Job ID = 4288961 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,693,065 reads read : 27,386,130 reads written : 13,693,065 reads 0-length : 13,693,065 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: 00:16:46 13693065 reads; of these: 13693065 (100.00%) were unpaired; of these: 2836042 (20.71%) aligned 0 times 8218261 (60.02%) aligned exactly 1 time 2638762 (19.27%) aligned >1 times 79.29% overall alignment rate Time searching: 00:16:47 Overall time: 00:16:47 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 1487214 / 10857023 = 0.1370 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 13:20:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Dec 2019 13:20:07: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:20:07: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:20:19: 1000000 INFO @ Tue, 10 Dec 2019 13:20:32: 2000000 INFO @ Tue, 10 Dec 2019 13:20:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Dec 2019 13:20:37: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:20:37: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:20:44: 3000000 INFO @ Tue, 10 Dec 2019 13:20:52: 1000000 INFO @ Tue, 10 Dec 2019 13:20:57: 4000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 13:21:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Dec 2019 13:21:07: #1 read tag files... INFO @ Tue, 10 Dec 2019 13:21:07: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 13:21:08: 2000000 INFO @ Tue, 10 Dec 2019 13:21:09: 5000000 INFO @ Tue, 10 Dec 2019 13:21:21: 6000000 INFO @ Tue, 10 Dec 2019 13:21:23: 3000000 INFO @ Tue, 10 Dec 2019 13:21:24: 1000000 INFO @ Tue, 10 Dec 2019 13:21:33: 7000000 INFO @ Tue, 10 Dec 2019 13:21:38: 4000000 INFO @ Tue, 10 Dec 2019 13:21:40: 2000000 INFO @ Tue, 10 Dec 2019 13:21:45: 8000000 INFO @ Tue, 10 Dec 2019 13:21:52: 5000000 INFO @ Tue, 10 Dec 2019 13:21:54: 3000000 INFO @ Tue, 10 Dec 2019 13:21:58: 9000000 INFO @ Tue, 10 Dec 2019 13:22:02: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:22:02: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:22:02: #1 total tags in treatment: 9369809 INFO @ Tue, 10 Dec 2019 13:22:02: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:22:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:22:02: #1 tags after filtering in treatment: 9369579 INFO @ Tue, 10 Dec 2019 13:22:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:22:02: #1 finished! INFO @ Tue, 10 Dec 2019 13:22:02: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:22:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:22:04: #2 number of paired peaks: 4949 INFO @ Tue, 10 Dec 2019 13:22:04: start model_add_line... INFO @ Tue, 10 Dec 2019 13:22:04: start X-correlation... INFO @ Tue, 10 Dec 2019 13:22:04: end of X-cor INFO @ Tue, 10 Dec 2019 13:22:04: #2 finished! INFO @ Tue, 10 Dec 2019 13:22:04: #2 predicted fragment length is 82 bps INFO @ Tue, 10 Dec 2019 13:22:04: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 10 Dec 2019 13:22:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.05_model.r WARNING @ Tue, 10 Dec 2019 13:22:04: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:22:04: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 10 Dec 2019 13:22:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:22:04: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:22:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:22:07: 6000000 INFO @ Tue, 10 Dec 2019 13:22:10: 4000000 INFO @ Tue, 10 Dec 2019 13:22:21: 7000000 INFO @ Tue, 10 Dec 2019 13:22:24: 5000000 INFO @ Tue, 10 Dec 2019 13:22:34: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:22:35: 8000000 INFO @ Tue, 10 Dec 2019 13:22:38: 6000000 INFO @ Tue, 10 Dec 2019 13:22:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.05_peaks.xls INFO @ Tue, 10 Dec 2019 13:22:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:22:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.05_summits.bed INFO @ Tue, 10 Dec 2019 13:22:49: Done! INFO @ Tue, 10 Dec 2019 13:22:49: 9000000 pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (621 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:22:51: 7000000 INFO @ Tue, 10 Dec 2019 13:22:54: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:22:54: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:22:54: #1 total tags in treatment: 9369809 INFO @ Tue, 10 Dec 2019 13:22:54: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:22:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:22:54: #1 tags after filtering in treatment: 9369579 INFO @ Tue, 10 Dec 2019 13:22:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:22:54: #1 finished! INFO @ Tue, 10 Dec 2019 13:22:54: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:22:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:22:55: #2 number of paired peaks: 4949 INFO @ Tue, 10 Dec 2019 13:22:55: start model_add_line... INFO @ Tue, 10 Dec 2019 13:22:55: start X-correlation... INFO @ Tue, 10 Dec 2019 13:22:55: end of X-cor INFO @ Tue, 10 Dec 2019 13:22:55: #2 finished! INFO @ Tue, 10 Dec 2019 13:22:55: #2 predicted fragment length is 82 bps INFO @ Tue, 10 Dec 2019 13:22:55: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 10 Dec 2019 13:22:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.10_model.r WARNING @ Tue, 10 Dec 2019 13:22:55: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:22:55: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 10 Dec 2019 13:22:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:22:55: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:22:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:23:05: 8000000 INFO @ Tue, 10 Dec 2019 13:23:18: 9000000 INFO @ Tue, 10 Dec 2019 13:23:23: #1 tag size is determined as 84 bps INFO @ Tue, 10 Dec 2019 13:23:23: #1 tag size = 84 INFO @ Tue, 10 Dec 2019 13:23:23: #1 total tags in treatment: 9369809 INFO @ Tue, 10 Dec 2019 13:23:23: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 13:23:23: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 10 Dec 2019 13:23:24: #1 tags after filtering in treatment: 9369579 INFO @ Tue, 10 Dec 2019 13:23:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 13:23:24: #1 finished! INFO @ Tue, 10 Dec 2019 13:23:24: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 13:23:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 13:23:25: #2 number of paired peaks: 4949 INFO @ Tue, 10 Dec 2019 13:23:25: start model_add_line... INFO @ Tue, 10 Dec 2019 13:23:25: start X-correlation... INFO @ Tue, 10 Dec 2019 13:23:25: end of X-cor INFO @ Tue, 10 Dec 2019 13:23:25: #2 finished! INFO @ Tue, 10 Dec 2019 13:23:25: #2 predicted fragment length is 82 bps INFO @ Tue, 10 Dec 2019 13:23:25: #2 alternative fragment length(s) may be 82 bps INFO @ Tue, 10 Dec 2019 13:23:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.20_model.r WARNING @ Tue, 10 Dec 2019 13:23:25: #2 Since the d (82) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 13:23:25: #2 You may need to consider one of the other alternative d(s): 82 WARNING @ Tue, 10 Dec 2019 13:23:25: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 10 Dec 2019 13:23:25: #3 Call peaks... INFO @ Tue, 10 Dec 2019 13:23:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 13:23:25: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:23:41: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.10_peaks.xls INFO @ Tue, 10 Dec 2019 13:23:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:23:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.10_summits.bed INFO @ Tue, 10 Dec 2019 13:23:41: Done! pass1 - making usageList (30 chroms): 2 millis pass2 - checking and writing primary data (397 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 13:23:55: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 13:24:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.20_peaks.xls INFO @ Tue, 10 Dec 2019 13:24:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 13:24:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5460581/SRX5460581.20_summits.bed INFO @ Tue, 10 Dec 2019 13:24:10: Done! pass1 - making usageList (22 chroms): 2 millis pass2 - checking and writing primary data (220 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。