Job ID = 4287220 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,796,489 reads read : 43,592,978 reads written : 21,796,489 reads 0-length : 21,796,489 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: 00:00:02 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:22:45 21796489 reads; of these: 21796489 (100.00%) were unpaired; of these: 559103 (2.57%) aligned 0 times 14557516 (66.79%) aligned exactly 1 time 6679870 (30.65%) aligned >1 times 97.43% overall alignment rate Time searching: 00:22:51 Overall time: 00:22:51 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] 882849 / 21237386 = 0.0416 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:24:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.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 12:24:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:24:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:24:38: 1000000 INFO @ Tue, 10 Dec 2019 12:24:45: 2000000 INFO @ Tue, 10 Dec 2019 12:24:52: 3000000 INFO @ Tue, 10 Dec 2019 12:24:59: 4000000 INFO @ Tue, 10 Dec 2019 12:25:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.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 12:25:01: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:25:01: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:25:06: 5000000 INFO @ Tue, 10 Dec 2019 12:25:07: 1000000 INFO @ Tue, 10 Dec 2019 12:25:13: 6000000 INFO @ Tue, 10 Dec 2019 12:25:14: 2000000 INFO @ Tue, 10 Dec 2019 12:25:20: 7000000 INFO @ Tue, 10 Dec 2019 12:25:20: 3000000 INFO @ Tue, 10 Dec 2019 12:25:26: 4000000 INFO @ Tue, 10 Dec 2019 12:25:27: 8000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:25:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.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 12:25:31: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:25:31: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:25:33: 5000000 INFO @ Tue, 10 Dec 2019 12:25:34: 9000000 INFO @ Tue, 10 Dec 2019 12:25:38: 1000000 INFO @ Tue, 10 Dec 2019 12:25:39: 6000000 INFO @ Tue, 10 Dec 2019 12:25:41: 10000000 INFO @ Tue, 10 Dec 2019 12:25:45: 2000000 INFO @ Tue, 10 Dec 2019 12:25:46: 7000000 INFO @ Tue, 10 Dec 2019 12:25:48: 11000000 INFO @ Tue, 10 Dec 2019 12:25:52: 3000000 INFO @ Tue, 10 Dec 2019 12:25:52: 8000000 INFO @ Tue, 10 Dec 2019 12:25:55: 12000000 INFO @ Tue, 10 Dec 2019 12:25:59: 9000000 INFO @ Tue, 10 Dec 2019 12:25:59: 4000000 INFO @ Tue, 10 Dec 2019 12:26:02: 13000000 INFO @ Tue, 10 Dec 2019 12:26:05: 10000000 INFO @ Tue, 10 Dec 2019 12:26:06: 5000000 INFO @ Tue, 10 Dec 2019 12:26:09: 14000000 INFO @ Tue, 10 Dec 2019 12:26:11: 11000000 INFO @ Tue, 10 Dec 2019 12:26:13: 6000000 INFO @ Tue, 10 Dec 2019 12:26:16: 15000000 INFO @ Tue, 10 Dec 2019 12:26:18: 12000000 INFO @ Tue, 10 Dec 2019 12:26:20: 7000000 INFO @ Tue, 10 Dec 2019 12:26:23: 16000000 INFO @ Tue, 10 Dec 2019 12:26:24: 13000000 INFO @ Tue, 10 Dec 2019 12:26:27: 8000000 INFO @ Tue, 10 Dec 2019 12:26:30: 17000000 INFO @ Tue, 10 Dec 2019 12:26:31: 14000000 INFO @ Tue, 10 Dec 2019 12:26:34: 9000000 INFO @ Tue, 10 Dec 2019 12:26:37: 18000000 INFO @ Tue, 10 Dec 2019 12:26:37: 15000000 INFO @ Tue, 10 Dec 2019 12:26:40: 10000000 INFO @ Tue, 10 Dec 2019 12:26:44: 19000000 INFO @ Tue, 10 Dec 2019 12:26:44: 16000000 INFO @ Tue, 10 Dec 2019 12:26:48: 11000000 INFO @ Tue, 10 Dec 2019 12:26:50: 17000000 INFO @ Tue, 10 Dec 2019 12:26:51: 20000000 INFO @ Tue, 10 Dec 2019 12:26:54: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:26:54: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:26:54: #1 total tags in treatment: 20354537 INFO @ Tue, 10 Dec 2019 12:26:54: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:26:54: #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 12:26:54: #1 tags after filtering in treatment: 20354413 INFO @ Tue, 10 Dec 2019 12:26:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:26:54: #1 finished! INFO @ Tue, 10 Dec 2019 12:26:54: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:26:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:26:56: 12000000 INFO @ Tue, 10 Dec 2019 12:26:57: #2 number of paired peaks: 5840 INFO @ Tue, 10 Dec 2019 12:26:57: start model_add_line... INFO @ Tue, 10 Dec 2019 12:26:57: 18000000 INFO @ Tue, 10 Dec 2019 12:26:57: start X-correlation... INFO @ Tue, 10 Dec 2019 12:26:57: end of X-cor INFO @ Tue, 10 Dec 2019 12:26:57: #2 finished! INFO @ Tue, 10 Dec 2019 12:26:57: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:26:57: #2 alternative fragment length(s) may be 51,217 bps INFO @ Tue, 10 Dec 2019 12:26:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.05_model.r WARNING @ Tue, 10 Dec 2019 12:26:57: #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 12:26:57: #2 You may need to consider one of the other alternative d(s): 51,217 WARNING @ Tue, 10 Dec 2019 12:26:57: #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 12:26:57: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:26:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:27:02: 13000000 INFO @ Tue, 10 Dec 2019 12:27:03: 19000000 INFO @ Tue, 10 Dec 2019 12:27:09: 14000000 INFO @ Tue, 10 Dec 2019 12:27:10: 20000000 INFO @ Tue, 10 Dec 2019 12:27:12: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:27:12: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:27:12: #1 total tags in treatment: 20354537 INFO @ Tue, 10 Dec 2019 12:27:12: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:27:12: #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 12:27:13: #1 tags after filtering in treatment: 20354413 INFO @ Tue, 10 Dec 2019 12:27:13: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:27:13: #1 finished! INFO @ Tue, 10 Dec 2019 12:27:13: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:27:13: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:27:15: #2 number of paired peaks: 5840 INFO @ Tue, 10 Dec 2019 12:27:15: start model_add_line... INFO @ Tue, 10 Dec 2019 12:27:15: start X-correlation... INFO @ Tue, 10 Dec 2019 12:27:15: end of X-cor INFO @ Tue, 10 Dec 2019 12:27:15: #2 finished! INFO @ Tue, 10 Dec 2019 12:27:15: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:27:15: #2 alternative fragment length(s) may be 51,217 bps INFO @ Tue, 10 Dec 2019 12:27:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.10_model.r WARNING @ Tue, 10 Dec 2019 12:27:15: #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 12:27:15: #2 You may need to consider one of the other alternative d(s): 51,217 WARNING @ Tue, 10 Dec 2019 12:27:15: #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 12:27:15: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:27:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:27:16: 15000000 INFO @ Tue, 10 Dec 2019 12:27:23: 16000000 INFO @ Tue, 10 Dec 2019 12:27:30: 17000000 INFO @ Tue, 10 Dec 2019 12:27:37: 18000000 INFO @ Tue, 10 Dec 2019 12:27:44: 19000000 INFO @ Tue, 10 Dec 2019 12:27:51: 20000000 INFO @ Tue, 10 Dec 2019 12:27:53: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:27:53: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:27:53: #1 total tags in treatment: 20354537 INFO @ Tue, 10 Dec 2019 12:27:53: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:27:53: #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 12:27:54: #1 tags after filtering in treatment: 20354413 INFO @ Tue, 10 Dec 2019 12:27:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:27:54: #1 finished! INFO @ Tue, 10 Dec 2019 12:27:54: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:27:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:27:56: #2 number of paired peaks: 5840 INFO @ Tue, 10 Dec 2019 12:27:56: start model_add_line... INFO @ Tue, 10 Dec 2019 12:27:56: start X-correlation... INFO @ Tue, 10 Dec 2019 12:27:56: end of X-cor INFO @ Tue, 10 Dec 2019 12:27:56: #2 finished! INFO @ Tue, 10 Dec 2019 12:27:56: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:27:56: #2 alternative fragment length(s) may be 51,217 bps INFO @ Tue, 10 Dec 2019 12:27:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.20_model.r WARNING @ Tue, 10 Dec 2019 12:27:56: #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 12:27:56: #2 You may need to consider one of the other alternative d(s): 51,217 WARNING @ Tue, 10 Dec 2019 12:27:56: #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 12:27:56: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:27:56: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:28:01: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:28:19: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:28:32: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:28:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:28:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.05_summits.bed INFO @ Tue, 10 Dec 2019 12:28:32: Done! pass1 - making usageList (55 chroms): 2 millis pass2 - checking and writing primary data (1486 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:28:50: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:28:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:28:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.10_summits.bed INFO @ Tue, 10 Dec 2019 12:28:50: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (867 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:29:00: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:29:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:29:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:29:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654056/SRX4654056.20_summits.bed INFO @ Tue, 10 Dec 2019 12:29:31: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (417 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。