Job ID = 4303109 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,266,404 reads read : 21,266,404 reads written : 21,266,404 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1164519.sra.cache’: 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: 00:07:46 21266404 reads; of these: 21266404 (100.00%) were unpaired; of these: 1402820 (6.60%) aligned 0 times 13365825 (62.85%) aligned exactly 1 time 6497759 (30.55%) aligned >1 times 93.40% overall alignment rate Time searching: 00:07:47 Overall time: 00:07:47 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] 3845922 / 19863584 = 0.1936 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:57:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.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 00:57:35: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:57:35: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:57:43: 1000000 INFO @ Thu, 12 Dec 2019 00:57:50: 2000000 INFO @ Thu, 12 Dec 2019 00:57:57: 3000000 INFO @ Thu, 12 Dec 2019 00:58:05: 4000000 INFO @ Thu, 12 Dec 2019 00:58:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.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 00:58:05: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:58:05: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:58:12: 1000000 INFO @ Thu, 12 Dec 2019 00:58:12: 5000000 INFO @ Thu, 12 Dec 2019 00:58:18: 2000000 INFO @ Thu, 12 Dec 2019 00:58:19: 6000000 INFO @ Thu, 12 Dec 2019 00:58:23: 3000000 INFO @ Thu, 12 Dec 2019 00:58:27: 7000000 INFO @ Thu, 12 Dec 2019 00:58:29: 4000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:58:34: 8000000 INFO @ Thu, 12 Dec 2019 00:58:34: 5000000 INFO @ Thu, 12 Dec 2019 00:58:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.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 00:58:36: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:58:36: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:58:40: 6000000 INFO @ Thu, 12 Dec 2019 00:58:41: 9000000 INFO @ Thu, 12 Dec 2019 00:58:43: 1000000 INFO @ Thu, 12 Dec 2019 00:58:45: 7000000 INFO @ Thu, 12 Dec 2019 00:58:49: 10000000 INFO @ Thu, 12 Dec 2019 00:58:50: 8000000 INFO @ Thu, 12 Dec 2019 00:58:51: 2000000 INFO @ Thu, 12 Dec 2019 00:58:55: 9000000 INFO @ Thu, 12 Dec 2019 00:58:56: 11000000 INFO @ Thu, 12 Dec 2019 00:58:58: 3000000 INFO @ Thu, 12 Dec 2019 00:59:01: 10000000 INFO @ Thu, 12 Dec 2019 00:59:03: 12000000 INFO @ Thu, 12 Dec 2019 00:59:06: 4000000 INFO @ Thu, 12 Dec 2019 00:59:06: 11000000 INFO @ Thu, 12 Dec 2019 00:59:11: 13000000 INFO @ Thu, 12 Dec 2019 00:59:12: 12000000 INFO @ Thu, 12 Dec 2019 00:59:13: 5000000 INFO @ Thu, 12 Dec 2019 00:59:17: 13000000 INFO @ Thu, 12 Dec 2019 00:59:18: 14000000 INFO @ Thu, 12 Dec 2019 00:59:20: 6000000 INFO @ Thu, 12 Dec 2019 00:59:22: 14000000 INFO @ Thu, 12 Dec 2019 00:59:25: 15000000 INFO @ Thu, 12 Dec 2019 00:59:27: 7000000 INFO @ Thu, 12 Dec 2019 00:59:28: 15000000 INFO @ Thu, 12 Dec 2019 00:59:33: 16000000 INFO @ Thu, 12 Dec 2019 00:59:33: 16000000 INFO @ Thu, 12 Dec 2019 00:59:33: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:59:33: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:59:33: #1 total tags in treatment: 16017662 INFO @ Thu, 12 Dec 2019 00:59:33: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:59:33: #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 00:59:33: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 00:59:33: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 00:59:33: #1 total tags in treatment: 16017662 INFO @ Thu, 12 Dec 2019 00:59:33: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:59:33: #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 00:59:34: #1 tags after filtering in treatment: 16017662 INFO @ Thu, 12 Dec 2019 00:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:59:34: #1 finished! INFO @ Thu, 12 Dec 2019 00:59:34: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:59:34: #1 tags after filtering in treatment: 16017662 INFO @ Thu, 12 Dec 2019 00:59:34: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:59:34: #1 finished! INFO @ Thu, 12 Dec 2019 00:59:34: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:59:34: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:59:34: 8000000 INFO @ Thu, 12 Dec 2019 00:59:35: #2 number of paired peaks: 249 WARNING @ Thu, 12 Dec 2019 00:59:35: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Thu, 12 Dec 2019 00:59:35: start model_add_line... INFO @ Thu, 12 Dec 2019 00:59:35: #2 number of paired peaks: 249 WARNING @ Thu, 12 Dec 2019 00:59:35: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Thu, 12 Dec 2019 00:59:35: start model_add_line... INFO @ Thu, 12 