Job ID = 2591019 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,696,307 reads read : 27,696,307 reads written : 27,696,307 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: 00:06:46 27696307 reads; of these: 27696307 (100.00%) were unpaired; of these: 4042483 (14.60%) aligned 0 times 20766747 (74.98%) aligned exactly 1 time 2887077 (10.42%) aligned >1 times 85.40% overall alignment rate Time searching: 00:06:46 Overall time: 00:06:46 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] 11617339 / 23653824 = 0.4911 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 00:55:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.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 00:55:21: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:55:21: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:55:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.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 00:55:22: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:55:22: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:55:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.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 00:55:23: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:55:23: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:55:29: 1000000 INFO @ Tue, 13 Aug 2019 00:55:29: 1000000 INFO @ Tue, 13 Aug 2019 00:55:30: 1000000 INFO @ Tue, 13 Aug 2019 00:55:36: 2000000 INFO @ Tue, 13 Aug 2019 00:55:36: 2000000 INFO @ Tue, 13 Aug 2019 00:55:38: 2000000 INFO @ Tue, 13 Aug 2019 00:55:43: 3000000 INFO @ Tue, 13 Aug 2019 00:55:44: 3000000 INFO @ Tue, 13 Aug 2019 00:55:45: 3000000 INFO @ Tue, 13 Aug 2019 00:55:50: 4000000 INFO @ Tue, 13 Aug 2019 00:55:51: 4000000 INFO @ Tue, 13 Aug 2019 00:55:52: 4000000 INFO @ Tue, 13 Aug 2019 00:55:57: 5000000 INFO @ Tue, 13 Aug 2019 00:55:58: 5000000 INFO @ Tue, 13 Aug 2019 00:55:59: 5000000 INFO @ Tue, 13 Aug 2019 00:56:04: 6000000 INFO @ Tue, 13 Aug 2019 00:56:05: 6000000 INFO @ Tue, 13 Aug 2019 00:56:07: 6000000 INFO @ Tue, 13 Aug 2019 00:56:11: 7000000 INFO @ Tue, 13 Aug 2019 00:56:12: 7000000 INFO @ Tue, 13 Aug 2019 00:56:14: 7000000 INFO @ Tue, 13 Aug 2019 00:56:18: 8000000 INFO @ Tue, 13 Aug 2019 00:56:19: 8000000 INFO @ Tue, 13 Aug 2019 00:56:21: 8000000 INFO @ Tue, 13 Aug 2019 00:56:25: 9000000 INFO @ Tue, 13 Aug 2019 00:56:27: 9000000 INFO @ Tue, 13 Aug 2019 00:56:28: 9000000 INFO @ Tue, 13 Aug 2019 00:56:32: 10000000 INFO @ Tue, 13 Aug 2019 00:56:34: 10000000 INFO @ Tue, 13 Aug 2019 00:56:35: 10000000 INFO @ Tue, 13 Aug 2019 00:56:40: 11000000 INFO @ Tue, 13 Aug 2019 00:56:41: 11000000 INFO @ Tue, 13 Aug 2019 00:56:42: 11000000 INFO @ Tue, 13 Aug 2019 00:56:47: 12000000 INFO @ Tue, 13 Aug 2019 00:56:47: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:56:47: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:56:47: #1 total tags in treatment: 12036485 INFO @ Tue, 13 Aug 2019 00:56:47: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:56:47: #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 00:56:47: #1 tags after filtering in treatment: 12036485 INFO @ Tue, 13 Aug 2019 00:56:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:56:47: #1 finished! INFO @ Tue, 13 Aug 2019 00:56:47: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:56:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:56:48: 12000000 INFO @ Tue, 13 Aug 2019 00:56:48: #2 number of paired peaks: 169 WARNING @ Tue, 13 Aug 2019 00:56:48: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 13 Aug 2019 00:56:48: start model_add_line... INFO @ Tue, 13 Aug 2019 00:56:48: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:56:48: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:56:48: #1 total tags in treatment: 12036485 INFO @ Tue, 13 Aug 2019 00:56:48: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:56:48: #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 00:56:48: start X-correlation... INFO @ Tue, 13 Aug 2019 00:56:48: end of X-cor INFO @ Tue, 13 Aug 2019 00:56:48: #2 finished! INFO @ Tue, 13 Aug 2019 00:56:48: #2 predicted fragment length is 97 bps INFO @ Tue, 13 Aug 2019 00:56:48: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 13 Aug 2019 00:56:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.05_model.r WARNING @ Tue, 13 Aug 2019 00:56:48: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:56:48: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 13 Aug 2019 00:56:48: #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 00:56:48: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:56:48: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:56:49: #1 tags after filtering in treatment: 12036485 INFO @ Tue, 13 Aug 2019 00:56:49: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:56:49: #1 finished! INFO @ Tue, 13 Aug 2019 00:56:49: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:56:49: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:56:50: #2 number of paired peaks: 169 WARNING @ Tue, 13 Aug 2019 00:56:50: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 13 Aug 2019 00:56:50: start model_add_line... INFO @ Tue, 13 Aug 2019 00:56:50: 12000000 INFO @ Tue, 13 Aug 2019 00:56:50: start X-correlation... INFO @ Tue, 13 Aug 2019 00:56:50: end of X-cor INFO @ Tue, 13 Aug 2019 00:56:50: #2 finished! INFO @ Tue, 13 Aug 2019 00:56:50: #2 predicted fragment length is 97 bps INFO @ Tue, 13 Aug 2019 00:56:50: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 13 Aug 2019 00:56:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.10_model.r WARNING @ Tue, 13 Aug 2019 00:56:50: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:56:50: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 13 Aug 2019 00:56:50: #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 00:56:50: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:56:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:56:50: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:56:50: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:56:50: #1 total tags in treatment: 12036485 INFO @ Tue, 13 Aug 2019 00:56:50: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:56:50: #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 00:56:50: #1 tags after filtering in treatment: 12036485 INFO @ Tue, 13 Aug 2019 00:56:50: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:56:50: #1 finished! INFO @ Tue, 13 Aug 2019 00:56:50: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:56:50: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:56:51: #2 number of paired peaks: 169 WARNING @ Tue, 13 Aug 2019 00:56:51: Fewer paired peaks (169) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 169 pairs to build model! INFO @ Tue, 13 Aug 2019 00:56:51: start model_add_line... INFO @ Tue, 13 Aug 2019 00:56:51: start X-correlation... INFO @ Tue, 13 Aug 2019 00:56:51: end of X-cor INFO @ Tue, 13 Aug 2019 00:56:51: #2 finished! INFO @ Tue, 13 Aug 2019 00:56:51: #2 predicted fragment length is 97 bps INFO @ Tue, 13 Aug 2019 00:56:51: #2 alternative fragment length(s) may be 97 bps INFO @ Tue, 13 Aug 2019 00:56:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.20_model.r WARNING @ Tue, 13 Aug 2019 00:56:51: #2 Since the d (97) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:56:51: #2 You may need to consider one of the other alternative d(s): 97 WARNING @ Tue, 13 Aug 2019 00:56:51: #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 00:56:51: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:56:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:57:22: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:57:24: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:57:25: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:57:39: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:57:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:57:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.05_summits.bed INFO @ Tue, 13 Aug 2019 00:57:39: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1714 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:57:41: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:57:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:57:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.10_summits.bed INFO @ Tue, 13 Aug 2019 00:57:41: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (877 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:57:43: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:57:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:57:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX661230/SRX661230.20_summits.bed INFO @ Tue, 13 Aug 2019 00:57:43: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (373 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。