Job ID = 2590835 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,360,324 reads read : 56,720,648 reads written : 28,360,324 reads 0-length : 28,360,324 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: 00:08:54 28360324 reads; of these: 28360324 (100.00%) were unpaired; of these: 8295096 (29.25%) aligned 0 times 14811128 (52.22%) aligned exactly 1 time 5254100 (18.53%) aligned >1 times 70.75% overall alignment rate Time searching: 00:08:54 Overall time: 00:08:54 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 12 files... [bam_rmdupse_core] 12538133 / 20065228 = 0.6249 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 23:47:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.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 23:47:23: #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/SRX5011072/SRX5011072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.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 23:47:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:47:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:47:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.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 23:47:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:47:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:47:33: 1000000 INFO @ Mon, 12 Aug 2019 23:47:34: 1000000 INFO @ Mon, 12 Aug 2019 23:47:35: 1000000 INFO @ Mon, 12 Aug 2019 23:47:43: 2000000 INFO @ Mon, 12 Aug 2019 23:47:44: 2000000 INFO @ Mon, 12 Aug 2019 23:47:45: 2000000 INFO @ Mon, 12 Aug 2019 23:47:52: 3000000 INFO @ Mon, 12 Aug 2019 23:47:53: 3000000 INFO @ Mon, 12 Aug 2019 23:47:55: 3000000 INFO @ Mon, 12 Aug 2019 23:48:01: 4000000 INFO @ Mon, 12 Aug 2019 23:48:02: 4000000 INFO @ Mon, 12 Aug 2019 23:48:04: 4000000 INFO @ Mon, 12 Aug 2019 23:48:10: 5000000 INFO @ Mon, 12 Aug 2019 23:48:11: 5000000 INFO @ Mon, 12 Aug 2019 23:48:14: 5000000 INFO @ Mon, 12 Aug 2019 23:48:19: 6000000 INFO @ Mon, 12 Aug 2019 23:48:20: 6000000 INFO @ Mon, 12 Aug 2019 23:48:23: 6000000 INFO @ Mon, 12 Aug 2019 23:48:28: 7000000 INFO @ Mon, 12 Aug 2019 23:48:29: 7000000 INFO @ Mon, 12 Aug 2019 23:48:32: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:48:32: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:48:32: #1 total tags in treatment: 7527095 INFO @ Mon, 12 Aug 2019 23:48:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:48:32: #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 23:48:32: #1 tags after filtering in treatment: 7527095 INFO @ Mon, 12 Aug 2019 23:48:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:48:32: #1 finished! INFO @ Mon, 12 Aug 2019 23:48:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:48:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:48:32: 7000000 INFO @ Mon, 12 Aug 2019 23:48:33: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:48:33: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:48:33: #1 total tags in treatment: 7527095 INFO @ Mon, 12 Aug 2019 23:48:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:48:33: #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 23:48:33: #2 number of paired peaks: 2561 INFO @ Mon, 12 Aug 2019 23:48:33: start model_add_line... INFO @ Mon, 12 Aug 2019 23:48:33: start X-correlation... INFO @ Mon, 12 Aug 2019 23:48:33: end of X-cor INFO @ Mon, 12 Aug 2019 23:48:33: #2 finished! INFO @ Mon, 12 Aug 2019 23:48:33: #2 predicted fragment length is 84 bps INFO @ Mon, 12 Aug 2019 23:48:33: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 12 Aug 2019 23:48:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.05_model.r INFO @ Mon, 12 Aug 2019 23:48:33: #1 tags after filtering in treatment: 7527095 INFO @ Mon, 12 Aug 2019 23:48:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:48:33: #1 finished! INFO @ Mon, 12 Aug 2019 23:48:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:48:33: #2 looking for paired plus/minus strand peaks... WARNING @ Mon, 12 Aug 2019 23:48:33: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:48:33: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 12 Aug 2019 23:48:33: #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 23:48:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:48:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:48:34: #2 number of paired peaks: 2561 INFO @ Mon, 12 Aug 2019 23:48:34: start model_add_line... INFO @ Mon, 12 Aug 2019 23:48:34: start X-correlation... INFO @ Mon, 12 Aug 2019 23:48:35: end of X-cor INFO @ Mon, 12 Aug 2019 23:48:35: #2 finished! INFO @ Mon, 12 Aug 2019 23:48:35: #2 predicted fragment length is 84 bps INFO @ Mon, 12 Aug 2019 23:48:35: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 12 Aug 2019 23:48:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.10_model.r WARNING @ Mon, 12 Aug 2019 23:48:35: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:48:35: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 12 Aug 2019 23:48:35: #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 23:48:35: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:48:35: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:48:37: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:48:37: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:48:37: #1 total tags in treatment: 7527095 INFO @ Mon, 12 Aug 2019 23:48:37: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:48:37: #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 23:48:37: #1 tags after filtering in treatment: 7527095 INFO @ Mon, 12 Aug 2019 23:48:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:48:37: #1 finished! INFO @ Mon, 12 Aug 2019 23:48:37: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:48:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:48:38: #2 number of paired peaks: 2561 INFO @ Mon, 12 Aug 2019 23:48:38: start model_add_line... INFO @ Mon, 12 Aug 2019 23:48:38: start X-correlation... INFO @ Mon, 12 Aug 2019 23:48:38: end of X-cor INFO @ Mon, 12 Aug 2019 23:48:38: #2 finished! INFO @ Mon, 12 Aug 2019 23:48:38: #2 predicted fragment length is 84 bps INFO @ Mon, 12 Aug 2019 23:48:38: #2 alternative fragment length(s) may be 84 bps INFO @ Mon, 12 Aug 2019 23:48:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.20_model.r WARNING @ Mon, 12 Aug 2019 23:48:38: #2 Since the d (84) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:48:38: #2 You may need to consider one of the other alternative d(s): 84 WARNING @ Mon, 12 Aug 2019 23:48:38: #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 23:48:38: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:48:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:48:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:48:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:49:00: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:49:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:49:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:49:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.05_summits.bed INFO @ Mon, 12 Aug 2019 23:49:08: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (6880 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:49:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:49:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:49:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.10_summits.bed INFO @ Mon, 12 Aug 2019 23:49:09: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3772 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:49:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:49:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:49:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011072/SRX5011072.20_summits.bed INFO @ Mon, 12 Aug 2019 23:49:11: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1793 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。