Job ID = 2003724 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,364,455 reads read : 58,728,910 reads written : 29,364,455 reads 0-length : 29,364,455 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: 00:33:12 29364455 reads; of these: 29364455 (100.00%) were unpaired; of these: 2496607 (8.50%) aligned 0 times 16209024 (55.20%) aligned exactly 1 time 10658824 (36.30%) aligned >1 times 91.50% overall alignment rate Time searching: 00:33:15 Overall time: 00:33:15 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] 5002387 / 26867848 = 0.1862 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 14:39:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.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 14:39:55: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:39:55: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:39:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.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 14:39:56: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:39:56: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:39:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.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 14:39:57: #1 read tag files... INFO @ Fri, 05 Jul 2019 14:39:57: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 14:40:04: 1000000 INFO @ Fri, 05 Jul 2019 14:40:06: 1000000 INFO @ Fri, 05 Jul 2019 14:40:07: 1000000 INFO @ Fri, 05 Jul 2019 14:40:13: 2000000 INFO @ Fri, 05 Jul 2019 14:40:15: 2000000 INFO @ Fri, 05 Jul 2019 14:40:18: 2000000 INFO @ Fri, 05 Jul 2019 14:40:21: 3000000 INFO @ Fri, 05 Jul 2019 14:40:24: 3000000 INFO @ Fri, 05 Jul 2019 14:40:29: 3000000 INFO @ Fri, 05 Jul 2019 14:40:30: 4000000 INFO @ Fri, 05 Jul 2019 14:40:33: 4000000 INFO @ Fri, 05 Jul 2019 14:40:39: 5000000 INFO @ Fri, 05 Jul 2019 14:40:40: 4000000 INFO @ Fri, 05 Jul 2019 14:40:41: 5000000 INFO @ Fri, 05 Jul 2019 14:40:47: 6000000 INFO @ Fri, 05 Jul 2019 14:40:50: 6000000 INFO @ Fri, 05 Jul 2019 14:40:51: 5000000 INFO @ Fri, 05 Jul 2019 14:40:55: 7000000 INFO @ Fri, 05 Jul 2019 14:40:58: 7000000 INFO @ Fri, 05 Jul 2019 14:41:02: 6000000 INFO @ Fri, 05 Jul 2019 14:41:04: 8000000 INFO @ Fri, 05 Jul 2019 14:41:08: 8000000 INFO @ Fri, 05 Jul 2019 14:41:13: 7000000 INFO @ Fri, 05 Jul 2019 14:41:13: 9000000 INFO @ Fri, 05 Jul 2019 14:41:17: 9000000 INFO @ Fri, 05 Jul 2019 14:41:23: 10000000 INFO @ Fri, 05 Jul 2019 14:41:23: 8000000 INFO @ Fri, 05 Jul 2019 14:41:26: 10000000 INFO @ Fri, 05 Jul 2019 14:41:32: 11000000 INFO @ Fri, 05 Jul 2019 14:41:34: 9000000 INFO @ Fri, 05 Jul 2019 14:41:36: 11000000 INFO @ Fri, 05 Jul 2019 14:41:41: 12000000 INFO @ Fri, 05 Jul 2019 14:41:44: 10000000 INFO @ Fri, 05 Jul 2019 14:41:45: 12000000 INFO @ Fri, 05 Jul 2019 14:41:50: 13000000 INFO @ Fri, 05 Jul 2019 14:41:54: 13000000 INFO @ Fri, 05 Jul 2019 14:41:55: 11000000 INFO @ Fri, 05 Jul 2019 14:41:59: 14000000 INFO @ Fri, 05 Jul 2019 14:42:03: 14000000 INFO @ Fri, 05 Jul 2019 14:42:05: 12000000 INFO @ Fri, 05 Jul 2019 14:42:09: 15000000 INFO @ Fri, 05 Jul 2019 14:42:13: 15000000 INFO @ Fri, 05 Jul 2019 14:42:16: 13000000 INFO @ Fri, 05 Jul 2019 14:42:18: 16000000 INFO @ Fri, 05 Jul 2019 14:42:22: 16000000 INFO @ Fri, 05 Jul 2019 14:42:26: 14000000 INFO @ Fri, 05 Jul 2019 14:42:27: 17000000 INFO @ Fri, 05 Jul 2019 14:42:31: 17000000 INFO @ Fri, 05 Jul 2019 14:42:36: 18000000 INFO @ Fri, 05 Jul 2019 14:42:37: 15000000 INFO @ Fri, 05 Jul 2019 14:42:40: 18000000 INFO @ Fri, 05 Jul 2019 14:42:45: 19000000 INFO @ Fri, 05 Jul 2019 14:42:47: 16000000 INFO @ Fri, 05 Jul 2019 14:42:49: 19000000 INFO @ Fri, 05 Jul 2019 14:42:54: 20000000 INFO @ Fri, 05 Jul 2019 14:42:58: 17000000 INFO @ Fri, 05 Jul 2019 14:42:58: 20000000 INFO @ Fri, 05 Jul 2019 14:43:03: 21000000 INFO @ Fri, 05 Jul 2019 14:43:07: 21000000 INFO @ Fri, 05 Jul 2019 14:43:08: 18000000 INFO @ Fri, 05 Jul 2019 14:43:11: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:43:11: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:43:11: #1 total tags in treatment: 21865461 INFO @ Fri, 05 Jul 2019 14:43:11: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:43:11: #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 14:43:12: #1 tags after filtering in treatment: 21865361 INFO @ Fri, 05 Jul 2019 14:43:12: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:43:12: #1 finished! INFO @ Fri, 05 Jul 2019 14:43:12: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:43:12: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:43:15: #2 number of paired peaks: 8265 INFO @ Fri, 05 Jul 2019 14:43:15: start model_add_line... INFO @ Fri, 05 Jul 2019 14:43:15: start X-correlation... INFO @ Fri, 05 Jul 2019 14:43:15: end of X-cor INFO @ Fri, 05 Jul 2019 14:43:15: #2 finished! INFO @ Fri, 05 Jul 2019 14:43:15: #2 predicted fragment length is 50 bps INFO @ Fri, 05 Jul 2019 14:43:15: #2 alternative fragment length(s) may be 50,216,409 bps INFO @ Fri, 05 Jul 2019 14:43:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.05_model.r