Job ID = 2590861 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,208,741 reads read : 58,417,482 reads written : 29,208,741 reads 0-length : 29,208,741 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: 00:13:17 29208741 reads; of these: 29208741 (100.00%) were unpaired; of these: 2269042 (7.77%) aligned 0 times 18562141 (63.55%) aligned exactly 1 time 8377558 (28.68%) aligned >1 times 92.23% overall alignment rate Time searching: 00:13:17 Overall time: 00:13:17 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] 13477309 / 26939699 = 0.5003 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 @ Tue, 13 Aug 2019 00:04:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.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 @ Tue, 13 Aug 2019 00:04:23: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:04:23: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:04:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.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 @ Tue, 13 Aug 2019 00:04:24: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:04:24: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:04:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.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 @ Tue, 13 Aug 2019 00:04:25: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:04:25: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:04:30: 1000000 INFO @ Tue, 13 Aug 2019 00:04:31: 1000000 INFO @ Tue, 13 Aug 2019 00:04:32: 1000000 INFO @ Tue, 13 Aug 2019 00:04:37: 2000000 INFO @ Tue, 13 Aug 2019 00:04:39: 2000000 INFO @ Tue, 13 Aug 2019 00:04:39: 2000000 INFO @ Tue, 13 Aug 2019 00:04:45: 3000000 INFO @ Tue, 13 Aug 2019 00:04:46: 3000000 INFO @ Tue, 13 Aug 2019 00:04:47: 3000000 INFO @ Tue, 13 Aug 2019 00:04:52: 4000000 INFO @ Tue, 13 Aug 2019 00:04:53: 4000000 INFO @ Tue, 13 Aug 2019 00:04:54: 4000000 INFO @ Tue, 13 Aug 2019 00:04:59: 5000000 INFO @ Tue, 13 Aug 2019 00:05:01: 5000000 INFO @ Tue, 13 Aug 2019 00:05:01: 5000000 INFO @ Tue, 13 Aug 2019 00:05:06: 6000000 INFO @ Tue, 13 Aug 2019 00:05:08: 6000000 INFO @ Tue, 13 Aug 2019 00:05:08: 6000000 INFO @ Tue, 13 Aug 2019 00:05:13: 7000000 INFO @ Tue, 13 Aug 2019 00:05:15: 7000000 INFO @ Tue, 13 Aug 2019 00:05:16: 7000000 INFO @ Tue, 13 Aug 2019 00:05:21: 8000000 INFO @ Tue, 13 Aug 2019 00:05:23: 8000000 INFO @ Tue, 13 Aug 2019 00:05:23: 8000000 INFO @ Tue, 13 Aug 2019 00:05:28: 9000000 INFO @ Tue, 13 Aug 2019 00:05:30: 9000000 INFO @ Tue, 13 Aug 2019 00:05:30: 9000000 INFO @ Tue, 13 Aug 2019 00:05:35: 10000000 INFO @ Tue, 13 Aug 2019 00:05:38: 10000000 INFO @ Tue, 13 Aug 2019 00:05:38: 10000000 INFO @ Tue, 13 Aug 2019 00:05:42: 11000000 INFO @ Tue, 13 Aug 2019 00:05:45: 11000000 INFO @ Tue, 13 Aug 2019 00:05:45: 11000000 INFO @ Tue, 13 Aug 2019 00:05:50: 12000000 INFO @ Tue, 13 Aug 2019 00:05:52: 12000000 INFO @ Tue, 13 Aug 2019 00:05:53: 12000000 INFO @ Tue, 13 Aug 2019 00:05:57: 13000000 INFO @ Tue, 13 Aug 2019 00:06:00: 13000000 INFO @ Tue, 13 Aug 2019 00:06:00: 13000000 INFO @ Tue, 13 Aug 2019 00:06:00: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:06:00: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:06:00: #1 total tags in treatment: 13462390 INFO @ Tue, 13 Aug 2019 00:06:00: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:06:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:06:01: #1 tags after filtering in treatment: 13462390 INFO @ Tue, 13 Aug 2019 00:06:01: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:06:01: #1 finished! INFO @ Tue, 13 Aug 2019 00:06:01: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:06:01: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:06:02: #2 number of paired peaks: 1137 INFO @ Tue, 13 Aug 2019 00:06:02: start model_add_line... INFO @ Tue, 13 Aug 2019 00:06:02: start X-correlation... INFO @ Tue, 13 Aug 2019 00:06:02: end of X-cor INFO @ Tue, 13 Aug 2019 00:06:02: #2 finished! INFO @ Tue, 13 Aug 2019 00:06:02: #2 predicted fragment length is 50 bps INFO @ Tue, 13 Aug 2019 00:06:02: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 13 Aug 2019 00:06:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.05_model.r WARNING @ Tue, 13 Aug 2019 00:06:02: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:06:02: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 