Job ID = 1294574 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,325,380 reads read : 15,325,380 reads written : 15,325,380 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:07:44 15325380 reads; of these: 15325380 (100.00%) were unpaired; of these: 820544 (5.35%) aligned 0 times 9330192 (60.88%) aligned exactly 1 time 5174644 (33.77%) aligned >1 times 94.65% overall alignment rate Time searching: 00:07:45 Overall time: 00:07:45 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] 2381981 / 14504836 = 0.1642 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 09:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.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 09:18:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:18:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.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 09:18:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:18:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:18:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.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 09:18:36: #1 read tag files... INFO @ Mon, 03 Jun 2019 09:18:36: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 09:18:43: 1000000 INFO @ Mon, 03 Jun 2019 09:18:44: 1000000 INFO @ Mon, 03 Jun 2019 09:18:45: 1000000 INFO @ Mon, 03 Jun 2019 09:18:50: 2000000 INFO @ Mon, 03 Jun 2019 09:18:53: 2000000 INFO @ Mon, 03 Jun 2019 09:18:54: 2000000 INFO @ Mon, 03 Jun 2019 09:18:58: 3000000 INFO @ Mon, 03 Jun 2019 09:19:01: 3000000 INFO @ Mon, 03 Jun 2019 09:19:03: 3000000 INFO @ Mon, 03 Jun 2019 09:19:05: 4000000 INFO @ Mon, 03 Jun 2019 09:19:09: 4000000 INFO @ Mon, 03 Jun 2019 09:19:11: 4000000 INFO @ Mon, 03 Jun 2019 09:19:12: 5000000 INFO @ Mon, 03 Jun 2019 09:19:18: 5000000 INFO @ Mon, 03 Jun 2019 09:19:19: 6000000 INFO @ Mon, 03 Jun 2019 09:19:20: 5000000 INFO @ Mon, 03 Jun 2019 09:19:26: 6000000 INFO @ Mon, 03 Jun 2019 09:19:27: 7000000 INFO @ Mon, 03 Jun 2019 09:19:29: 6000000 INFO @ Mon, 03 Jun 2019 09:19:34: 8000000 INFO @ Mon, 03 Jun 2019 09:19:34: 7000000 INFO @ Mon, 03 Jun 2019 09:19:37: 7000000 INFO @ Mon, 03 Jun 2019 09:19:41: 9000000 INFO @ Mon, 03 Jun 2019 09:19:42: 8000000 INFO @ Mon, 03 Jun 2019 09:19:45: 8000000 INFO @ Mon, 03 Jun 2019 09:19:48: 10000000 INFO @ Mon, 03 Jun 2019 09:19:50: 9000000 INFO @ Mon, 03 Jun 2019 09:19:53: 9000000 INFO @ Mon, 03 Jun 2019 09:19:55: 11000000 INFO @ Mon, 03 Jun 2019 09:19:59: 10000000 INFO @ Mon, 03 Jun 2019 09:20:01: 10000000 INFO @ Mon, 03 Jun 2019 09:20:02: 12000000 INFO @ Mon, 03 Jun 2019 09:20:03: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:20:03: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:20:03: #1 total tags in treatment: 12122855 INFO @ Mon, 03 Jun 2019 09:20:03: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:20:03: #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 09:20:04: #1 tags after filtering in treatment: 12122855 INFO @ Mon, 03 Jun 2019 09:20:04: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:20:04: #1 finished! INFO @ Mon, 03 Jun 2019 09:20:04: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:20:04: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:20:05: #2 number of paired peaks: 539 WARNING @ Mon, 03 Jun 2019 09:20:05: Fewer paired peaks (539) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 539 pairs to build model! INFO @ Mon, 03 Jun 2019 09:20:05: start model_add_line... INFO @ Mon, 03 Jun 2019 09:20:05: start X-correlation... INFO @ Mon, 03 Jun 2019 09:20:05: end of X-cor INFO @ Mon, 03 Jun 2019 09:20:05: #2 finished! INFO @ Mon, 03 Jun 2019 09:20:05: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:20:05: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:20:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.20_model.r WARNING @ Mon, 03 Jun 2019 09:20:05: #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, 03 Jun 2019 09:20:05: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:20:05: #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 09:20:05: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:20:05: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:20:07: 11000000 INFO @ Mon, 03 Jun 2019 09:20:09: 11000000 INFO @ Mon, 03 Jun 2019 09:20:15: 12000000 INFO @ Mon, 03 Jun 2019 09:20:16: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:20:16: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:20:16: #1 total tags in treatment: 12122855 