WARNING @ Fri, 05 Jul 2019 14:43:15: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 14:43:15: #2 You may need to consider one of the other alternative d(s): 50,216,409 WARNING @ Fri, 05 Jul 2019 14:43:15: #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 14:43:15: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:43:15: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:43:16: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:43:16: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:43:16: #1 total tags in treatment: 21865461 INFO @ Fri, 05 Jul 2019 14:43:16: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:43:16: #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 14:43:16: #1 tags after filtering in treatment: 21865361 INFO @ Fri, 05 Jul 2019 14:43:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:43:16: #1 finished! INFO @ Fri, 05 Jul 2019 14:43:16: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:43:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:43:18: 19000000 INFO @ Fri, 05 Jul 2019 14:43:19: #2 number of paired peaks: 8265 INFO @ Fri, 05 Jul 2019 14:43:19: start model_add_line... INFO @ Fri, 05 Jul 2019 14:43:19: start X-correlation... INFO @ Fri, 05 Jul 2019 14:43:19: end of X-cor INFO @ Fri, 05 Jul 2019 14:43:19: #2 finished! INFO @ Fri, 05 Jul 2019 14:43:19: #2 predicted fragment length is 50 bps INFO @ Fri, 05 Jul 2019 14:43:19: #2 alternative fragment length(s) may be 50,216,409 bps INFO @ Fri, 05 Jul 2019 14:43:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.20_model.r WARNING @ Fri, 05 Jul 2019 14:43:19: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 14:43:19: #2 You may need to consider one of the other alternative d(s): 50,216,409 WARNING @ Fri, 05 Jul 2019 14:43:19: #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 14:43:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:43:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:43:28: 20000000 INFO @ Fri, 05 Jul 2019 14:43:39: 21000000 INFO @ Fri, 05 Jul 2019 14:43:47: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 14:43:47: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 14:43:47: #1 total tags in treatment: 21865461 INFO @ Fri, 05 Jul 2019 14:43:47: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 14:43:47: #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 14:43:48: #1 tags after filtering in treatment: 21865361 INFO @ Fri, 05 Jul 2019 14:43:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 14:43:48: #1 finished! INFO @ Fri, 05 Jul 2019 14:43:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 14:43:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 14:43:51: #2 number of paired peaks: 8265 INFO @ Fri, 05 Jul 2019 14:43:51: start model_add_line... INFO @ Fri, 05 Jul 2019 14:43:51: start X-correlation... INFO @ Fri, 05 Jul 2019 14:43:51: end of X-cor INFO @ Fri, 05 Jul 2019 14:43:51: #2 finished! INFO @ Fri, 05 Jul 2019 14:43:51: #2 predicted fragment length is 50 bps INFO @ Fri, 05 Jul 2019 14:43:51: #2 alternative fragment length(s) may be 50,216,409 bps INFO @ Fri, 05 Jul 2019 14:43:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.10_model.r WARNING @ Fri, 05 Jul 2019 14:43:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 14:43:51: #2 You may need to consider one of the other alternative d(s): 50,216,409 WARNING @ Fri, 05 Jul 2019 14:43:51: #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 14:43:51: #3 Call peaks... INFO @ Fri, 05 Jul 2019 14:43:51: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 14:44:23: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:44:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 14:44:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.05_peaks.xls INFO @ Fri, 05 Jul 2019 14:44:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:44:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.05_summits.bed INFO @ Fri, 05 Jul 2019 14:44:56: Done! pass1 - making usageList (70 chroms): 2 millis pass2 - checking and writing primary data (2099 records, 4 fields): 14 millis INFO @ Fri, 05 Jul 2019 14:44:59: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:45:00: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.20_peaks.xls INFO @ Fri, 05 Jul 2019 14:45:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:45:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.20_summits.bed INFO @ Fri, 05 Jul 2019 14:45:01: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (723 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 14:45:31: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.10_peaks.xls INFO @ Fri, 05 Jul 2019 14:45:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 14:45:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5333725/SRX5333725.10_summits.bed INFO @ Fri, 05 Jul 2019 14:45:31: Done! pass1 - making usageList (57 chroms): 2 millis pass2 - checking and writing primary data (1338 records, 4 fields): 616 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。