Job ID = 1294300 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,268,284 reads read : 13,268,284 reads written : 13,268,284 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: 00:06:52 13268284 reads; of these: 13268284 (100.00%) were unpaired; of these: 282726 (2.13%) aligned 0 times 8679753 (65.42%) aligned exactly 1 time 4305805 (32.45%) aligned >1 times 97.87% overall alignment rate Time searching: 00:06:52 Overall time: 00:06:52 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] 1188664 / 12985558 = 0.0915 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 06:27:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.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 06:27:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:27:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:27:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.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 06:27:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:27:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:27:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.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 06:27:05: #1 read tag files... INFO @ Mon, 03 Jun 2019 06:27:05: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 06:27:14: 1000000 INFO @ Mon, 03 Jun 2019 06:27:14: 1000000 INFO @ Mon, 03 Jun 2019 06:27:15: 1000000 INFO @ Mon, 03 Jun 2019 06:27:23: 2000000 INFO @ Mon, 03 Jun 2019 06:27:23: 2000000 INFO @ Mon, 03 Jun 2019 06:27:25: 2000000 INFO @ Mon, 03 Jun 2019 06:27:32: 3000000 INFO @ Mon, 03 Jun 2019 06:27:32: 3000000 INFO @ Mon, 03 Jun 2019 06:27:35: 3000000 INFO @ Mon, 03 Jun 2019 06:27:40: 4000000 INFO @ Mon, 03 Jun 2019 06:27:40: 4000000 INFO @ Mon, 03 Jun 2019 06:27:45: 4000000 INFO @ Mon, 03 Jun 2019 06:27:49: 5000000 INFO @ Mon, 03 Jun 2019 06:27:49: 5000000 INFO @ Mon, 03 Jun 2019 06:27:54: 5000000 INFO @ Mon, 03 Jun 2019 06:27:57: 6000000 INFO @ Mon, 03 Jun 2019 06:27:57: 6000000 INFO @ Mon, 03 Jun 2019 06:28:04: 6000000 INFO @ Mon, 03 Jun 2019 06:28:06: 7000000 INFO @ Mon, 03 Jun 2019 06:28:06: 7000000 INFO @ Mon, 03 Jun 2019 06:28:13: 7000000 INFO @ Mon, 03 Jun 2019 06:28:14: 8000000 INFO @ Mon, 03 Jun 2019 06:28:14: 8000000 INFO @ Mon, 03 Jun 2019 06:28:23: 9000000 INFO @ Mon, 03 Jun 2019 06:28:23: 9000000 INFO @ Mon, 03 Jun 2019 06:28:23: 8000000 INFO @ Mon, 03 Jun 2019 06:28:31: 10000000 INFO @ Mon, 03 Jun 2019 06:28:31: 10000000 INFO @ Mon, 03 Jun 2019 06:28:33: 9000000 INFO @ Mon, 03 Jun 2019 06:28:39: 11000000 INFO @ Mon, 03 Jun 2019 06:28:39: 11000000 INFO @ Mon, 03 Jun 2019 06:28:42: 10000000 INFO @ Mon, 03 Jun 2019 06:28:46: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:28:46: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:28:46: #1 total tags in treatment: 11796894 INFO @ Mon, 03 Jun 2019 06:28:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:28:46: #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 06:28:46: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:28:46: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:28:46: #1 total tags in treatment: 11796894 INFO @ Mon, 03 Jun 2019 06:28:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:28:46: #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 06:28:46: #1 tags after filtering in treatment: 11796894 INFO @ Mon, 03 Jun 2019 06:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:28:46: #1 finished! INFO @ Mon, 03 Jun 2019 06:28:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:28:46: #1 tags after filtering in treatment: 11796894 INFO @ Mon, 03 Jun 2019 06:28:46: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:28:46: #1 finished! INFO @ Mon, 03 Jun 2019 06:28:46: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:28:46: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:28:48: #2 number of paired peaks: 1083 INFO @ Mon, 03 Jun 2019 06:28:48: start model_add_line... INFO @ Mon, 03 Jun 2019 06:28:48: #2 number of paired peaks: 1083 INFO @ Mon, 03 Jun 2019 06:28:48: start model_add_line... INFO @ Mon, 03 Jun 2019 06:28:48: start X-correlation... INFO @ Mon, 03 Jun 2019 06:28:48: end of X-cor INFO @ Mon, 03 Jun 2019 06:28:48: #2 finished! INFO @ Mon, 03 Jun 2019 06:28:48: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 06:28:48: #2 alternative fragment length(s) may be 3,68 bps INFO @ Mon, 03 Jun 2019 06:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.20_model.r WARNING @ Mon, 03 Jun 2019 06:28:48: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:28:48: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Mon, 03 Jun 2019 06:28:48: #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 06:28:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:28:48: start X-correlation... INFO @ Mon, 03 Jun 2019 06:28:48: end of X-cor INFO @ Mon, 03 Jun 2019 06:28:48: #2 finished! INFO @ Mon, 03 Jun 2019 06:28:48: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 06:28:48: #2 alternative fragment length(s) may be 3,68 bps INFO @ Mon, 03 Jun 2019 06:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.05_model.r WARNING @ Mon, 03 Jun 2019 06:28:48: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:28:48: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Mon, 03 Jun 2019 06:28:48: #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 06:28:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:28:52: 11000000 INFO @ Mon, 03 Jun 2019 06:28:59: #1 tag size is determined as 68 bps INFO @ Mon, 03 Jun 2019 06:28:59: #1 tag size = 68 INFO @ Mon, 03 Jun 2019 06:28:59: #1 total tags in treatment: 11796894 INFO @ Mon, 03 Jun 2019 06:28:59: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 06:28:59: #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 06:28:59: #1 tags after filtering in treatment: 11796894 INFO @ Mon, 03 Jun 2019 06:28:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 06:28:59: #1 finished! INFO @ Mon, 03 Jun 2019 06:28:59: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 06:28:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 06:29:01: #2 number of paired peaks: 1083 INFO @ Mon, 03 Jun 2019 06:29:01: start model_add_line... INFO @ Mon, 03 Jun 2019 06:29:01: start X-correlation... INFO @ Mon, 03 Jun 2019 06:29:01: end of X-cor INFO @ Mon, 03 Jun 2019 06:29:01: #2 finished! INFO @ Mon, 03 Jun 2019 06:29:01: #2 predicted fragment length is 68 bps INFO @ Mon, 03 Jun 2019 06:29:01: #2 alternative fragment length(s) may be 3,68 bps INFO @ Mon, 03 Jun 2019 06:29:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.10_model.r WARNING @ Mon, 03 Jun 2019 06:29:01: #2 Since the d (68) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 03 Jun 2019 06:29:01: #2 You may need to consider one of the other alternative d(s): 3,68 WARNING @ Mon, 03 Jun 2019 06:29:01: #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 06:29:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 06:29:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 06:29:20: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:29:21: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:29:34: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 06:29:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.20_peaks.xls INFO @ Mon, 03 Jun 2019 06:29:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:29:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.20_summits.bed INFO @ Mon, 03 Jun 2019 06:29:36: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (740 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.05_peaks.xls INFO @ Mon, 03 Jun 2019 06:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.05_summits.bed INFO @ Mon, 03 Jun 2019 06:29:37: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (2980 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 06:29:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.10_peaks.xls INFO @ Mon, 03 Jun 2019 06:29:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 06:29:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX2422630/SRX2422630.10_summits.bed INFO @ Mon, 03 Jun 2019 06:29:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1679 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。