 number of paired peaks: 822 WARNING @ Mon, 12 Aug 2019 23:49:32: Fewer paired peaks (822) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 822 pairs to build model! INFO @ Mon, 12 Aug 2019 23:49:32: start model_add_line... INFO @ Mon, 12 Aug 2019 23:49:32: start X-correlation... INFO @ Mon, 12 Aug 2019 23:49:32: end of X-cor INFO @ Mon, 12 Aug 2019 23:49:32: #2 finished! INFO @ Mon, 12 Aug 2019 23:49:32: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 23:49:32: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 12 Aug 2019 23:49:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.10_model.r WARNING @ Mon, 12 Aug 2019 23:49:32: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:49:32: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 12 Aug 2019 23:49:32: #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 23:49:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:49:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:49:33: #2 number of paired peaks: 822 WARNING @ Mon, 12 Aug 2019 23:49:33: Fewer paired peaks (822) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 822 pairs to build model! INFO @ Mon, 12 Aug 2019 23:49:33: start model_add_line... INFO @ Mon, 12 Aug 2019 23:49:33: start X-correlation... INFO @ Mon, 12 Aug 2019 23:49:33: end of X-cor INFO @ Mon, 12 Aug 2019 23:49:33: #2 finished! INFO @ Mon, 12 Aug 2019 23:49:33: #2 predicted fragment length is 51 bps INFO @ Mon, 12 Aug 2019 23:49:33: #2 alternative fragment length(s) may be 51 bps INFO @ Mon, 12 Aug 2019 23:49:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.20_model.r WARNING @ Mon, 12 Aug 2019 23:49:33: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:49:33: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Mon, 12 Aug 2019 23:49:33: #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 23:49:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:49:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:50:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:50:12: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:50:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:50:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:50:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.10_summits.bed INFO @ Mon, 12 Aug 2019 23:50:32: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (3197 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:50:32: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:50:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:50:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.05_summits.bed INFO @ Mon, 12 Aug 2019 23:50:32: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4932 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:50:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:50:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:50:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011056/SRX5011056.20_summits.bed INFO @ Mon, 12 Aug 2019 23:50:33: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (1454 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。