Job ID = 2590607 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,773,290 reads read : 57,546,580 reads written : 28,773,290 reads 0-length : 28,773,290 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: 00:20:44 28773290 reads; of these: 28773290 (100.00%) were unpaired; of these: 590872 (2.05%) aligned 0 times 6770450 (23.53%) aligned exactly 1 time 21411968 (74.42%) aligned >1 times 97.95% overall alignment rate Time searching: 00:20:44 Overall time: 00:20:44 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] 11827426 / 28182418 = 0.4197 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 23:08:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.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 23:08:24: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:08:24: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:08:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.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 23:08:25: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:08:25: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:08:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.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 23:08:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 23:08:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 23:08:31: 1000000 INFO @ Mon, 12 Aug 2019 23:08:33: 1000000 INFO @ Mon, 12 Aug 2019 23:08:35: 1000000 INFO @ Mon, 12 Aug 2019 23:08:39: 2000000 INFO @ Mon, 12 Aug 2019 23:08:41: 2000000 INFO @ Mon, 12 Aug 2019 23:08:43: 2000000 INFO @ Mon, 12 Aug 2019 23:08:46: 3000000 INFO @ Mon, 12 Aug 2019 23:08:49: 3000000 INFO @ Mon, 12 Aug 2019 23:08:51: 3000000 INFO @ Mon, 12 Aug 2019 23:08:53: 4000000 INFO @ Mon, 12 Aug 2019 23:08:57: 4000000 INFO @ Mon, 12 Aug 2019 23:08:59: 4000000 INFO @ Mon, 12 Aug 2019 23:09:00: 5000000 INFO @ Mon, 12 Aug 2019 23:09:05: 5000000 INFO @ Mon, 12 Aug 2019 23:09:07: 6000000 INFO @ Mon, 12 Aug 2019 23:09:07: 5000000 INFO @ Mon, 12 Aug 2019 23:09:13: 6000000 INFO @ Mon, 12 Aug 2019 23:09:13: 7000000 INFO @ Mon, 12 Aug 2019 23:09:16: 6000000 INFO @ Mon, 12 Aug 2019 23:09:21: 8000000 INFO @ Mon, 12 Aug 2019 23:09:21: 7000000 INFO @ Mon, 12 Aug 2019 23:09:25: 7000000 INFO @ Mon, 12 Aug 2019 23:09:28: 9000000 INFO @ Mon, 12 Aug 2019 23:09:29: 8000000 INFO @ Mon, 12 Aug 2019 23:09:33: 8000000 INFO @ Mon, 12 Aug 2019 23:09:35: 10000000 INFO @ Mon, 12 Aug 2019 23:09:37: 9000000 INFO @ Mon, 12 Aug 2019 23:09:41: 9000000 INFO @ Mon, 12 Aug 2019 23:09:42: 11000000 INFO @ Mon, 12 Aug 2019 23:09:45: 10000000 INFO @ Mon, 12 Aug 2019 23:09:48: 12000000 INFO @ Mon, 12 Aug 2019 23:09:49: 10000000 INFO @ Mon, 12 Aug 2019 23:09:53: 11000000 INFO @ Mon, 12 Aug 2019 23:09:55: 13000000 INFO @ Mon, 12 Aug 2019 23:09:57: 11000000 INFO @ Mon, 12 Aug 2019 23:10:01: 12000000 INFO @ Mon, 12 Aug 2019 23:10:02: 14000000 INFO @ Mon, 12 Aug 2019 23:10:06: 12000000 INFO @ Mon, 12 Aug 2019 23:10:08: 13000000 INFO @ Mon, 12 Aug 2019 23:10:09: 15000000 INFO @ Mon, 12 Aug 2019 23:10:14: 13000000 INFO @ Mon, 12 Aug 2019 23:10:15: 16000000 INFO @ Mon, 12 Aug 2019 23:10:16: 14000000 INFO @ Mon, 12 Aug 2019 23:10:18: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:10:18: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:10:18: #1 total tags in treatment: 16354992 INFO @ Mon, 12 Aug 2019 23:10:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:10:18: #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 23:10:18: #1 tags after filtering in treatment: 16354992 INFO @ Mon, 12 Aug 2019 23:10:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:10:18: #1 finished! INFO @ Mon, 12 Aug 2019 23:10:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:10:20: #2 number of paired peaks: 3997 INFO @ Mon, 12 Aug 2019 23:10:20: start model_add_line... INFO @ Mon, 12 Aug 2019 23:10:21: start X-correlation... INFO @ Mon, 12 Aug 2019 23:10:21: end of X-cor INFO @ Mon, 12 Aug 2019 23:10:21: #2 finished! INFO @ Mon, 12 Aug 2019 23:10:21: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 23:10:21: #2 alternative fragment length(s) may be 3,42 bps INFO @ Mon, 12 Aug 2019 23:10:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.05_model.r WARNING @ Mon, 12 Aug 2019 23:10:21: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:10:21: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Mon, 12 Aug 2019 23:10:21: #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 23:10:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:10:22: 14000000 INFO @ Mon, 12 Aug 2019 