Job ID = 4303113 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,517,831 reads read : 9,517,831 reads written : 9,517,831 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:10 9517831 reads; of these: 9517831 (100.00%) were unpaired; of these: 147208 (1.55%) aligned 0 times 6411023 (67.36%) aligned exactly 1 time 2959600 (31.10%) aligned >1 times 98.45% overall alignment rate Time searching: 00:03:11 Overall time: 00:03:11 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_rmdupse_core] 244503 / 9370623 = 0.0261 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:56:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.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 @ Thu, 12 Dec 2019 00:56:37: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:56:37: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:56:46: 1000000 INFO @ Thu, 12 Dec 2019 00:56:55: 2000000 INFO @ Thu, 12 Dec 2019 00:57:03: 3000000 INFO @ Thu, 12 Dec 2019 00:57:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.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 @ Thu, 12 Dec 2019 00:57:06: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:57:06: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:57:12: 4000000 INFO @ Thu, 12 Dec 2019 00:57:15: 1000000 INFO @ Thu, 12 Dec 2019 00:57:21: 5000000 INFO @ Thu, 12 Dec 2019 00:57:24: 2000000 INFO @ Thu, 12 Dec 2019 00:57:30: 6000000 INFO @ Thu, 12 Dec 2019 00:57:33: 3000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:57:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.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 @ Thu, 12 Dec 2019 00:57:36: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:57:36: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:57:40: 7000000 INFO @ Thu, 12 Dec 2019 00:57:43: 4000000 INFO @ Thu, 12 Dec 2019 00:57:46: 1000000 INFO @ Thu, 12 Dec 2019 00:57:49: 8000000 INFO @ Thu, 12 Dec 2019 00:57:52: 5000000 INFO @ Thu, 12 Dec 2019 00:57:55: 2000000 INFO @ Thu, 12 Dec 2019 00:57:59: 9000000 INFO @ Thu, 12 Dec 2019 00:58:00: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 00:58:00: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 00:58:00: #1 total tags in treatment: 9126120 INFO @ Thu, 12 Dec 2019 00:58:00: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:58:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:58:00: #1 tags after filtering in treatment: 9126120 INFO @ Thu, 12 Dec 2019 00:58:00: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:58:00: #1 finished! INFO @ Thu, 12 Dec 2019 00:58:00: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:58:00: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:58:00: #2 number of paired peaks: 103 WARNING @ Thu, 12 Dec 2019 00:58:00: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Thu, 12 Dec 2019 00:58:00: start model_add_line... INFO @ Thu, 12 Dec 2019 00:58:00: start X-correlation... INFO @ Thu, 12 Dec 2019 00:58:00: end of X-cor INFO @ Thu, 12 Dec 2019 00:58:00: #2 finished! INFO @ Thu, 12 Dec 2019 00:58:00: #2 predicted fragment length is 53 bps INFO @ Thu, 12 Dec 2019 00:58:00: #2 alternative fragment length(s) may be 53 bps INFO @ Thu, 12 Dec 2019 00:58:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.05_model.r WARNING @ Thu, 12 Dec 2019 00:58:00: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:58:00: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Thu, 12 Dec 2019 00:58:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:58:00: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:58:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:58:01: 6000000 INFO @ Thu, 12 Dec 2019 00:58:04: 3000000 INFO @ Thu, 12 Dec 2019 00:58:10: 7000000 INFO @ Thu, 12 Dec 2019 00:58:13: 4000000 INFO @ Thu, 12 Dec 2019 00:58:17: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:58:20: 8000000 INFO @ Thu, 12 Dec 2019 00:58:22: 5000000 INFO @ Thu, 12 Dec 2019 00:58:26: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:58:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:58:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.05_summits.bed INFO @ Thu, 12 Dec 2019 00:58:26: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1892 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:58:28: 9000000 INFO @ Thu, 12 Dec 2019 00:58:29: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 00:58:29: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 00:58:29: #1 total tags in treatment: 9126120 INFO @ Thu, 12 Dec 2019 00:58:29: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:58:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:58:30: #1 tags after filtering in treatment: 9126120 INFO @ Thu, 12 Dec 2019 00:58:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:58:30: #1 finished! INFO @ Thu, 12 Dec 2019 00:58:30: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:58:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:58:30: #2 number of paired peaks: 103 WARNING @ Thu, 12 Dec 2019 00:58:30: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Thu, 12 Dec 2019 00:58:30: start model_add_line... INFO @ Thu, 12 Dec 2019 00:58:30: start X-correlation... INFO @ Thu, 12 Dec 2019 00:58:30: end of X-cor INFO @ Thu, 12 Dec 2019 00:58:30: #2 finished! INFO @ Thu, 12 Dec 2019 00:58:30: #2 predicted fragment length is 53 bps INFO @ Thu, 12 Dec 2019 00:58:30: #2 alternative fragment length(s) may be 53 bps INFO @ Thu, 12 Dec 2019 00:58:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.10_model.r WARNING @ Thu, 12 Dec 2019 00:58:30: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:58:30: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Thu, 12 Dec 2019 00:58:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:58:30: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:58:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:58:31: 6000000 INFO @ Thu, 12 Dec 2019 00:58:40: 7000000 INFO @ Thu, 12 Dec 2019 00:58:46: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:58:48: 8000000 INFO @ Thu, 12 Dec 2019 00:58:56: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:58:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:58:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.10_summits.bed INFO @ Thu, 12 Dec 2019 00:58:56: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (1108 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:58:57: 9000000 INFO @ Thu, 12 Dec 2019 00:58:58: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 00:58:58: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 00:58:58: #1 total tags in treatment: 9126120 INFO @ Thu, 12 Dec 2019 00:58:58: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:58:58: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:58:58: #1 tags after filtering in treatment: 9126120 INFO @ Thu, 12 Dec 2019 00:58:58: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:58:58: #1 finished! INFO @ Thu, 12 Dec 2019 00:58:58: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:58:58: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:58:58: #2 number of paired peaks: 103 WARNING @ Thu, 12 Dec 2019 00:58:58: Fewer paired peaks (103) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 103 pairs to build model! INFO @ Thu, 12 Dec 2019 00:58:58: start model_add_line... INFO @ Thu, 12 Dec 2019 00:58:58: start X-correlation... INFO @ Thu, 12 Dec 2019 00:58:58: end of X-cor INFO @ Thu, 12 Dec 2019 00:58:58: #2 finished! INFO @ Thu, 12 Dec 2019 00:58:58: #2 predicted fragment length is 53 bps INFO @ Thu, 12 Dec 2019 00:58:58: #2 alternative fragment length(s) may be 53 bps INFO @ Thu, 12 Dec 2019 00:58:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.20_model.r WARNING @ Thu, 12 Dec 2019 00:58:59: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:58:59: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Thu, 12 Dec 2019 00:58:59: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:58:59: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:59:15: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:59:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:59:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:59:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474523/SRX474523.20_summits.bed INFO @ Thu, 12 Dec 2019 00:59:24: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (311 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。