Job ID = 2590304 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,351,050 reads read : 19,351,050 reads written : 19,351,050 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:09:34 19351050 reads; of these: 19351050 (100.00%) were unpaired; of these: 799810 (4.13%) aligned 0 times 12282950 (63.47%) aligned exactly 1 time 6268290 (32.39%) aligned >1 times 95.87% overall alignment rate Time searching: 00:09:35 Overall time: 00:09:35 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] 3134497 / 18551240 = 0.1690 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 20:55:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.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 20:55:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:55:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:55:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.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 20:55:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:55:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:55:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.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 20:55:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:55:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:55:57: 1000000 INFO @ Mon, 12 Aug 2019 20:55:58: 1000000 INFO @ Mon, 12 Aug 2019 20:56:01: 1000000 INFO @ Mon, 12 Aug 2019 20:56:04: 2000000 INFO @ Mon, 12 Aug 2019 20:56:05: 2000000 INFO @ Mon, 12 Aug 2019 20:56:08: 2000000 INFO @ Mon, 12 Aug 2019 20:56:11: 3000000 INFO @ Mon, 12 Aug 2019 20:56:12: 3000000 INFO @ Mon, 12 Aug 2019 20:56:17: 3000000 INFO @ Mon, 12 Aug 2019 20:56:17: 4000000 INFO @ Mon, 12 Aug 2019 20:56:18: 4000000 INFO @ Mon, 12 Aug 2019 20:56:24: 5000000 INFO @ Mon, 12 Aug 2019 20:56:25: 5000000 INFO @ Mon, 12 Aug 2019 20:56:25: 4000000 INFO @ Mon, 12 Aug 2019 20:56:31: 6000000 INFO @ Mon, 12 Aug 2019 20:56:32: 6000000 INFO @ Mon, 12 Aug 2019 20:56:34: 5000000 INFO @ Mon, 12 Aug 2019 20:56:37: 7000000 INFO @ Mon, 12 Aug 2019 20:56:38: 7000000 INFO @ Mon, 12 Aug 2019 20:56:42: 6000000 INFO @ Mon, 12 Aug 2019 20:56:44: 8000000 INFO @ Mon, 12 Aug 2019 20:56:45: 8000000 INFO @ Mon, 12 Aug 2019 20:56:50: 7000000 INFO @ Mon, 12 Aug 2019 20:56:51: 9000000 INFO @ Mon, 12 Aug 2019 20:56:52: 9000000 INFO @ Mon, 12 Aug 2019 20:56:57: 10000000 INFO @ Mon, 12 Aug 2019 20:56:58: 10000000 INFO @ Mon, 12 Aug 2019 20:56:59: 8000000 INFO @ Mon, 12 Aug 2019 20:57:04: 11000000 INFO @ Mon, 12 Aug 2019 20:57:05: 11000000 INFO @ Mon, 12 Aug 2019 20:57:07: 9000000 INFO @ Mon, 12 Aug 2019 20:57:11: 12000000 INFO @ Mon, 12 Aug 2019 20:57:12: 12000000 INFO @ Mon, 12 Aug 2019 20:57:15: 10000000 INFO @ Mon, 12 Aug 2019 20:57:17: 13000000 INFO @ Mon, 12 Aug 2019 20:57:18: 13000000 INFO @ Mon, 12 Aug 2019 20:57:23: 11000000 INFO @ Mon, 12 Aug 2019 20:57:24: 14000000 INFO @ Mon, 12 Aug 2019 20:57:25: 14000000 INFO @ Mon, 12 Aug 2019 20:57:31: 15000000 INFO @ Mon, 12 Aug 2019 20:57:32: 15000000 INFO @ Mon, 12 Aug 2019 20:57:32: 12000000 INFO @ Mon, 12 Aug 2019 20:57:34: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:57:34: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:57:34: #1 total tags in treatment: 15416743 INFO @ Mon, 12 Aug 2019 20:57:34: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:57:34: #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 20:57:34: #1 tags after filtering in treatment: 15416743 INFO @ Mon, 12 Aug 2019 20:57:34: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:57:34: #1 finished! INFO @ Mon, 12 Aug 2019 20:57:34: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:57:34: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:57:35: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:57:35: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:57:35: #1 total tags in treatment: 15416743 INFO @ Mon, 12 Aug 2019 20:57:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:57:35: #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 20:57:35: #1 tags after filtering in treatment: 15416743 INFO @ Mon, 12 Aug 2019 20:57:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:57:35: #1 finished! INFO @ Mon, 12 Aug 2019 20:57:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:57:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:57:35: #2 number of paired peaks: 685 WARNING @ Mon, 12 Aug 2019 20:57:35: Fewer paired peaks (685) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 685 pairs to build model! INFO @ Mon, 12 Aug 2019 20:57:35: start model_add_line... INFO @ Mon, 12 Aug 