Job ID = 4288822 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 31,319,212 reads read : 62,638,424 reads written : 31,319,212 reads 0-length : 31,319,212 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: 00:00:01 Multiseed full-index search: 00:14:13 31319212 reads; of these: 31319212 (100.00%) were unpaired; of these: 20704654 (66.11%) aligned 0 times 7516402 (24.00%) aligned exactly 1 time 3098156 (9.89%) aligned >1 times 33.89% overall alignment rate Time searching: 00:14:16 Overall time: 00:14:16 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] 2277109 / 10614558 = 0.2145 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:35:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.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 12:35:33: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:35:33: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:35:40: 1000000 INFO @ Tue, 10 Dec 2019 12:35:47: 2000000 INFO @ Tue, 10 Dec 2019 12:35:55: 3000000 INFO @ Tue, 10 Dec 2019 12:36:02: 4000000 INFO @ Tue, 10 Dec 2019 12:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.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 12:36:03: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:36:03: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:36:10: 5000000 INFO @ Tue, 10 Dec 2019 12:36:10: 1000000 INFO @ Tue, 10 Dec 2019 12:36:17: 2000000 INFO @ Tue, 10 Dec 2019 12:36:17: 6000000 INFO @ Tue, 10 Dec 2019 12:36:24: 3000000 INFO @ Tue, 10 Dec 2019 12:36:25: 7000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:36:31: 4000000 INFO @ Tue, 10 Dec 2019 12:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.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 12:36:33: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:36:33: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:36:33: 8000000 INFO @ Tue, 10 Dec 2019 12:36:36: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:36:36: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:36:36: #1 total tags in treatment: 8337449 INFO @ Tue, 10 Dec 2019 12:36:36: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:36:36: #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 12:36:36: #1 tags after filtering in treatment: 8337222 INFO @ Tue, 10 Dec 2019 12:36:36: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:36:36: #1 finished! INFO @ Tue, 10 Dec 2019 12:36:36: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:36:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:36:38: 5000000 INFO @ Tue, 10 Dec 2019 12:36:38: #2 number of paired peaks: 40980 INFO @ Tue, 10 Dec 2019 12:36:38: start model_add_line... INFO @ Tue, 10 Dec 2019 12:36:39: start X-correlation... INFO @ Tue, 10 Dec 2019 12:36:39: end of X-cor INFO @ Tue, 10 Dec 2019 12:36:39: #2 finished! INFO @ Tue, 10 Dec 2019 12:36:39: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 12:36:39: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 10 Dec 2019 12:36:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.05_model.r WARNING @ Tue, 10 Dec 2019 12:36:39: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:36:39: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 10 Dec 2019 12:36:39: #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 12:36:39: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:36:39: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:36:40: 1000000 INFO @ Tue, 10 Dec 2019 12:36:45: 6000000 INFO @ Tue, 10 Dec 2019 12:36:48: 2000000 INFO @ Tue, 10 Dec 2019 12:36:52: 7000000 INFO @ Tue, 10 Dec 2019 12:36:55: 3000000 INFO @ Tue, 10 Dec 2019 12:36:59: 8000000 INFO @ Tue, 10 Dec 2019 12:37:01: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:37:01: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:37:01: #1 total tags in treatment: 8337449 INFO @ Tue, 10 Dec 2019 12:37:01: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:37:01: #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 12:37:02: #1 tags after filtering in treatment: 8337222 INFO @ Tue, 10 Dec 2019 12:37:02: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:37:02: #1 finished! INFO @ Tue, 10 Dec 2019 12:37:02: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:37:02: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:37:02: 4000000 INFO @ Tue, 10 Dec 2019 12:37:04: #2 number of paired peaks: 40980 INFO @ Tue, 10 Dec 2019 12:37:04: start model_add_line... INFO @ Tue, 10 Dec 2019 12:37:04: start X-correlation... INFO @ Tue, 10 Dec 2019 12:37:04: end of X-cor INFO @ Tue, 10 Dec 2019 12:37:04: #2 finished! INFO @ Tue, 10 Dec 2019 12:37:04: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 12:37:04: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 10 Dec 2019 12:37:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.10_model.r WARNING @ Tue, 10 Dec 2019 12:37:04: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:37:04: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 10 Dec 2019 12:37:04: #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 12:37:04: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:37:04: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:37:05: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:37:10: 5000000 INFO @ Tue, 10 Dec 2019 12:37:17: 6000000 INFO @ Tue, 10 Dec 2019 12:37:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.05_summits.bed INFO @ Tue, 10 Dec 2019 12:37:20: Done! pass1 - making usageList (137 chroms): 8 millis pass2 - checking and writing primary data (33250 records, 4 fields): 46 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:37:25: 7000000 INFO @ Tue, 10 Dec 2019 12:37:31: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:37:32: 8000000 INFO @ Tue, 10 Dec 2019 12:37:35: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:37:35: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:37:35: #1 total tags in treatment: 8337449 INFO @ Tue, 10 Dec 2019 12:37:35: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:37:35: #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 12:37:35: #1 tags after filtering in treatment: 8337222 INFO @ Tue, 10 Dec 2019 12:37:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:37:35: #1 finished! INFO @ Tue, 10 Dec 2019 12:37:35: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:37:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:37:38: #2 number of paired peaks: 40980 INFO @ Tue, 10 Dec 2019 12:37:38: start model_add_line... INFO @ Tue, 10 Dec 2019 12:37:38: start X-correlation... INFO @ Tue, 10 Dec 2019 12:37:38: end of X-cor INFO @ Tue, 10 Dec 2019 12:37:38: #2 finished! INFO @ Tue, 10 Dec 2019 12:37:38: #2 predicted fragment length is 52 bps INFO @ Tue, 10 Dec 2019 12:37:38: #2 alternative fragment length(s) may be 52 bps INFO @ Tue, 10 Dec 2019 12:37:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.20_model.r WARNING @ Tue, 10 Dec 2019 12:37:38: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:37:38: #2 You may need to consider one of the other alternative d(s): 52 WARNING @ Tue, 10 Dec 2019 12:37:38: #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 12:37:38: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:37:38: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:37:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:37:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:37:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.10_summits.bed INFO @ Tue, 10 Dec 2019 12:37:45: Done! pass1 - making usageList (92 chroms): 3 millis pass2 - checking and writing primary data (14864 records, 4 fields): 23 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:38:04: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:38:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:38:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:38:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654070/SRX4654070.20_summits.bed INFO @ Tue, 10 Dec 2019 12:38:18: Done! pass1 - making usageList (54 chroms): 3 millis pass2 - checking and writing primary data (4574 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。