Job ID = 4287274 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,218,950 reads read : 30,437,900 reads written : 15,218,950 reads 0-length : 15,218,950 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: 00:08:54 15218950 reads; of these: 15218950 (100.00%) were unpaired; of these: 7798475 (51.24%) aligned 0 times 4998811 (32.85%) aligned exactly 1 time 2421664 (15.91%) aligned >1 times 48.76% overall alignment rate Time searching: 00:08:58 Overall time: 00:08:58 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] 516655 / 7420475 = 0.0696 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Tue, 10 Dec 2019 12:12:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.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 12:12:03: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:12:03: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:12:11: 1000000 INFO @ Tue, 10 Dec 2019 12:12:19: 2000000 INFO @ Tue, 10 Dec 2019 12:12:27: 3000000 INFO @ Tue, 10 Dec 2019 12:12:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.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 12:12:33: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:12:33: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:12:36: 4000000 INFO @ Tue, 10 Dec 2019 12:12:42: 1000000 INFO @ Tue, 10 Dec 2019 12:12:45: 5000000 INFO @ Tue, 10 Dec 2019 12:12:52: 2000000 INFO @ Tue, 10 Dec 2019 12:12:55: 6000000 BedGraph に変換中... INFO @ Tue, 10 Dec 2019 12:13:00: 3000000 INFO @ Tue, 10 Dec 2019 12:13:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.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 12:13:03: #1 read tag files... INFO @ Tue, 10 Dec 2019 12:13:03: #1 read treatment tags... INFO @ Tue, 10 Dec 2019 12:13:04: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:13:04: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:13:04: #1 total tags in treatment: 6903820 INFO @ Tue, 10 Dec 2019 12:13:04: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:13:04: #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 12:13:04: #1 tags after filtering in treatment: 6903571 INFO @ Tue, 10 Dec 2019 12:13:04: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:13:04: #1 finished! INFO @ Tue, 10 Dec 2019 12:13:04: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:13:04: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:13:06: #2 number of paired peaks: 6655 INFO @ Tue, 10 Dec 2019 12:13:06: start model_add_line... INFO @ Tue, 10 Dec 2019 12:13:06: start X-correlation... INFO @ Tue, 10 Dec 2019 12:13:06: end of X-cor INFO @ Tue, 10 Dec 2019 12:13:06: #2 finished! INFO @ Tue, 10 Dec 2019 12:13:06: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:13:06: #2 alternative fragment length(s) may be 51,133,220,574,593 bps INFO @ Tue, 10 Dec 2019 12:13:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.05_model.r WARNING @ Tue, 10 Dec 2019 12:13:06: #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 12:13:06: #2 You may need to consider one of the other alternative d(s): 51,133,220,574,593 WARNING @ Tue, 10 Dec 2019 12:13:06: #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 12:13:06: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:13:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:13:09: 4000000 INFO @ Tue, 10 Dec 2019 12:13:11: 1000000 INFO @ Tue, 10 Dec 2019 12:13:17: 5000000 INFO @ Tue, 10 Dec 2019 12:13:18: 2000000 INFO @ Tue, 10 Dec 2019 12:13:26: 3000000 INFO @ Tue, 10 Dec 2019 12:13:26: 6000000 INFO @ Tue, 10 Dec 2019 12:13:28: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:13:33: 4000000 INFO @ Tue, 10 Dec 2019 12:13:34: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:13:34: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:13:34: #1 total tags in treatment: 6903820 INFO @ Tue, 10 Dec 2019 12:13:34: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:13:34: #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 12:13:35: #1 tags after filtering in treatment: 6903571 INFO @ Tue, 10 Dec 2019 12:13:35: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:13:35: #1 finished! INFO @ Tue, 10 Dec 2019 12:13:35: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:13:35: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:13:36: #2 number of paired peaks: 6655 INFO @ Tue, 10 Dec 2019 12:13:36: start model_add_line... INFO @ Tue, 10 Dec 2019 12:13:36: start X-correlation... INFO @ Tue, 10 Dec 2019 12:13:36: end of X-cor INFO @ Tue, 10 Dec 2019 12:13:36: #2 finished! INFO @ Tue, 10 Dec 2019 12:13:36: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:13:36: #2 alternative fragment length(s) may be 51,133,220,574,593 bps INFO @ Tue, 10 Dec 2019 12:13:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.10_model.r WARNING @ Tue, 10 Dec 2019 12:13:36: #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 12:13:36: #2 You may need to consider one of the other alternative d(s): 51,133,220,574,593 WARNING @ Tue, 10 Dec 2019 12:13:36: #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 12:13:36: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:13:36: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:13:39: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.05_peaks.xls INFO @ Tue, 10 Dec 2019 12:13:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.05_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:13:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.05_summits.bed INFO @ Tue, 10 Dec 2019 12:13:39: Done! pass1 - making usageList (44 chroms): 2 millis pass2 - checking and writing primary data (796 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:13:40: 5000000 INFO @ Tue, 10 Dec 2019 12:13:48: 6000000 INFO @ Tue, 10 Dec 2019 12:13:55: #1 tag size is determined as 51 bps INFO @ Tue, 10 Dec 2019 12:13:55: #1 tag size = 51 INFO @ Tue, 10 Dec 2019 12:13:55: #1 total tags in treatment: 6903820 INFO @ Tue, 10 Dec 2019 12:13:55: #1 user defined the maximum tags... INFO @ Tue, 10 Dec 2019 12:13:55: #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 12:13:55: #1 tags after filtering in treatment: 6903571 INFO @ Tue, 10 Dec 2019 12:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 10 Dec 2019 12:13:55: #1 finished! INFO @ Tue, 10 Dec 2019 12:13:55: #2 Build Peak Model... INFO @ Tue, 10 Dec 2019 12:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 10 Dec 2019 12:13:57: #2 number of paired peaks: 6655 INFO @ Tue, 10 Dec 2019 12:13:57: start model_add_line... INFO @ Tue, 10 Dec 2019 12:13:57: start X-correlation... INFO @ Tue, 10 Dec 2019 12:13:57: end of X-cor INFO @ Tue, 10 Dec 2019 12:13:57: #2 finished! INFO @ Tue, 10 Dec 2019 12:13:57: #2 predicted fragment length is 51 bps INFO @ Tue, 10 Dec 2019 12:13:57: #2 alternative fragment length(s) may be 51,133,220,574,593 bps INFO @ Tue, 10 Dec 2019 12:13:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.20_model.r WARNING @ Tue, 10 Dec 2019 12:13:57: #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 12:13:57: #2 You may need to consider one of the other alternative d(s): 51,133,220,574,593 WARNING @ Tue, 10 Dec 2019 12:13:57: #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 12:13:57: #3 Call peaks... INFO @ Tue, 10 Dec 2019 12:13:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 10 Dec 2019 12:13:59: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:14:10: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.10_peaks.xls INFO @ Tue, 10 Dec 2019 12:14:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.10_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:14:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.10_summits.bed INFO @ Tue, 10 Dec 2019 12:14:10: Done! pass1 - making usageList (33 chroms): 2 millis pass2 - checking and writing primary data (446 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 10 Dec 2019 12:14:19: #3 Call peaks for each chromosome... INFO @ Tue, 10 Dec 2019 12:14:30: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.20_peaks.xls INFO @ Tue, 10 Dec 2019 12:14:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.20_peaks.narrowPeak INFO @ Tue, 10 Dec 2019 12:14:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX4654059/SRX4654059.20_summits.bed INFO @ Tue, 10 Dec 2019 12:14:30: Done! pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (176 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。