Job ID = 2003634 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,293,908 reads read : 10,293,908 reads written : 10,293,908 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:03:59 10293908 reads; of these: 10293908 (100.00%) were unpaired; of these: 863432 (8.39%) aligned 0 times 5905227 (57.37%) aligned exactly 1 time 3525249 (34.25%) aligned >1 times 91.61% overall alignment rate Time searching: 00:04:02 Overall time: 00:04:02 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_rmdupse_core] 641262 / 9430476 = 0.0680 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... INFO @ Fri, 05 Jul 2019 12:40:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.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 @ Fri, 05 Jul 2019 12:40:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:40:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:40:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.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 @ Fri, 05 Jul 2019 12:40:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:40:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:40:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.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 @ Fri, 05 Jul 2019 12:40:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:40:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:41:01: 1000000 INFO @ Fri, 05 Jul 2019 12:41:02: 1000000 INFO @ Fri, 05 Jul 2019 12:41:03: 1000000 INFO @ Fri, 05 Jul 2019 12:41:07: 2000000 INFO @ Fri, 05 Jul 2019 12:41:08: 2000000 INFO @ Fri, 05 Jul 2019 12:41:09: 2000000 INFO @ Fri, 05 Jul 2019 12:41:12: 3000000 INFO @ Fri, 05 Jul 2019 12:41:14: 3000000 INFO @ Fri, 05 Jul 2019 12:41:15: 3000000 INFO @ Fri, 05 Jul 2019 12:41:17: 4000000 INFO @ Fri, 05 Jul 2019 12:41:20: 4000000 INFO @ Fri, 05 Jul 2019 12:41:21: 4000000 INFO @ Fri, 05 Jul 2019 12:41:22: 5000000 INFO @ Fri, 05 Jul 2019 12:41:26: 5000000 INFO @ Fri, 05 Jul 2019 12:41:27: 5000000 INFO @ Fri, 05 Jul 2019 12:41:28: 6000000 INFO @ Fri, 05 Jul 2019 12:41:32: 6000000 INFO @ Fri, 05 Jul 2019 12:41:33: 7000000 INFO @ Fri, 05 Jul 2019 12:41:33: 6000000 INFO @ Fri, 05 Jul 2019 12:41:38: 7000000 INFO @ Fri, 05 Jul 2019 12:41:39: 8000000 INFO @ Fri, 05 Jul 2019 12:41:39: 7000000 INFO @ Fri, 05 Jul 2019 12:41:43: #1 tag size is determined as 29 bps INFO @ Fri, 05 Jul 2019 12:41:43: #1 tag size = 29 INFO @ Fri, 05 Jul 2019 12:41:43: #1 total tags in treatment: 8789214 INFO @ Fri, 05 Jul 2019 12:41:43: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:41:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:41:43: #1 tags after filtering in treatment: 8789016 INFO @ Fri, 05 Jul 2019 12:41:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:41:43: #1 finished! INFO @ Fri, 05 Jul 2019 12:41:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:41:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:41:44: 8000000 INFO @ Fri, 05 Jul 2019 12:41:45: #2 number of paired peaks: 7176 INFO @ Fri, 05 Jul 2019 12:41:45: start model_add_line... INFO @ Fri, 05 Jul 2019 12:41:45: start X-correlation... INFO @ Fri, 05 Jul 2019 12:41:45: end of X-cor INFO @ Fri, 05 Jul 2019 12:41:45: #2 finished! INFO @ Fri, 05 Jul 2019 12:41:45: #2 predicted fragment length is 31 bps INFO @ Fri, 05 Jul 2019 12:41:45: #2 alternative fragment length(s) may be 31,104,207 bps INFO @ Fri, 05 Jul 2019 12:41:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.10_model.r WARNING @ Fri, 05 Jul 2019 12:41:45: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:41:45: #2 You may need to consider one of the other alternative d(s): 31,104,207 WARNING @ Fri, 05 Jul 2019 12:41:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:41:45: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:41:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:41:45: 8000000 INFO @ Fri, 05 Jul 2019 12:41:49: #1 tag size is determined as 29 bps INFO @ Fri, 05 Jul 2019 12:41:49: #1 tag size = 29 INFO @ Fri, 05 Jul 2019 12:41:49: #1 total tags in treatment: 8789214 INFO @ Fri, 05 Jul 2019 12:41:49: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:41:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:41:49: #1 tags after filtering in treatment: 8789016 INFO @ Fri, 05 Jul 2019 12:41:49: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:41:49: #1 finished! INFO @ Fri, 05 Jul 2019 12:41:49: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:41:49: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:41:50: #1 tag size is determined as 29 bps INFO @ Fri, 05 Jul 2019 12:41:51: #2 number of paired peaks: 7176 INFO @ Fri, 05 Jul 2019 12:41:51: start model_add_line... INFO @ Fri, 05 Jul 2019 12:41:51: #1 tag size = 29 INFO @ Fri, 05 Jul 2019 12:41:51: #1 total tags in treatment: 8789214 INFO @ Fri, 05 Jul 2019 12:41:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:41:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 12:41:51: start X-correlation... INFO @ Fri, 05 Jul 2019 12:41:51: end of X-cor INFO @ Fri, 05 Jul 2019 12:41:51: #2 finished! INFO @ Fri, 05 Jul 2019 12:41:51: #2 predicted fragment length is 31 bps INFO @ Fri, 05 Jul 2019 12:41:51: #2 alternative fragment length(s) may be 31,104,207 bps INFO @ Fri, 05 Jul 2019 12:41:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.05_model.r WARNING @ Fri, 05 Jul 2019 12:41:51: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:41:51: #2 You may need to consider one of the other alternative d(s): 31,104,207 WARNING @ Fri, 05 Jul 2019 12:41:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:41:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:41:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:41:51: #1 tags after filtering in treatment: 8789016 INFO @ Fri, 05 Jul 2019 12:41:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:41:51: #1 finished! INFO @ Fri, 05 Jul 2019 12:41:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:41:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:41:53: #2 number of paired peaks: 7176 INFO @ Fri, 05 Jul 2019 12:41:53: start model_add_line... INFO @ Fri, 05 Jul 2019 12:41:53: start X-correlation... INFO @ Fri, 05 Jul 2019 12:41:53: end of X-cor INFO @ Fri, 05 Jul 2019 12:41:53: #2 finished! INFO @ Fri, 05 Jul 2019 12:41:53: #2 predicted fragment length is 31 bps INFO @ Fri, 05 Jul 2019 12:41:53: #2 alternative fragment length(s) may be 31,104,207 bps INFO @ Fri, 05 Jul 2019 12:41:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.20_model.r WARNING @ Fri, 05 Jul 2019 12:41:53: #2 Since the d (31) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 12:41:53: #2 You may need to consider one of the other alternative d(s): 31,104,207 WARNING @ Fri, 05 Jul 2019 12:41:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 05 Jul 2019 12:41:53: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:41:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:42:02: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:42:08: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:42:10: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:42:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:42:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:42:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.10_summits.bed INFO @ Fri, 05 Jul 2019 12:42:11: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (662 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 12:42:18: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:42:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:42:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.05_summits.bed INFO @ Fri, 05 Jul 2019 12:42:18: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (1307 records, 4 fields): 4 millis INFO @ Fri, 05 Jul 2019 12:42:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:42:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:42:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX204156/SRX204156.20_summits.bed INFO @ Fri, 05 Jul 2019 12:42:19: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (171 records, 4 fields): 2 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。