Job ID = 2590597 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,403,846 reads read : 40,807,692 reads written : 20,403,846 reads 0-length : 20,403,846 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: 00:11:50 20403846 reads; of these: 20403846 (100.00%) were unpaired; of these: 381667 (1.87%) aligned 0 times 5838834 (28.62%) aligned exactly 1 time 14183345 (69.51%) aligned >1 times 98.13% overall alignment rate Time searching: 00:11:50 Overall time: 00:11:50 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] 7022146 / 20022179 = 0.3507 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 22:51:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.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 22:51:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:51:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:51:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.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 22:51:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:51:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:51:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.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 22:51:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 22:51:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 22:51:41: 1000000 INFO @ Mon, 12 Aug 2019 22:51:42: 1000000 INFO @ Mon, 12 Aug 2019 22:51:43: 1000000 INFO @ Mon, 12 Aug 2019 22:51:49: 2000000 INFO @ Mon, 12 Aug 2019 22:51:50: 2000000 INFO @ Mon, 12 Aug 2019 22:51:51: 2000000 INFO @ Mon, 12 Aug 2019 22:51:56: 3000000 INFO @ Mon, 12 Aug 2019 22:51:58: 3000000 INFO @ Mon, 12 Aug 2019 22:52:00: 3000000 INFO @ Mon, 12 Aug 2019 22:52:02: 4000000 INFO @ Mon, 12 Aug 2019 22:52:07: 4000000 INFO @ Mon, 12 Aug 2019 22:52:09: 4000000 INFO @ Mon, 12 Aug 2019 22:52:10: 5000000 INFO @ Mon, 12 Aug 2019 22:52:15: 5000000 INFO @ Mon, 12 Aug 2019 22:52:17: 6000000 INFO @ Mon, 12 Aug 2019 22:52:17: 5000000 INFO @ Mon, 12 Aug 2019 22:52:24: 6000000 INFO @ Mon, 12 Aug 2019 22:52:24: 7000000 INFO @ Mon, 12 Aug 2019 22:52:25: 6000000 INFO @ Mon, 12 Aug 2019 22:52:31: 8000000 INFO @ Mon, 12 Aug 2019 22:52:32: 7000000 INFO @ Mon, 12 Aug 2019 22:52:33: 7000000 INFO @ Mon, 12 Aug 2019 22:52:38: 9000000 INFO @ Mon, 12 Aug 2019 22:52:40: 8000000 INFO @ Mon, 12 Aug 2019 22:52:41: 8000000 INFO @ Mon, 12 Aug 2019 22:52:44: 10000000 INFO @ Mon, 12 Aug 2019 22:52:47: 9000000 INFO @ Mon, 12 Aug 2019 22:52:49: 9000000 INFO @ Mon, 12 Aug 2019 22:52:51: 11000000 INFO @ Mon, 12 Aug 2019 22:52:55: 10000000 INFO @ Mon, 12 Aug 2019 22:52:58: 10000000 INFO @ Mon, 12 Aug 2019 22:52:58: 12000000 INFO @ Mon, 12 Aug 2019 22:53:03: 11000000 INFO @ Mon, 12 Aug 2019 22:53:05: 13000000 INFO @ Mon, 12 Aug 2019 22:53:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:53:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:53:05: #1 total tags in treatment: 13000033 INFO @ Mon, 12 Aug 2019 22:53:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:53:05: #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 22:53:05: #1 tags after filtering in treatment: 13000033 INFO @ Mon, 12 Aug 2019 22:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:53:05: #1 finished! INFO @ Mon, 12 Aug 2019 22:53:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:53:07: 11000000 INFO @ Mon, 12 Aug 2019 22:53:07: #2 number of paired peaks: 3822 INFO @ Mon, 12 Aug 2019 22:53:07: start model_add_line... INFO @ Mon, 12 Aug 2019 22:53:07: start X-correlation... INFO @ Mon, 12 Aug 2019 22:53:07: end of X-cor INFO @ Mon, 12 Aug 2019 22:53:07: #2 finished! INFO @ Mon, 12 Aug 2019 22:53:07: #2 predicted fragment length is 65 bps INFO @ Mon, 12 Aug 2019 22:53:07: #2 alternative fragment length(s) may be 4,65 bps INFO @ Mon, 12 Aug 2019 22:53:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.20_model.r WARNING @ Mon, 12 Aug 2019 22:53:07: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:53:07: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Mon, 12 Aug 2019 22:53:07: #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 22:53:07: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:53:07: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:53:10: 12000000 INFO @ Mon, 12 Aug 2019 22:53:15: 12000000 INFO @ Mon, 12 Aug 2019 22:53:17: 13000000 INFO @ Mon, 12 Aug 2019 