Job ID = 1295524 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,228,362 reads read : 21,228,362 reads written : 21,228,362 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: 00:07:14 21228362 reads; of these: 21228362 (100.00%) were unpaired; of these: 2532143 (11.93%) aligned 0 times 14018569 (66.04%) aligned exactly 1 time 4677650 (22.03%) aligned >1 times 88.07% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 3905127 / 18696219 = 0.2089 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 14:19:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.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 14:19:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:19:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:19:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.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 14:19:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:19:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:19:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.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 14:19:11: #1 read tag files... INFO @ Mon, 03 Jun 2019 14:19:11: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 14:19:19: 1000000 INFO @ Mon, 03 Jun 2019 14:19:20: 1000000 INFO @ Mon, 03 Jun 2019 14:19:20: 1000000 INFO @ Mon, 03 Jun 2019 14:19:27: 2000000 INFO @ Mon, 03 Jun 2019 14:19:29: 2000000 INFO @ Mon, 03 Jun 2019 14:19:29: 2000000 INFO @ Mon, 03 Jun 2019 14:19:34: 3000000 INFO @ Mon, 03 Jun 2019 14:19:37: 3000000 INFO @ Mon, 03 Jun 2019 14:19:37: 3000000 INFO @ Mon, 03 Jun 2019 14:19:42: 4000000 INFO @ Mon, 03 Jun 2019 14:19:45: 4000000 INFO @ Mon, 03 Jun 2019 14:19:46: 4000000 INFO @ Mon, 03 Jun 2019 14:19:49: 5000000 INFO @ Mon, 03 Jun 2019 14:19:54: 5000000 INFO @ Mon, 03 Jun 2019 14:19:56: 5000000 INFO @ Mon, 03 Jun 2019 14:19:59: 6000000 INFO @ Mon, 03 Jun 2019 14:20:03: 6000000 INFO @ Mon, 03 Jun 2019 14:20:04: 6000000 INFO @ Mon, 03 Jun 2019 14:20:07: 7000000 INFO @ Mon, 03 Jun 2019 14:20:11: 7000000 INFO @ Mon, 03 Jun 2019 14:20:13: 7000000 INFO @ Mon, 03 Jun 2019 14:20:14: 8000000 INFO @ Mon, 03 Jun 2019 14:20:20: 8000000 INFO @ Mon, 03 Jun 2019 14:20:21: 8000000 INFO @ Mon, 03 Jun 2019 14:20:22: 9000000 INFO @ Mon, 03 Jun 2019 14:20:29: 9000000 INFO @ Mon, 03 Jun 2019 14:20:29: 9000000 INFO @ Mon, 03 Jun 2019 14:20:30: 10000000 INFO @ Mon, 03 Jun 2019 14:20:37: 10000000 INFO @ Mon, 03 Jun 2019 14:20:37: 10000000 INFO @ Mon, 03 Jun 2019 14:20:38: 11000000 INFO @ Mon, 03 Jun 2019 14:20:46: 12000000 INFO @ Mon, 03 Jun 2019 14:20:46: 11000000 INFO @ Mon, 03 Jun 2019 14:20:46: 11000000 INFO @ Mon, 03 Jun 2019 14:20:53: 13000000 INFO @ Mon, 03 Jun 2019 14:20:54: 12000000 INFO @ Mon, 03 Jun 2019 14:20:55: 12000000 INFO @ Mon, 03 Jun 2019 14:21:01: 14000000 INFO @ Mon, 03 Jun 2019 14:21:02: 13000000 INFO @ Mon, 03 Jun 2019 14:21:03: 13000000 INFO @ Mon, 03 Jun 2019 14:21:07: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 14:21:07: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 14:21:07: #1 total tags in treatment: 14791092 INFO @ Mon, 03 Jun 2019 14:21:07: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:21:07: #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 14:21:07: #1 tags after filtering in treatment: 14791092 INFO @ Mon, 03 Jun 2019 14:21:07: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:21:07: #1 finished! INFO @ Mon, 03 Jun 2019 14:21:07: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:21:07: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:21:09: #2 number of paired peaks: 518 WARNING @ Mon, 03 Jun 2019 14:21:09: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Mon, 03 Jun 2019 14:21:09: start model_add_line... INFO @ Mon, 03 Jun 2019 14:21:09: start X-correlation... INFO @ Mon, 03 Jun 2019 14:21:09: end of X-cor INFO @ Mon, 03 Jun 2019 14:21:09: #2 finished! INFO @ Mon, 03 Jun 2019 14:21:09: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 14:21:09: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 03 Jun 2019 14:21:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.20_model.r WARNING @ Mon, 03 Jun 2019 14:21:09: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:21:09: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 03 Jun 2019 14:21:09: #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 14:21:09: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:21:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:21:10: 14000000 INFO @ Mon, 03 Jun 2019 14:21:11: 