Dec 2019 00:59:35: start X-correlation... INFO @ Thu, 12 Dec 2019 00:59:35: end of X-cor INFO @ Thu, 12 Dec 2019 00:59:35: #2 finished! INFO @ Thu, 12 Dec 2019 00:59:35: #2 predicted fragment length is 45 bps INFO @ Thu, 12 Dec 2019 00:59:35: #2 alternative fragment length(s) may be 45 bps INFO @ Thu, 12 Dec 2019 00:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.10_model.r INFO @ Thu, 12 Dec 2019 00:59:35: start X-correlation... INFO @ Thu, 12 Dec 2019 00:59:35: end of X-cor INFO @ Thu, 12 Dec 2019 00:59:35: #2 finished! INFO @ Thu, 12 Dec 2019 00:59:35: #2 predicted fragment length is 45 bps INFO @ Thu, 12 Dec 2019 00:59:35: #2 alternative fragment length(s) may be 45 bps INFO @ Thu, 12 Dec 2019 00:59:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.05_model.r WARNING @ Thu, 12 Dec 2019 00:59:35: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:59:35: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Thu, 12 Dec 2019 00:59:35: #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 00:59:35: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:59:35: #3 Pre-compute pvalue-qvalue table... WARNING @ Thu, 12 Dec 2019 00:59:35: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:59:35: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Thu, 12 Dec 2019 00:59:35: #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 00:59:35: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:59:35: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:59:41: 9000000 INFO @ Thu, 12 Dec 2019 00:59:48: 10000000 INFO @ Thu, 12 Dec 2019 00:59:55: 11000000 INFO @ Thu, 12 Dec 2019 01:00:01: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:00:02: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:00:02: 12000000 INFO @ Thu, 12 Dec 2019 01:00:09: 13000000 INFO @ Thu, 12 Dec 2019 01:00:16: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:00:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:00:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.10_summits.bed INFO @ Thu, 12 Dec 2019 01:00:16: Done! INFO @ Thu, 12 Dec 2019 01:00:16: 14000000 pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1733 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:00:17: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:00:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:00:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.05_summits.bed INFO @ Thu, 12 Dec 2019 01:00:17: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2038 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:00:23: 15000000 INFO @ Thu, 12 Dec 2019 01:00:30: 16000000 INFO @ Thu, 12 Dec 2019 01:00:30: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:00:30: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:00:30: #1 total tags in treatment: 16017662 INFO @ Thu, 12 Dec 2019 01:00:30: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:00:30: #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 01:00:30: #1 tags after filtering in treatment: 16017662 INFO @ Thu, 12 Dec 2019 01:00:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:00:30: #1 finished! INFO @ Thu, 12 Dec 2019 01:00:30: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:00:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:00:31: #2 number of paired peaks: 249 WARNING @ Thu, 12 Dec 2019 01:00:31: Fewer paired peaks (249) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 249 pairs to build model! INFO @ Thu, 12 Dec 2019 01:00:31: start model_add_line... INFO @ Thu, 12 Dec 2019 01:00:31: start X-correlation... INFO @ Thu, 12 Dec 2019 01:00:31: end of X-cor INFO @ Thu, 12 Dec 2019 01:00:31: #2 finished! INFO @ Thu, 12 Dec 2019 01:00:31: #2 predicted fragment length is 45 bps INFO @ Thu, 12 Dec 2019 01:00:31: #2 alternative fragment length(s) may be 45 bps INFO @ Thu, 12 Dec 2019 01:00:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.20_model.r WARNING @ Thu, 12 Dec 2019 01:00:31: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 01:00:31: #2 You may need to consider one of the other alternative d(s): 45 WARNING @ Thu, 12 Dec 2019 01:00:31: #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 01:00:31: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:00:31: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:00:58: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:01:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:01:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:01:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX467095/SRX467095.20_summits.bed INFO @ Thu, 12 Dec 2019 01:01:14: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (1266 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。