22:53:17: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:53:17: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:53:17: #1 total tags in treatment: 13000033 INFO @ Mon, 12 Aug 2019 22:53:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:53:17: #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 22:53:18: #1 tags after filtering in treatment: 13000033 INFO @ Mon, 12 Aug 2019 22:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:53:18: #1 finished! INFO @ Mon, 12 Aug 2019 22:53:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:53:19: #2 number of paired peaks: 3822 INFO @ Mon, 12 Aug 2019 22:53:19: start model_add_line... INFO @ Mon, 12 Aug 2019 22:53:19: start X-correlation... INFO @ Mon, 12 Aug 2019 22:53:20: end of X-cor INFO @ Mon, 12 Aug 2019 22:53:20: #2 finished! INFO @ Mon, 12 Aug 2019 22:53:20: #2 predicted fragment length is 65 bps INFO @ Mon, 12 Aug 2019 22:53:20: #2 alternative fragment length(s) may be 4,65 bps INFO @ Mon, 12 Aug 2019 22:53:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.10_model.r WARNING @ Mon, 12 Aug 2019 22:53:20: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:53:20: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Mon, 12 Aug 2019 22:53:20: #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 22:53:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:53:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:53:23: 13000000 INFO @ Mon, 12 Aug 2019 22:53:23: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 22:53:23: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 22:53:23: #1 total tags in treatment: 13000033 INFO @ Mon, 12 Aug 2019 22:53:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 22:53:23: #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 22:53:24: #1 tags after filtering in treatment: 13000033 INFO @ Mon, 12 Aug 2019 22:53:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 22:53:24: #1 finished! INFO @ Mon, 12 Aug 2019 22:53:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 22:53:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 22:53:25: #2 number of paired peaks: 3822 INFO @ Mon, 12 Aug 2019 22:53:25: start model_add_line... INFO @ Mon, 12 Aug 2019 22:53:26: start X-correlation... INFO @ Mon, 12 Aug 2019 22:53:26: end of X-cor INFO @ Mon, 12 Aug 2019 22:53:26: #2 finished! INFO @ Mon, 12 Aug 2019 22:53:26: #2 predicted fragment length is 65 bps INFO @ Mon, 12 Aug 2019 22:53:26: #2 alternative fragment length(s) may be 4,65 bps INFO @ Mon, 12 Aug 2019 22:53:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.05_model.r WARNING @ Mon, 12 Aug 2019 22:53:26: #2 Since the d (65) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 22:53:26: #2 You may need to consider one of the other alternative d(s): 4,65 WARNING @ Mon, 12 Aug 2019 22:53:26: #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 22:53:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 22:53:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 22:53:44: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:53:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:54:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 22:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.20_peaks.xls INFO @ Mon, 12 Aug 2019 22:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.20_summits.bed INFO @ Mon, 12 Aug 2019 22:54:02: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (2166 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:54:13: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.10_peaks.xls INFO @ Mon, 12 Aug 2019 22:54:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:54:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.10_summits.bed INFO @ Mon, 12 Aug 2019 22:54:13: Done! pass1 - making usageList (14 chroms): 4 millis pass2 - checking and writing primary data (7374 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 22:54:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.05_peaks.xls INFO @ Mon, 12 Aug 2019 22:54:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 22:54:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX4923183/SRX4923183.05_summits.bed INFO @ Mon, 12 Aug 2019 22:54:20: Done! pass1 - making usageList (14 chroms): 7 millis pass2 - checking and writing primary data (15116 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。