13 Aug 2019 00:06:02: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:06:02: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:06:02: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:06:03: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:06:03: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:06:03: #1 total tags in treatment: 13462390 INFO @ Tue, 13 Aug 2019 00:06:03: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:06:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:06:03: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:06:03: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:06:03: #1 total tags in treatment: 13462390 INFO @ Tue, 13 Aug 2019 00:06:03: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:06:03: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:06:04: #1 tags after filtering in treatment: 13462390 INFO @ Tue, 13 Aug 2019 00:06:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:06:04: #1 finished! INFO @ Tue, 13 Aug 2019 00:06:04: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:06:04: #1 tags after filtering in treatment: 13462390 INFO @ Tue, 13 Aug 2019 00:06:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:06:04: #1 finished! INFO @ Tue, 13 Aug 2019 00:06:04: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:06:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:06:05: #2 number of paired peaks: 1137 INFO @ Tue, 13 Aug 2019 00:06:05: start model_add_line... INFO @ Tue, 13 Aug 2019 00:06:05: #2 number of paired peaks: 1137 INFO @ Tue, 13 Aug 2019 00:06:05: start model_add_line... INFO @ Tue, 13 Aug 2019 00:06:05: start X-correlation... INFO @ Tue, 13 Aug 2019 00:06:05: end of X-cor INFO @ Tue, 13 Aug 2019 00:06:05: #2 finished! INFO @ Tue, 13 Aug 2019 00:06:05: #2 predicted fragment length is 50 bps INFO @ Tue, 13 Aug 2019 00:06:05: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 13 Aug 2019 00:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.10_model.r WARNING @ Tue, 13 Aug 2019 00:06:05: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:06:05: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 13 Aug 2019 00:06:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:06:05: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:06:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:06:05: start X-correlation... INFO @ Tue, 13 Aug 2019 00:06:05: end of X-cor INFO @ Tue, 13 Aug 2019 00:06:05: #2 finished! INFO @ Tue, 13 Aug 2019 00:06:05: #2 predicted fragment length is 50 bps INFO @ Tue, 13 Aug 2019 00:06:05: #2 alternative fragment length(s) may be 50 bps INFO @ Tue, 13 Aug 2019 00:06:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.20_model.r WARNING @ Tue, 13 Aug 2019 00:06:05: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:06:05: #2 You may need to consider one of the other alternative d(s): 50 WARNING @ Tue, 13 Aug 2019 00:06:05: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:06:05: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:06:05: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:06:38: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:06:41: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:06:41: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:06:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:06:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:06:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.05_summits.bed INFO @ Tue, 13 Aug 2019 00:06:56: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4733 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:06:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:06:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:06:59: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:06:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.20_summits.bed INFO @ Tue, 13 Aug 2019 00:06:59: Done! INFO @ Tue, 13 Aug 2019 00:06:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:06:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5011095/SRX5011095.10_summits.bed INFO @ Tue, 13 Aug 2019 00:06:59: Done! pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (1984 records, 4 fields): 8 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3276 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。