Job ID = 1295070 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,633,065 reads read : 15,633,065 reads written : 15,633,065 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:08:12 15633065 reads; of these: 15633065 (100.00%) were unpaired; of these: 3528767 (22.57%) aligned 0 times 7231506 (46.26%) aligned exactly 1 time 4872792 (31.17%) aligned >1 times 77.43% overall alignment rate Time searching: 00:08:12 Overall time: 00:08:12 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] 2543036 / 12104298 = 0.2101 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, 03 Jun 2019 11:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.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, 03 Jun 2019 11:52:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:52:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.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, 03 Jun 2019 11:52:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:52:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:52:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.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, 03 Jun 2019 11:52:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:52:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:52:22: 1000000 INFO @ Mon, 03 Jun 2019 11:52:23: 1000000 INFO @ Mon, 03 Jun 2019 11:52:23: 1000000 INFO @ Mon, 03 Jun 2019 11:52:32: 2000000 INFO @ Mon, 03 Jun 2019 11:52:32: 2000000 INFO @ Mon, 03 Jun 2019 11:52:33: 2000000 INFO @ Mon, 03 Jun 2019 11:52:40: 3000000 INFO @ Mon, 03 Jun 2019 11:52:42: 3000000 INFO @ Mon, 03 Jun 2019 11:52:43: 3000000 INFO @ Mon, 03 Jun 2019 11:52:49: 4000000 INFO @ Mon, 03 Jun 2019 11:52:52: 4000000 INFO @ Mon, 03 Jun 2019 11:52:53: 4000000 INFO @ Mon, 03 Jun 2019 11:52:58: 5000000 INFO @ Mon, 03 Jun 2019 11:53:01: 5000000 INFO @ Mon, 03 Jun 2019 11:53:03: 5000000 INFO @ Mon, 03 Jun 2019 11:53:07: 6000000 INFO @ Mon, 03 Jun 2019 11:53:11: 6000000 INFO @ Mon, 03 Jun 2019 11:53:13: 6000000 INFO @ Mon, 03 Jun 2019 11:53:15: 7000000 INFO @ Mon, 03 Jun 2019 11:53:20: 7000000 INFO @ Mon, 03 Jun 2019 11:53:22: 7000000 INFO @ Mon, 03 Jun 2019 11:53:23: 8000000 INFO @ Mon, 03 Jun 2019 11:53:30: 8000000 INFO @ Mon, 03 Jun 2019 11:53:31: 9000000 INFO @ Mon, 03 Jun 2019 11:53:33: 8000000 INFO @ Mon, 03 Jun 2019 11:53:36: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:53:36: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:53:36: #1 total tags in treatment: 9561262 INFO @ Mon, 03 Jun 2019 11:53:36: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:53:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:53:36: #1 tags after filtering in treatment: 9561262 INFO @ Mon, 03 Jun 2019 11:53:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:53:36: #1 finished! INFO @ Mon, 03 Jun 2019 11:53:36: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:53:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:53:37: #2 number of paired peaks: 563 WARNING @ Mon, 03 Jun 2019 11:53:37: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Mon, 03 Jun 2019 11:53:37: start model_add_line... INFO @ Mon, 03 Jun 2019 11:53:37: start X-correlation... INFO @ Mon, 03 Jun 2019 11:53:37: end of X-cor INFO @ Mon, 03 Jun 2019 11:53:37: #2 finished! INFO @ Mon, 03 Jun 2019 11:53:37: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 11:53:37: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 11:53:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.05_model.r WARNING @ Mon, 03 Jun 2019 11:53:37: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:53:37: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 11:53:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:53:37: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:53:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:53:40: 9000000 INFO @ Mon, 03 Jun 2019 11:53:42: 9000000 INFO @ Mon, 03 Jun 2019 11:53:46: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:53:46: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:53:46: #1 total tags in treatment: 9561262 INFO @ Mon, 03 Jun 2019 11:53:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:53:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:53:46: #1 tags after filtering in treatment: 9561262 INFO @ Mon, 03 Jun 2019 11:53:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:53:46: #1 finished! INFO @ Mon, 03 Jun 2019 11:53:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:53:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:53:47: #2 number of paired peaks: 563 WARNING @ Mon, 03 Jun 2019 11:53:47: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Mon, 03 Jun 2019 11:53:47: start model_add_line... INFO @ Mon, 03 Jun 2019 11:53:47: start X-correlation... INFO @ Mon, 03 Jun 2019 11:53:47: end of X-cor INFO @ Mon, 03 Jun 2019 11:53:47: #2 finished! INFO @ Mon, 03 Jun 2019 11:53:47: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 11:53:47: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 11:53:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.20_model.r WARNING @ Mon, 03 Jun 2019 11:53:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:53:47: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 11:53:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:53:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:53:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:53:48: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 11:53:48: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 11:53:48: #1 total tags in treatment: 9561262 INFO @ Mon, 03 Jun 2019 11:53:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:53:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 11:53:48: #1 tags after filtering in treatment: 9561262 INFO @ Mon, 03 Jun 2019 11:53:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:53:48: #1 finished! INFO @ Mon, 03 Jun 2019 11:53:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:53:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:53:49: #2 number of paired peaks: 563 WARNING @ Mon, 03 Jun 2019 11:53:49: Fewer paired peaks (563) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 563 pairs to build model! INFO @ Mon, 03 Jun 2019 11:53:49: start model_add_line... INFO @ Mon, 03 Jun 2019 11:53:49: start X-correlation... INFO @ Mon, 03 Jun 2019 11:53:49: end of X-cor INFO @ Mon, 03 Jun 2019 11:53:49: #2 finished! INFO @ Mon, 03 Jun 2019 11:53:49: #2 predicted fragment length is 49 bps INFO @ Mon, 03 Jun 2019 11:53:49: #2 alternative fragment length(s) may be 49 bps INFO @ Mon, 03 Jun 2019 11:53:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.10_model.r WARNING @ Mon, 03 Jun 2019 11:53:49: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 11:53:49: #2 You may need to consider one of the other alternative d(s): 49 WARNING @ Mon, 03 Jun 2019 11:53:49: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 03 Jun 2019 11:53:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:53:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:54:07: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:54:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:54:18: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:54:23: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:54:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:54:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.05_summits.bed INFO @ Mon, 03 Jun 2019 11:54:23: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1922 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:54:31: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:54:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:54:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.20_summits.bed INFO @ Mon, 03 Jun 2019 11:54:31: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1025 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:54:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:54:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:54:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3167260/SRX3167260.10_summits.bed INFO @ Mon, 03 Jun 2019 11:54:33: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1286 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。