Job ID = 2003738 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,820,826 reads read : 59,641,652 reads written : 29,820,826 reads 0-length : 29,820,826 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:30:26 29820826 reads; of these: 29820826 (100.00%) were unpaired; of these: 1758453 (5.90%) aligned 0 times 17202003 (57.68%) aligned exactly 1 time 10860370 (36.42%) aligned >1 times 94.10% overall alignment rate Time searching: 00:30:27 Overall time: 00:30:27 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] 4535812 / 28062373 = 0.1616 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 14:48:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.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 14:48:24: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:48:24: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:48:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.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 14:48:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:48:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:48:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.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 14:48:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:48:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:48:31: 1000000 INFO @ Fri, 05 Jul 2019 14:48:32: 1000000 INFO @ Fri, 05 Jul 2019 14:48:33: 1000000 INFO @ Fri, 05 Jul 2019 14:48:38: 2000000 INFO @ Fri, 05 Jul 2019 14:48:39: 2000000 INFO @ Fri, 05 Jul 2019 14:48:40: 2000000 INFO @ Fri, 05 Jul 2019 14:48:45: 3000000 INFO @ Fri, 05 Jul 2019 14:48:46: 3000000 INFO @ Fri, 05 Jul 2019 14:48:47: 3000000 INFO @ Fri, 05 Jul 2019 14:48:52: 4000000 INFO @ Fri, 05 Jul 2019 14:48:53: 4000000 INFO @ Fri, 05 Jul 2019 14:48:54: 4000000 INFO @ Fri, 05 Jul 2019 14:48:59: 5000000 INFO @ Fri, 05 Jul 2019 14:49:00: 5000000 INFO @ Fri, 05 Jul 2019 14:49:01: 5000000 INFO @ Fri, 05 Jul 2019 14:49:06: 6000000 INFO @ Fri, 05 Jul 2019 14:49:07: 6000000 INFO @ Fri, 05 Jul 2019 14:49:08: 6000000 INFO @ Fri, 05 Jul 2019 14:49:12: 7000000 INFO @ Fri, 05 Jul 2019 14:49:13: 7000000 INFO @ Fri, 05 Jul 2019 14:49:14: 7000000 INFO @ Fri, 05 Jul 2019 14:49:19: 8000000 INFO @ Fri, 05 Jul 2019 14:49:20: 8000000 INFO @ Fri, 05 Jul 2019 14:49:21: 8000000 INFO @ Fri, 05 Jul 2019 14:49:26: 9000000 INFO @ Fri, 05 Jul 2019 14:49:27: 9000000 INFO @ Fri, 05 Jul 2019 14:49:28: 9000000 INFO @ Fri, 05 Jul 2019 14:49:33: 10000000 INFO @ Fri, 05 Jul 2019 14:49:33: 10000000 INFO @ Fri, 05 Jul 2019 14:49:35: 10000000 INFO @ Fri, 05 Jul 2019 14:49:39: 11000000 INFO @ Fri, 05 Jul 2019 14:49:40: 11000000 INFO @ Fri, 05 Jul 2019 14:49:41: 11000000 INFO @ Fri, 05 Jul 2019 14:49:46: 12000000 INFO @ Fri, 05 Jul 2019 14:49:47: 12000000 INFO @ Fri, 05 Jul 2019 14:49:48: 12000000 INFO @ Fri, 05 Jul 2019 14:49:53: 13000000 INFO @ Fri, 05 Jul 2019 14:49:54: 13000000 INFO @ Fri, 05 Jul 2019 14:49:55: 13000000 INFO @ Fri, 05 Jul 2019 14:50:00: 14000000 INFO @ Fri, 05 Jul 2019 14:50:01: 14000000 INFO @ Fri, 05 Jul 2019 14:50:02: 14000000 INFO @ Fri, 05 Jul 2019 14:50:07: 15000000 INFO @ Fri, 05 Jul 2019 14:50:08: 15000000 INFO @ Fri, 05 Jul 2019 14:50:08: 15000000 INFO @ Fri, 05 Jul 2019 14:50:17: 16000000 INFO @ Fri, 05 Jul 2019 14:50:17: 16000000 INFO @ Fri, 05 Jul 2019 14:50:17: 16000000 INFO @ Fri, 05 Jul 2019 14:50:24: 17000000 INFO @ Fri, 05 Jul 2019 14:50:24: 17000000 INFO @ Fri, 05 Jul 2019 14:50:24: 17000000 INFO @ Fri, 05 Jul 2019 14:50:31: 18000000 INFO @ Fri, 05 Jul 2019 14:50:31: 18000000 INFO @ Fri, 05 Jul 2019 14:50:31: 18000000 INFO @ Fri, 05 Jul 2019 14:50:38: 19000000 INFO @ Fri, 05 Jul 2019 14:50:38: 19000000 INFO @ Fri, 05 Jul 2019 14:50:39: 19000000 INFO @ Fri, 05 Jul 2019 14:50:45: 20000000 INFO @ Fri, 05 Jul 2019 14:50:45: 20000000 INFO @ Fri, 05 Jul 2019 14:50:45: 20000000 INFO @ Fri, 05 Jul 2019 14:50:52: 21000000 INFO @ Fri, 05 Jul 2019 14:50:52: 21000000 INFO @ Fri, 05 Jul 2019 14:50:52: 21000000 INFO @ Fri, 05 Jul 2019 14:50:59: 22000000 INFO @ Fri, 05 Jul 2019 14:50:59: 22000000 INFO @ Fri, 05 Jul 2019 14:50:59: 22000000 INFO @ Fri, 05 Jul 2019 14:51:06: 23000000 INFO @ Fri, 05 Jul 2019 14:51:06: 23000000 INFO @ Fri, 05 Jul 2019 14:51:06: 23000000 INFO @ Fri, 05 Jul 2019 14:51:09: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:51:09: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:51:09: #1 total tags in treatment: 23526561 INFO @ Fri, 05 Jul 2019 14:51:09: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:51:09: #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 14:51:10: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:51:10: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:51:10: #1 total tags in treatment: 23526561 INFO @ Fri, 05 Jul 2019 14:51:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:51:10: #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 14:51:10: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:51:10: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:51:10: #1 total tags in treatment: 23526561 INFO @ Fri, 05 Jul 2019 14:51:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:51:10: #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 14:51:10: #1 tags after filtering in treatment: 23526474 INFO @ Fri, 05 Jul 2019 14:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:51:10: #1 finished! INFO @ Fri, 05 Jul 2019 14:51:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:51:10: #1 tags after filtering in treatment: 23526474 INFO @ Fri, 05 Jul 2019 14:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:51:10: #1 finished! INFO @ Fri, 05 Jul 2019 14:51:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:51:10: #1 tags after filtering in treatment: 23526474 INFO @ Fri, 05 Jul 2019 14:51:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:51:10: #1 finished! INFO @ Fri, 05 Jul 2019 14:51:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:51:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:51:13: #2 number of paired peaks: 16540 INFO @ Fri, 05 Jul 2019 14:51:13: start model_add_line... INFO @ Fri, 05 Jul 2019 14:51:14: start X-correlation... INFO @ Fri, 05 Jul 2019 14:51:14: end of X-cor INFO @ Fri, 05 Jul 2019 14:51:14: #2 finished! INFO @ Fri, 05 Jul 2019 14:51:14: #2 predicted fragment length is 52 bps INFO @ Fri, 05 Jul 2019 14:51:14: #2 alternative fragment length(s) may be 52,110 bps INFO @ Fri, 05 Jul 2019 14:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.10_model.r WARNING @ Fri, 05 Jul 2019 14:51:14: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 14:51:14: #2 You may need to consider one of the other alternative d(s): 52,110 WARNING @ Fri, 05 Jul 2019 14:51:14: #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 14:51:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:51:14: #2 number of paired peaks: 16540 INFO @ Fri, 05 Jul 2019 14:51:14: start model_add_line... INFO @ Fri, 05 Jul 2019 14:51:14: #2 number of paired peaks: 16540 INFO @ Fri, 05 Jul 2019 14:51:14: start model_add_line... INFO @ Fri, 05 Jul 2019 14:51:14: start X-correlation... INFO @ Fri, 05 Jul 2019 14:51:14: end of X-cor INFO @ Fri, 05 Jul 2019 14:51:14: #2 finished! INFO @ Fri, 05 Jul 2019 14:51:14: #2 predicted fragment length is 52 bps INFO @ Fri, 05 Jul 2019 14:51:14: #2 alternative fragment length(s) may be 52,110 bps INFO @ Fri, 05 Jul 2019 14:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.20_model.r WARNING @ Fri, 05 Jul 2019 14:51:14: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 14:51:14: #2 You may need to consider one of the other alternative d(s): 52,110 WARNING @ Fri, 05 Jul 2019 14:51:14: #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 14:51:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:51:14: start X-correlation... INFO @ Fri, 05 Jul 2019 14:51:14: end of X-cor INFO @ Fri, 05 Jul 2019 14:51:14: #2 finished! INFO @ Fri, 05 Jul 2019 14:51:14: #2 predicted fragment length is 52 bps INFO @ Fri, 05 Jul 2019 14:51:14: #2 alternative fragment length(s) may be 52,110 bps INFO @ Fri, 05 Jul 2019 14:51:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.05_model.r WARNING @ Fri, 05 Jul 2019 14:51:14: #2 Since the d (52) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 14:51:14: #2 You may need to consider one of the other alternative d(s): 52,110 WARNING @ Fri, 05 Jul 2019 14:51:14: #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 14:51:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:51:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:52:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:52:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:52:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.05_summits.bed INFO @ Fri, 05 Jul 2019 14:53:04: Done! INFO @ Fri, 05 Jul 2019 14:53:04: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:53:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:53:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.20_summits.bed INFO @ Fri, 05 Jul 2019 14:53:04: Done! pass1 - making usageList (59 chroms): 2 millis pass2 - checking and writing primary data (2242 records, 4 fields): 12 millis pass1 - making usageList (37 chroms): 2 millis pass2 - checking and writing primary data (690 records, 4 fields): 5 millis INFO @ Fri, 05 Jul 2019 14:53:05: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:53:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:53:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333730/SRX5333730.10_summits.bed INFO @ Fri, 05 Jul 2019 14:53:05: Done! pass1 - making usageList (47 chroms): 2 millis pass2 - checking and writing primary data (1306 records, 4 fields): 7 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。