2019 20:57:36: start X-correlation... INFO @ Mon, 12 Aug 2019 20:57:36: end of X-cor INFO @ Mon, 12 Aug 2019 20:57:36: #2 finished! INFO @ Mon, 12 Aug 2019 20:57:36: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 20:57:36: #2 alternative fragment length(s) may be 4,42 bps INFO @ Mon, 12 Aug 2019 20:57:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.05_model.r WARNING @ Mon, 12 Aug 2019 20:57:36: #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 20:57:36: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Mon, 12 Aug 2019 20:57:36: #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 20:57:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:57:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:57:36: #2 number of paired peaks: 685 WARNING @ Mon, 12 Aug 2019 20:57:36: Fewer paired peaks (685) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 685 pairs to build model! INFO @ Mon, 12 Aug 2019 20:57:36: start model_add_line... INFO @ Mon, 12 Aug 2019 20:57:37: start X-correlation... INFO @ Mon, 12 Aug 2019 20:57:37: end of X-cor INFO @ Mon, 12 Aug 2019 20:57:37: #2 finished! INFO @ Mon, 12 Aug 2019 20:57:37: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 20:57:37: #2 alternative fragment length(s) may be 4,42 bps INFO @ Mon, 12 Aug 2019 20:57:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.10_model.r WARNING @ Mon, 12 Aug 2019 20:57:37: #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 20:57:37: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Mon, 12 Aug 2019 20:57:37: #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 20:57:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:57:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:57:40: 13000000 INFO @ Mon, 12 Aug 2019 20:57:48: 14000000 INFO @ Mon, 12 Aug 2019 20:57:56: 15000000 INFO @ Mon, 12 Aug 2019 20:58:00: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:58:00: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:58:00: #1 total tags in treatment: 15416743 INFO @ Mon, 12 Aug 2019 20:58:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:58:00: #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 20:58:00: #1 tags after filtering in treatment: 15416743 INFO @ Mon, 12 Aug 2019 20:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:58:00: #1 finished! INFO @ Mon, 12 Aug 2019 20:58:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:58:01: #2 number of paired peaks: 685 WARNING @ Mon, 12 Aug 2019 20:58:01: Fewer paired peaks (685) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 685 pairs to build model! INFO @ Mon, 12 Aug 2019 20:58:01: start model_add_line... INFO @ Mon, 12 Aug 2019 20:58:02: start X-correlation... INFO @ Mon, 12 Aug 2019 20:58:02: end of X-cor INFO @ Mon, 12 Aug 2019 20:58:02: #2 finished! INFO @ Mon, 12 Aug 2019 20:58:02: #2 predicted fragment length is 42 bps INFO @ Mon, 12 Aug 2019 20:58:02: #2 alternative fragment length(s) may be 4,42 bps INFO @ Mon, 12 Aug 2019 20:58:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.20_model.r WARNING @ Mon, 12 Aug 2019 20:58:02: #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 20:58:02: #2 You may need to consider one of the other alternative d(s): 4,42 WARNING @ Mon, 12 Aug 2019 20:58:02: #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 20:58:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:58:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:58:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:58:17: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:58:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:58:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.05_summits.bed INFO @ Mon, 12 Aug 2019 20:58:35: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (3306 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:58:36: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:58:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:58:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.10_summits.bed INFO @ Mon, 12 Aug 2019 20:58:36: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2574 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:58:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:59:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:59:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:59:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX318799/SRX318799.20_summits.bed INFO @ Mon, 12 Aug 2019 20:59:01: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1437 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。