Job ID = 4287229 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,911,736 reads read : 43,823,472 reads written : 21,911,736 reads 0-length : 21,911,736 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:21:40 21911736 reads; of these: 21911736 (100.00%) were unpaired; of these: 502409 (2.29%) aligned 0 times 14658537 (66.90%) aligned exactly 1 time 6750790 (30.81%) aligned >1 times 97.71% overall alignment rate Time searching: 00:21:44 Overall time: 00:21:44 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 12 files... [bam_rmdupse_core] 949207 / 21409327 = 0.0443 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:24:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.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 12:24:28: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:24:28: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:24:34: 1000000 INFO @ Tue, 10 Dec 2019 12:24:41: 2000000 INFO @ Tue, 10 Dec 2019 12:24:48: 3000000 INFO @ Tue, 10 Dec 2019 12:24:55: 4000000 INFO @ Tue, 10 Dec 2019 12:24:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.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 12:24:58: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:24:58: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:25:02: 5000000 INFO @ Tue, 10 Dec 2019 12:25:06: 1000000 INFO @ Tue, 10 Dec 2019 12:25:09: 6000000 INFO @ Tue, 10 Dec 2019 12:25:14: 2000000 INFO @ Tue, 10 Dec 2019 12:25:15: 7000000 INFO @ Tue, 10 Dec 2019 12:25:21: 3000000 INFO @ Tue, 10 Dec 2019 12:25:22: 8000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:25:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.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 12:25:28: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:25:28: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:25:29: 4000000 INFO @ Tue, 10 Dec 2019 12:25:29: 9000000 INFO @ Tue, 10 Dec 2019 12:25:36: 1000000 INFO @ Tue, 10 Dec 2019 12:25:36: 10000000 INFO @ Tue, 10 Dec 2019 12:25:37: 5000000 INFO @ Tue, 10 Dec 2019 12:25:44: 11000000 INFO @ Tue, 10 Dec 2019 12:25:44: 2000000 INFO @ Tue, 10 Dec 2019 12:25:46: 6000000 INFO @ Tue, 10 Dec 2019 12:25:51: 12000000 INFO @ Tue, 10 Dec 2019 12:25:53: 3000000 INFO @ Tue, 10 Dec 2019 12:25:54: 7000000 INFO @ Tue, 10 Dec 2019 12:25:58: 13000000 INFO @ Tue, 10 Dec 2019 12:26:02: 4000000 INFO @ Tue, 10 Dec 2019 12:26:03: 8000000 INFO @ Tue, 10 Dec 2019 12:26:05: 14000000 INFO @ Tue, 10 Dec 2019 12:26:10: 5000000 INFO @ Tue, 10 Dec 2019 12:26:12: 9000000 INFO @ Tue, 10 Dec 2019 12:26:12: 15000000 INFO @ Tue, 10 Dec 2019 12:26:19: 16000000 INFO @ Tue, 10 Dec 2019 12:26:19: 6000000 INFO @ Tue, 10 Dec 2019 12:26:20: 10000000 INFO @ Tue, 10 Dec 2019 12:26:26: 17000000 INFO @ Tue, 10 Dec 2019 12:26:28: 7000000 INFO @ Tue, 10 Dec 2019 12:26:29: 11000000 INFO @ Tue, 10 Dec 2019 12:26:33: 18000000 INFO @ Tue, 10 Dec 2019 12:26:36: 8000000 INFO @ Tue, 10 Dec 2019 12:26:37: 12000000 INFO @ Tue, 10 Dec 2019 12:26:40: 19000000 INFO @ Tue, 10 Dec 2019 12:26:45: 9000000 INFO @ Tue, 10 Dec 2019 12:26:46: 13000000 INFO @ Tue, 10 Dec 2019 12:26:48: 20000000 INFO @ Tue, 10 Dec 2019 12:26:51: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:26:51: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:26:51: #1 total tags in treatment: 20460120 INFO @ Tue, 10 Dec 2019 12:26:51: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:26:51: #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 12:26:52: #1 tags after filtering in treatment: 20459999 INFO @ Tue, 10 Dec 2019 12:26:52: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:26:52: #1 finished! INFO @ Tue, 10 Dec 2019 12:26:52: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:26:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:26:53: 10000000 INFO @ Tue, 10 Dec 2019 12:26:54: #2 number of paired peaks: 6014 INFO @ Tue, 10 Dec 2019 12:26:54: start model_add_line... INFO @ Tue, 10 Dec 2019 12:26:54: start X-correlation... INFO @ Tue, 10 Dec 2019 12:26:54: end of X-cor INFO @ Tue, 10 Dec 2019 12:26:54: #2 finished! INFO @ Tue, 10 Dec 2019 12:26:54: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:26:54: #2 alternative fragment length(s) may be 51,217 bps INFO @ Tue, 10 Dec 2019 12:26:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.05_model.r WARNING @ Tue, 10 Dec 2019 12:26:54: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:26:54: #2 You may need to consider one of the other alternative d(s): 51,217 WARNING @ Tue, 10 Dec 2019 12:26:54: #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 12:26:54: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:26:54: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:26:55: 14000000 INFO @ Tue, 10 Dec 2019 12:27:02: 11000000 INFO @ Tue, 10 Dec 2019 12:27:03: 15000000 INFO @ Tue, 10 Dec 2019 12:27:10: 12000000 INFO @ Tue, 10 Dec 2019 