14000000 INFO @ Mon, 03 Jun 2019 14:21:16: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 14:21:16: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 14:21:16: #1 total tags in treatment: 14791092 INFO @ Mon, 03 Jun 2019 14:21:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:21:16: #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 14:21:16: #1 tags after filtering in treatment: 14791092 INFO @ Mon, 03 Jun 2019 14:21:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:21:16: #1 finished! INFO @ Mon, 03 Jun 2019 14:21:16: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:21:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:21:18: #2 number of paired peaks: 518 WARNING @ Mon, 03 Jun 2019 14:21:18: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Mon, 03 Jun 2019 14:21:18: start model_add_line... INFO @ Mon, 03 Jun 2019 14:21:18: start X-correlation... INFO @ Mon, 03 Jun 2019 14:21:18: end of X-cor INFO @ Mon, 03 Jun 2019 14:21:18: #2 finished! INFO @ Mon, 03 Jun 2019 14:21:18: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 14:21:18: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 03 Jun 2019 14:21:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.10_model.r WARNING @ Mon, 03 Jun 2019 14:21:18: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:21:18: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 03 Jun 2019 14:21:18: #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 14:21:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:21:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:21:18: #1 tag size is determined as 46 bps INFO @ Mon, 03 Jun 2019 14:21:18: #1 tag size = 46 INFO @ Mon, 03 Jun 2019 14:21:18: #1 total tags in treatment: 14791092 INFO @ Mon, 03 Jun 2019 14:21:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 14:21:18: #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 14:21:18: #1 tags after filtering in treatment: 14791092 INFO @ Mon, 03 Jun 2019 14:21:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 14:21:18: #1 finished! INFO @ Mon, 03 Jun 2019 14:21:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 14:21:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 14:21:20: #2 number of paired peaks: 518 WARNING @ Mon, 03 Jun 2019 14:21:20: Fewer paired peaks (518) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 518 pairs to build model! INFO @ Mon, 03 Jun 2019 14:21:20: start model_add_line... INFO @ Mon, 03 Jun 2019 14:21:20: start X-correlation... INFO @ Mon, 03 Jun 2019 14:21:20: end of X-cor INFO @ Mon, 03 Jun 2019 14:21:20: #2 finished! INFO @ Mon, 03 Jun 2019 14:21:20: #2 predicted fragment length is 77 bps INFO @ Mon, 03 Jun 2019 14:21:20: #2 alternative fragment length(s) may be 77 bps INFO @ Mon, 03 Jun 2019 14:21:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.05_model.r WARNING @ Mon, 03 Jun 2019 14:21:20: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 14:21:20: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Mon, 03 Jun 2019 14:21:20: #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 14:21:20: #3 Call peaks... INFO @ Mon, 03 Jun 2019 14:21:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 14:21:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:21:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:22:01: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 14:22:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.20_peaks.xls INFO @ Mon, 03 Jun 2019 14:22:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:22:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.20_summits.bed INFO @ Mon, 03 Jun 2019 14:22:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1340 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:22:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.10_peaks.xls INFO @ Mon, 03 Jun 2019 14:22:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:22:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.10_summits.bed INFO @ Mon, 03 Jun 2019 14:22:19: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (2849 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 14:22:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.05_peaks.xls INFO @ Mon, 03 Jun 2019 14:22:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 14:22:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX359797/SRX359797.05_summits.bed INFO @ Mon, 03 Jun 2019 14:22:22: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (4887 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。