23:10:24: 15000000 INFO @ Mon, 12 Aug 2019 23:10:30: 15000000 INFO @ Mon, 12 Aug 2019 23:10:31: 16000000 INFO @ Mon, 12 Aug 2019 23:10:34: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:10:34: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:10:34: #1 total tags in treatment: 16354992 INFO @ Mon, 12 Aug 2019 23:10:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:10:34: #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 23:10:35: #1 tags after filtering in treatment: 16354992 INFO @ Mon, 12 Aug 2019 23:10:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:10:35: #1 finished! INFO @ Mon, 12 Aug 2019 23:10:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:10:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:10:37: #2 number of paired peaks: 3997 INFO @ Mon, 12 Aug 2019 23:10:37: start model_add_line... INFO @ Mon, 12 Aug 2019 23:10:37: start X-correlation... INFO @ Mon, 12 Aug 2019 23:10:37: end of X-cor INFO @ Mon, 12 Aug 2019 23:10:37: #2 finished! INFO @ Mon, 12 Aug 2019 23:10:37: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 23:10:37: #2 alternative fragment length(s) may be 3,42 bps INFO @ Mon, 12 Aug 2019 23:10:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.10_model.r WARNING @ Mon, 12 Aug 2019 23:10:37: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:10:37: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Mon, 12 Aug 2019 23:10:37: #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 23:10:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:10:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:10:38: 16000000 INFO @ Mon, 12 Aug 2019 23:10:41: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 23:10:41: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 23:10:41: #1 total tags in treatment: 16354992 INFO @ Mon, 12 Aug 2019 23:10:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 23:10:41: #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 23:10:41: #1 tags after filtering in treatment: 16354992 INFO @ Mon, 12 Aug 2019 23:10:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 23:10:41: #1 finished! INFO @ Mon, 12 Aug 2019 23:10:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 23:10:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 23:10:43: #2 number of paired peaks: 3997 INFO @ Mon, 12 Aug 2019 23:10:43: start model_add_line... INFO @ Mon, 12 Aug 2019 23:10:43: start X-correlation... INFO @ Mon, 12 Aug 2019 23:10:43: end of X-cor INFO @ Mon, 12 Aug 2019 23:10:43: #2 finished! INFO @ Mon, 12 Aug 2019 23:10:43: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 23:10:43: #2 alternative fragment length(s) may be 3,42 bps INFO @ Mon, 12 Aug 2019 23:10:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.20_model.r WARNING @ Mon, 12 Aug 2019 23:10:43: #2 Since the d (42) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 23:10:43: #2 You may need to consider one of the other alternative d(s): 3,42 WARNING @ Mon, 12 Aug 2019 23:10:43: #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 23:10:43: #3 Call peaks... INFO @ Mon, 12 Aug 2019 23:10:43: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 23:11:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:11:20: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 23:11:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.05_peaks.xls INFO @ Mon, 12 Aug 2019 23:11:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:11:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.05_summits.bed INFO @ Mon, 12 Aug 2019 23:11:26: Done! pass1 - making usageList (14 chroms): 8 millis INFO @ Mon, 12 Aug 2019 23:11:27: #3 Call peaks for each chromosome... pass2 - checking and writing primary data (17672 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:11:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.10_peaks.xls INFO @ Mon, 12 Aug 2019 23:11:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:11:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.10_summits.bed INFO @ Mon, 12 Aug 2019 23:11:41: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7766 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 23:11:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.20_peaks.xls INFO @ Mon, 12 Aug 2019 23:11:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 23:11:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923191/SRX4923191.20_summits.bed INFO @ Mon, 12 Aug 2019 23:11:49: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (1506 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。