INFO @ Mon, 03 Jun 2019 09:20:16: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:20:16: #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 09:20:17: #1 tags after filtering in treatment: 12122855 INFO @ Mon, 03 Jun 2019 09:20:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:20:17: #1 finished! INFO @ Mon, 03 Jun 2019 09:20:17: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:20:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:20:17: 12000000 INFO @ Mon, 03 Jun 2019 09:20:18: #2 number of paired peaks: 539 WARNING @ Mon, 03 Jun 2019 09:20:18: Fewer paired peaks (539) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 539 pairs to build model! INFO @ Mon, 03 Jun 2019 09:20:18: start model_add_line... INFO @ Mon, 03 Jun 2019 09:20:18: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 09:20:18: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 09:20:18: #1 total tags in treatment: 12122855 INFO @ Mon, 03 Jun 2019 09:20:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 09:20:18: #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 09:20:18: start X-correlation... INFO @ Mon, 03 Jun 2019 09:20:18: end of X-cor INFO @ Mon, 03 Jun 2019 09:20:18: #2 finished! INFO @ Mon, 03 Jun 2019 09:20:18: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:20:18: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:20:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.05_model.r WARNING @ Mon, 03 Jun 2019 09:20:18: #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, 03 Jun 2019 09:20:18: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:20:18: #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 09:20:18: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:20:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:20:18: #1 tags after filtering in treatment: 12122855 INFO @ Mon, 03 Jun 2019 09:20:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 09:20:18: #1 finished! INFO @ Mon, 03 Jun 2019 09:20:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 09:20:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 09:20:19: #2 number of paired peaks: 539 WARNING @ Mon, 03 Jun 2019 09:20:19: Fewer paired peaks (539) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 539 pairs to build model! INFO @ Mon, 03 Jun 2019 09:20:19: start model_add_line... INFO @ Mon, 03 Jun 2019 09:20:19: start X-correlation... INFO @ Mon, 03 Jun 2019 09:20:19: end of X-cor INFO @ Mon, 03 Jun 2019 09:20:19: #2 finished! INFO @ Mon, 03 Jun 2019 09:20:19: #2 predicted fragment length is 45 bps INFO @ Mon, 03 Jun 2019 09:20:19: #2 alternative fragment length(s) may be 45 bps INFO @ Mon, 03 Jun 2019 09:20:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.10_model.r WARNING @ Mon, 03 Jun 2019 09:20:19: #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, 03 Jun 2019 09:20:19: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Mon, 03 Jun 2019 09:20:19: #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 09:20:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 09:20:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 09:20:38: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:20:51: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:20:52: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 09:20:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.20_peaks.xls INFO @ Mon, 03 Jun 2019 09:20:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:20:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.20_summits.bed INFO @ Mon, 03 Jun 2019 09:20:54: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1464 records, 4 fields): 40 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:21:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.05_peaks.xls INFO @ Mon, 03 Jun 2019 09:21:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:21:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.05_summits.bed INFO @ Mon, 03 Jun 2019 09:21:07: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (2149 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 09:21:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.10_peaks.xls INFO @ Mon, 03 Jun 2019 09:21:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 09:21:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX287750/SRX287750.10_summits.bed INFO @ Mon, 03 Jun 2019 09:21:09: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1836 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。