Job ID = 4288815 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,327,073 reads read : 40,654,146 reads written : 20,327,073 reads 0-length : 20,327,073 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:45 20327073 reads; of these: 20327073 (100.00%) were unpaired; of these: 450513 (2.22%) aligned 0 times 13691032 (67.35%) aligned exactly 1 time 6185528 (30.43%) aligned >1 times 97.78% overall alignment rate Time searching: 00:18:48 Overall time: 00:18:48 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] 896074 / 19876560 = 0.0451 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:39:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.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 12:39:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:39:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:39:23: 1000000 INFO @ Tue, 10 Dec 2019 12:39:29: 2000000 INFO @ Tue, 10 Dec 2019 12:39:36: 3000000 INFO @ Tue, 10 Dec 2019 12:39:43: 4000000 INFO @ Tue, 10 Dec 2019 12:39:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.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 12:39:46: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:39:46: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:39:49: 5000000 INFO @ Tue, 10 Dec 2019 12:39:54: 1000000 INFO @ Tue, 10 Dec 2019 12:39:56: 6000000 INFO @ Tue, 10 Dec 2019 12:40:02: 2000000 INFO @ Tue, 10 Dec 2019 12:40:03: 7000000 INFO @ Tue, 10 Dec 2019 12:40:09: 8000000 INFO @ Tue, 10 Dec 2019 12:40:09: 3000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:40:16: 9000000 INFO @ Tue, 10 Dec 2019 12:40:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.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 12:40:16: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:40:16: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:40:17: 4000000 INFO @ Tue, 10 Dec 2019 12:40:23: 10000000 INFO @ Tue, 10 Dec 2019 12:40:24: 1000000 INFO @ Tue, 10 Dec 2019 12:40:25: 5000000 INFO @ Tue, 10 Dec 2019 12:40:29: 11000000 INFO @ Tue, 10 Dec 2019 12:40:31: 2000000 INFO @ Tue, 10 Dec 2019 12:40:32: 6000000 INFO @ Tue, 10 Dec 2019 12:40:36: 12000000 INFO @ Tue, 10 Dec 2019 12:40:38: 3000000 INFO @ Tue, 10 Dec 2019 12:40:40: 7000000 INFO @ Tue, 10 Dec 2019 12:40:43: 13000000 INFO @ Tue, 10 Dec 2019 12:40:46: 4000000 INFO @ Tue, 10 Dec 2019 12:40:48: 8000000 INFO @ Tue, 10 Dec 2019 12:40:49: 14000000 INFO @ Tue, 10 Dec 2019 12:40:53: 5000000 INFO @ Tue, 10 Dec 2019 12:40:56: 9000000 INFO @ Tue, 10 Dec 2019 12:40:56: 15000000 INFO @ Tue, 10 Dec 2019 12:41:01: 6000000 INFO @ Tue, 10 Dec 2019 12:41:03: 16000000 INFO @ Tue, 10 Dec 2019 12:41:03: 10000000 INFO @ Tue, 10 Dec 2019 12:41:08: 7000000 INFO @ Tue, 10 Dec 2019 12:41:10: 17000000 INFO @ Tue, 10 Dec 2019 12:41:11: 11000000 INFO @ Tue, 10 Dec 2019 12:41:16: 8000000 INFO @ Tue, 10 Dec 2019 12:41:17: 18000000 INFO @ Tue, 10 Dec 2019 12:41:19: 12000000 INFO @ Tue, 10 Dec 2019 12:41:23: 9000000 INFO @ Tue, 10 Dec 2019 12:41:24: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:41:24: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:41:24: #1 total tags in treatment: 18980486 INFO @ Tue, 10 Dec 2019 12:41:24: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:41:24: #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 12:41:24: #1 tags after filtering in treatment: 18980353 INFO @ Tue, 10 Dec 2019 12:41:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:41:24: #1 finished! INFO @ Tue, 10 Dec 2019 12:41:24: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:41:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:41:26: #2 number of paired peaks: 5763 INFO @ Tue, 10 Dec 2019 12:41:26: start model_add_line... INFO @ Tue, 10 Dec 2019 12:41:27: start X-correlation... INFO @ Tue, 10 Dec 2019 12:41:27: end of X-cor INFO @ Tue, 10 Dec 2019 12:41:27: #2 finished! INFO @ Tue, 10 Dec 2019 12:41:27: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:41:27: #2 alternative fragment length(s) may be 51,500 bps INFO @ Tue, 10 Dec 2019 12:41:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.05_model.r WARNING @ Tue, 10 Dec 2019 12:41:27: #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 12:41:27: #2 You may need to consider one of the other alternative d(s): 51,500 WARNING @ Tue, 10 Dec 2019 12:41:27: #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 12:41:27: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:41:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:41:27: 13000000 INFO @ Tue, 10 Dec 2019 12:41:31: 10000000 INFO @ Tue, 10 Dec 2019 12:41:34: 14000000 INFO @ Tue, 10 Dec 2019 12:41:38: 11000000 INFO @ Tue, 10 Dec 2019 12:41:42: 15000000 INFO @ Tue, 10 Dec 2019 12:41:46: 12000000 