12:27:11: 16000000 INFO @ Tue, 10 Dec 2019 12:27:17: 13000000 INFO @ Tue, 10 Dec 2019 12:27:19: 17000000 INFO @ Tue, 10 Dec 2019 12:27:25: 14000000 INFO @ Tue, 10 Dec 2019 12:27:27: 18000000 INFO @ Tue, 10 Dec 2019 12:27:33: 15000000 INFO @ Tue, 10 Dec 2019 12:27:35: 19000000 INFO @ Tue, 10 Dec 2019 12:27:41: 16000000 INFO @ Tue, 10 Dec 2019 12:27:43: 20000000 INFO @ Tue, 10 Dec 2019 12:27:47: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:27:47: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:27:47: #1 total tags in treatment: 20460120 INFO @ Tue, 10 Dec 2019 12:27:47: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:27:47: #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 12:27:47: #1 tags after filtering in treatment: 20459999 INFO @ Tue, 10 Dec 2019 12:27:47: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:27:47: #1 finished! INFO @ Tue, 10 Dec 2019 12:27:47: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:27:47: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:27:49: 17000000 INFO @ Tue, 10 Dec 2019 12:27:50: #2 number of paired peaks: 6014 INFO @ Tue, 10 Dec 2019 12:27:50: start model_add_line... INFO @ Tue, 10 Dec 2019 12:27:50: start X-correlation... INFO @ Tue, 10 Dec 2019 12:27:50: end of X-cor INFO @ Tue, 10 Dec 2019 12:27:50: #2 finished! INFO @ Tue, 10 Dec 2019 12:27:50: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:27:50: #2 alternative fragment length(s) may be 51,217 bps INFO @ Tue, 10 Dec 2019 12:27:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.10_model.r WARNING @ Tue, 10 Dec 2019 12:27:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:27:50: #2 You may need to consider one of the other alternative d(s): 51,217 WARNING @ Tue, 10 Dec 2019 12:27:50: #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 12:27:50: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:27:50: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:27:57: 18000000 INFO @ Tue, 10 Dec 2019 12:27:58: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:28:04: 19000000 INFO @ Tue, 10 Dec 2019 12:28:12: 20000000 INFO @ Tue, 10 Dec 2019 12:28:16: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:28:16: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:28:16: #1 total tags in treatment: 20460120 INFO @ Tue, 10 Dec 2019 12:28:16: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:28:16: #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 12:28:17: #1 tags after filtering in treatment: 20459999 INFO @ Tue, 10 Dec 2019 12:28:17: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:28:17: #1 finished! INFO @ Tue, 10 Dec 2019 12:28:17: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:28:17: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:28:19: #2 number of paired peaks: 6014 INFO @ Tue, 10 Dec 2019 12:28:19: start model_add_line... INFO @ Tue, 10 Dec 2019 12:28:19: start X-correlation... INFO @ Tue, 10 Dec 2019 12:28:19: end of X-cor INFO @ Tue, 10 Dec 2019 12:28:19: #2 finished! INFO @ Tue, 10 Dec 2019 12:28:19: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:28:19: #2 alternative fragment length(s) may be 51,217 bps INFO @ Tue, 10 Dec 2019 12:28:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.20_model.r WARNING @ Tue, 10 Dec 2019 12:28:19: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 10 Dec 2019 12:28:19: #2 You may need to consider one of the other alternative d(s): 51,217 WARNING @ Tue, 10 Dec 2019 12:28:19: #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 12:28:19: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:28:19: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:28:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:28:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:28:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.05_summits.bed INFO @ Tue, 10 Dec 2019 12:28:29: Done! pass1 - making usageList (56 chroms): 3 millis pass2 - checking and writing primary data (1514 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:28:53: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:29:23: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:29:24: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:29:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:29:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.10_summits.bed INFO @ Tue, 10 Dec 2019 12:29:24: Done! pass1 - making usageList (43 chroms): 2 millis pass2 - checking and writing primary data (881 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:29:54: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:29:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:29:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654057/SRX4654057.20_summits.bed INFO @ Tue, 10 Dec 2019 12:29:54: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (415 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。