Job ID = 2590843 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,473,053 reads read : 25,473,053 reads written : 25,473,053 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: 00:08:33 25473053 reads; of these: 25473053 (100.00%) were unpaired; of these: 7429178 (29.16%) aligned 0 times 13191474 (51.79%) aligned exactly 1 time 4852401 (19.05%) aligned >1 times 70.84% overall alignment rate Time searching: 00:08:33 Overall time: 00:08:33 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] 9889143 / 18043875 = 0.5481 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 23:51:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.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 23:51:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:51:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:51:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.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 23:51:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:51:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:51:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.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 23:51:13: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:51:13: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:51:20: 1000000 INFO @ Mon, 12 Aug 2019 23:51:20: 1000000 INFO @ Mon, 12 Aug 2019 23:51:21: 1000000 INFO @ Mon, 12 Aug 2019 23:51:28: 2000000 INFO @ Mon, 12 Aug 2019 23:51:29: 2000000 INFO @ Mon, 12 Aug 2019 23:51:30: 2000000 INFO @ Mon, 12 Aug 2019 23:51:37: 3000000 INFO @ Mon, 12 Aug 2019 23:51:38: 3000000 INFO @ Mon, 12 Aug 2019 23:51:39: 3000000 INFO @ Mon, 12 Aug 2019 23:51:45: 4000000 INFO @ Mon, 12 Aug 2019 23:51:46: 4000000 INFO @ Mon, 12 Aug 2019 23:51:48: 4000000 INFO @ Mon, 12 Aug 2019 23:51:53: 5000000 INFO @ Mon, 12 Aug 2019 23:51:54: 5000000 INFO @ Mon, 12 Aug 2019 23:51:57: 5000000 INFO @ Mon, 12 Aug 2019 23:52:01: 6000000 INFO @ Mon, 12 Aug 2019 23:52:02: 6000000 INFO @ Mon, 12 Aug 2019 23:52:06: 6000000 INFO @ Mon, 12 Aug 2019 23:52:09: 7000000 INFO @ Mon, 12 Aug 2019 23:52:10: 7000000 INFO @ Mon, 12 Aug 2019 23:52:16: 7000000 INFO @ Mon, 12 Aug 2019 23:52:17: 8000000 INFO @ Mon, 12 Aug 2019 23:52:18: 8000000 INFO @ Mon, 12 Aug 2019 23:52:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:52:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:52:18: #1 total tags in treatment: 8154732 INFO @ Mon, 12 Aug 2019 23:52:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:52:18: #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 23:52:19: #1 tags after filtering in treatment: 8154732 INFO @ Mon, 12 Aug 2019 23:52:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:52:19: #1 finished! INFO @ Mon, 12 Aug 2019 23:52:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:52:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:52:19: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:52:19: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:52:19: #1 total tags in treatment: 8154732 INFO @ Mon, 12 Aug 2019 23:52:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:52:19: #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 23:52:20: #1 tags after filtering in treatment: 8154732 INFO @ Mon, 12 Aug 2019 23:52:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:52:20: #1 finished! INFO @ Mon, 12 Aug 2019 23:52:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:52:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:52:20: #2 number of paired peaks: 2715 INFO @ Mon, 12 Aug 2019 23:52:20: start model_add_line... INFO @ Mon, 12 Aug 2019 23:52:20: start X-correlation... INFO @ Mon, 12 Aug 2019 23:52:20: end of X-cor INFO @ Mon, 12 Aug 2019 23:52:20: #2 finished! INFO @ Mon, 12 Aug 2019 23:52:20: #2 predicted fragment length is 85 bps INFO @ Mon, 12 Aug 2019 23:52:20: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 12 Aug 2019 23:52:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.10_model.r WARNING @ Mon, 12 Aug 2019 23:52:20: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:52:20: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 12 Aug 2019 23:52:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 23:52:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:52:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:52:21: #2 number of paired peaks: 2715 INFO @ Mon, 12 Aug 2019 23:52:21: start model_add_line... INFO @ Mon, 12 Aug 2019 23:52:21: start X-correlation... INFO @ Mon, 12 Aug 2019 23:52:21: end of X-cor INFO @ Mon, 12 Aug 2019 23:52:21: #2 finished! INFO @ Mon, 12 Aug 2019 23:52:21: #2 predicted fragment length is 85 bps INFO @ Mon, 12 Aug 2019 23:52:21: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 12 Aug 2019 23:52:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.20_model.r WARNING @ Mon, 12 Aug 2019 23:52:21: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:52:21: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 12 Aug 2019 23:52:21: #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 23:52:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:52:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:52:24: 8000000 INFO @ Mon, 12 Aug 2019 23:52:26: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:52:26: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:52:26: #1 total tags in treatment: 8154732 INFO @ Mon, 12 Aug 2019 23:52:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:52:26: #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 23:52:26: #1 tags after filtering in treatment: 8154732 INFO @ Mon, 12 Aug 2019 23:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:52:26: #1 finished! INFO @ Mon, 12 Aug 2019 23:52:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:52:27: #2 number of paired peaks: 2715 INFO @ Mon, 12 Aug 2019 23:52:27: start model_add_line... INFO @ Mon, 12 Aug 2019 23:52:27: start X-correlation... INFO @ Mon, 12 Aug 2019 23:52:27: end of X-cor INFO @ Mon, 12 Aug 2019 23:52:27: #2 finished! INFO @ Mon, 12 Aug 2019 23:52:27: #2 predicted fragment length is 85 bps INFO @ Mon, 12 Aug 2019 23:52:27: #2 alternative fragment length(s) may be 85 bps INFO @ Mon, 12 Aug 2019 23:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.05_model.r WARNING @ Mon, 12 Aug 2019 23:52:27: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:52:27: #2 You may need to consider one of the other alternative d(s): 85 WARNING @ Mon, 12 Aug 2019 23:52:27: #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 23:52:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:52:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:52:45: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:52:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:52:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.10_summits.bed INFO @ Mon, 12 Aug 2019 23:52:56: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (5077 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:52:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:52:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:52:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.20_summits.bed INFO @ Mon, 12 Aug 2019 23:52:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2681 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:53:03: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:53:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:53:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011078/SRX5011078.05_summits.bed INFO @ Mon, 12 Aug 2019 23:53:03: Done! pass1 - making usageList (15 chroms): 4 millis pass2 - checking and writing primary data (8680 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。