INFO @ Tue, 10 Dec 2019 12:41:50: 16000000 INFO @ Tue, 10 Dec 2019 12:41:53: 13000000 INFO @ Tue, 10 Dec 2019 12:41:58: 17000000 INFO @ Tue, 10 Dec 2019 12:42:00: 14000000 INFO @ Tue, 10 Dec 2019 12:42:06: 18000000 INFO @ Tue, 10 Dec 2019 12:42:08: 15000000 INFO @ Tue, 10 Dec 2019 12:42:13: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:42:13: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:42:13: #1 total tags in treatment: 18980486 INFO @ Tue, 10 Dec 2019 12:42:13: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:42:13: #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 12:42:14: #1 tags after filtering in treatment: 18980353 INFO @ Tue, 10 Dec 2019 12:42:14: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:42:14: #1 finished! INFO @ Tue, 10 Dec 2019 12:42:14: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:42:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:42:15: 16000000 INFO @ Tue, 10 Dec 2019 12:42:16: #2 number of paired peaks: 5763 INFO @ Tue, 10 Dec 2019 12:42:16: start model_add_line... INFO @ Tue, 10 Dec 2019 12:42:16: start X-correlation... INFO @ Tue, 10 Dec 2019 12:42:16: end of X-cor INFO @ Tue, 10 Dec 2019 12:42:16: #2 finished! INFO @ Tue, 10 Dec 2019 12:42:16: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:42:16: #2 alternative fragment length(s) may be 51,500 bps INFO @ Tue, 10 Dec 2019 12:42:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.10_model.r WARNING @ Tue, 10 Dec 2019 12:42:16: #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 12:42:16: #2 You may need to consider one of the other alternative d(s): 51,500 WARNING @ Tue, 10 Dec 2019 12:42:16: #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 12:42:16: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:42:16: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:42:23: 17000000 INFO @ Tue, 10 Dec 2019 12:42:27: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:42:30: 18000000 INFO @ Tue, 10 Dec 2019 12:42:37: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:42:37: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:42:37: #1 total tags in treatment: 18980486 INFO @ Tue, 10 Dec 2019 12:42:37: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:42:37: #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 12:42:38: #1 tags after filtering in treatment: 18980353 INFO @ Tue, 10 Dec 2019 12:42:38: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:42:38: #1 finished! INFO @ Tue, 10 Dec 2019 12:42:38: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:42:38: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:42:40: #2 number of paired peaks: 5763 INFO @ Tue, 10 Dec 2019 12:42:40: start model_add_line... INFO @ Tue, 10 Dec 2019 12:42:41: start X-correlation... INFO @ Tue, 10 Dec 2019 12:42:41: end of X-cor INFO @ Tue, 10 Dec 2019 12:42:41: #2 finished! INFO @ Tue, 10 Dec 2019 12:42:41: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:42:41: #2 alternative fragment length(s) may be 51,500 bps INFO @ Tue, 10 Dec 2019 12:42:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.20_model.r WARNING @ Tue, 10 Dec 2019 12:42:41: #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 12:42:41: #2 You may need to consider one of the other alternative d(s): 51,500 WARNING @ Tue, 10 Dec 2019 12:42:41: #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 12:42:41: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:42:41: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:42:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:42:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:42:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.05_summits.bed INFO @ Tue, 10 Dec 2019 12:42:56: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (1382 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:43:17: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:43:41: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:43:46: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:43:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:43:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.10_summits.bed INFO @ Tue, 10 Dec 2019 12:43:46: Done! pass1 - making usageList (42 chroms): 1 millis pass2 - checking and writing primary data (824 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:44:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:44:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:44:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654069/SRX4654069.20_summits.bed INFO @ Tue, 10 Dec 2019 12:44:10: Done! pass1 - making usageList (31 chroms): 2 millis pass2 - checking and writing primary data (381 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。