Job ID = 4178597 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 2,413,696 reads read : 4,827,392 reads written : 2,413,696 reads 0-length : 2,413,696 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: 00:00:54 2413696 reads; of these: 2413696 (100.00%) were unpaired; of these: 878 (0.04%) aligned 0 times 1692033 (70.10%) aligned exactly 1 time 720785 (29.86%) aligned >1 times 99.96% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 121190 / 2412818 = 0.0502 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 13:13:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.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, 05 Dec 2019 13:13:11: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:13:11: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:13:16: 1000000 INFO @ Thu, 05 Dec 2019 13:13:22: 2000000 INFO @ Thu, 05 Dec 2019 13:13:23: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:13:23: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:13:23: #1 total tags in treatment: 2291628 INFO @ Thu, 05 Dec 2019 13:13:23: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:13:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:13:23: #1 tags after filtering in treatment: 2291628 INFO @ Thu, 05 Dec 2019 13:13:23: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:13:23: #1 finished! INFO @ Thu, 05 Dec 2019 13:13:23: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:13:23: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:13:23: #2 number of paired peaks: 855 WARNING @ Thu, 05 Dec 2019 13:13:23: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Thu, 05 Dec 2019 13:13:23: start model_add_line... INFO @ Thu, 05 Dec 2019 13:13:23: start X-correlation... INFO @ Thu, 05 Dec 2019 13:13:23: end of X-cor INFO @ Thu, 05 Dec 2019 13:13:23: #2 finished! INFO @ Thu, 05 Dec 2019 13:13:23: #2 predicted fragment length is 66 bps INFO @ Thu, 05 Dec 2019 13:13:23: #2 alternative fragment length(s) may be 66 bps INFO @ Thu, 05 Dec 2019 13:13:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.05_model.r WARNING @ Thu, 05 Dec 2019 13:13:24: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:13:24: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Thu, 05 Dec 2019 13:13:24: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:13:24: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:13:24: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:13:28: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:13:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.05_peaks.xls INFO @ Thu, 05 Dec 2019 13:13:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:13:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.05_summits.bed INFO @ Thu, 05 Dec 2019 13:13:31: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (788 records, 4 fields): 18 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 13:13:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.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, 05 Dec 2019 13:13:41: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:13:41: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:13:46: 1000000 INFO @ Thu, 05 Dec 2019 13:13:52: 2000000 INFO @ Thu, 05 Dec 2019 13:13:53: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:13:53: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:13:53: #1 total tags in treatment: 2291628 INFO @ Thu, 05 Dec 2019 13:13:53: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:13:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:13:53: #1 tags after filtering in treatment: 2291628 INFO @ Thu, 05 Dec 2019 13:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:13:53: #1 finished! INFO @ Thu, 05 Dec 2019 13:13:53: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:13:53: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:13:53: #2 number of paired peaks: 855 WARNING @ Thu, 05 Dec 2019 13:13:53: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Thu, 05 Dec 2019 13:13:53: start model_add_line... INFO @ Thu, 05 Dec 2019 13:13:53: start X-correlation... INFO @ Thu, 05 Dec 2019 13:13:53: end of X-cor INFO @ Thu, 05 Dec 2019 13:13:53: #2 finished! INFO @ Thu, 05 Dec 2019 13:13:53: #2 predicted fragment length is 66 bps INFO @ Thu, 05 Dec 2019 13:13:53: #2 alternative fragment length(s) may be 66 bps INFO @ Thu, 05 Dec 2019 13:13:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.10_model.r WARNING @ Thu, 05 Dec 2019 13:13:53: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:13:53: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Thu, 05 Dec 2019 13:13:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:13:53: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:13:53: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:13:58: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:14:00: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.10_peaks.xls INFO @ Thu, 05 Dec 2019 13:14:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:14:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.10_summits.bed INFO @ Thu, 05 Dec 2019 13:14:01: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (304 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 05 Dec 2019 13:14:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.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, 05 Dec 2019 13:14:13: #1 read tag files... INFO @ Thu, 05 Dec 2019 13:14:13: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 13:14:18: 1000000 INFO @ Thu, 05 Dec 2019 13:14:24: 2000000 INFO @ Thu, 05 Dec 2019 13:14:25: #1 tag size is determined as 51 bps INFO @ Thu, 05 Dec 2019 13:14:25: #1 tag size = 51 INFO @ Thu, 05 Dec 2019 13:14:25: #1 total tags in treatment: 2291628 INFO @ Thu, 05 Dec 2019 13:14:25: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 13:14:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 13:14:25: #1 tags after filtering in treatment: 2291628 INFO @ Thu, 05 Dec 2019 13:14:25: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 13:14:25: #1 finished! INFO @ Thu, 05 Dec 2019 13:14:25: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 13:14:25: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 13:14:26: #2 number of paired peaks: 855 WARNING @ Thu, 05 Dec 2019 13:14:26: Fewer paired peaks (855) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 855 pairs to build model! INFO @ Thu, 05 Dec 2019 13:14:26: start model_add_line... INFO @ Thu, 05 Dec 2019 13:14:26: start X-correlation... INFO @ Thu, 05 Dec 2019 13:14:26: end of X-cor INFO @ Thu, 05 Dec 2019 13:14:26: #2 finished! INFO @ Thu, 05 Dec 2019 13:14:26: #2 predicted fragment length is 66 bps INFO @ Thu, 05 Dec 2019 13:14:26: #2 alternative fragment length(s) may be 66 bps INFO @ Thu, 05 Dec 2019 13:14:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.20_model.r WARNING @ Thu, 05 Dec 2019 13:14:26: #2 Since the d (66) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 05 Dec 2019 13:14:26: #2 You may need to consider one of the other alternative d(s): 66 WARNING @ Thu, 05 Dec 2019 13:14:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 05 Dec 2019 13:14:26: #3 Call peaks... INFO @ Thu, 05 Dec 2019 13:14:26: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 13:14:30: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 13:14:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.20_peaks.xls INFO @ Thu, 05 Dec 2019 13:14:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 13:14:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX6420691/SRX6420691.20_summits.bed INFO @ Thu, 05 Dec 2019 13:14:34: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (110 records, 4 fields): 40 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。