Job ID = 2002213 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,574,916 reads read : 26,574,916 reads written : 26,574,916 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: 00:00:00 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:26:08 26574916 reads; of these: 26574916 (100.00%) were unpaired; of these: 462830 (1.74%) aligned 0 times 17676054 (66.51%) aligned exactly 1 time 8436032 (31.74%) aligned >1 times 98.26% overall alignment rate Time searching: 00:26:09 Overall time: 00:26:09 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] 654135 / 26112086 = 0.0251 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 12:29:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.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 12:29:13: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:29:13: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:29:14: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.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 12:29:14: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:29:14: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:29:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.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 12:29:15: #1 read tag files... INFO @ Fri, 05 Jul 2019 12:29:15: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 12:29:21: 1000000 INFO @ Fri, 05 Jul 2019 12:29:22: 1000000 INFO @ Fri, 05 Jul 2019 12:29:25: 1000000 INFO @ Fri, 05 Jul 2019 12:29:29: 2000000 INFO @ Fri, 05 Jul 2019 12:29:29: 2000000 INFO @ Fri, 05 Jul 2019 12:29:35: 2000000 INFO @ Fri, 05 Jul 2019 12:29:36: 3000000 INFO @ Fri, 05 Jul 2019 12:29:37: 3000000 INFO @ Fri, 05 Jul 2019 12:29:44: 3000000 INFO @ Fri, 05 Jul 2019 12:29:44: 4000000 INFO @ Fri, 05 Jul 2019 12:29:44: 4000000 INFO @ Fri, 05 Jul 2019 12:29:52: 5000000 INFO @ Fri, 05 Jul 2019 12:29:52: 5000000 INFO @ Fri, 05 Jul 2019 12:29:53: 4000000 INFO @ Fri, 05 Jul 2019 12:29:59: 6000000 INFO @ Fri, 05 Jul 2019 12:30:00: 6000000 INFO @ Fri, 05 Jul 2019 12:30:03: 5000000 INFO @ Fri, 05 Jul 2019 12:30:07: 7000000 INFO @ Fri, 05 Jul 2019 12:30:07: 7000000 INFO @ Fri, 05 Jul 2019 12:30:12: 6000000 INFO @ Fri, 05 Jul 2019 12:30:14: 8000000 INFO @ Fri, 05 Jul 2019 12:30:15: 8000000 INFO @ Fri, 05 Jul 2019 12:30:21: 9000000 INFO @ Fri, 05 Jul 2019 12:30:21: 7000000 INFO @ Fri, 05 Jul 2019 12:30:23: 9000000 INFO @ Fri, 05 Jul 2019 12:30:28: 10000000 INFO @ Fri, 05 Jul 2019 12:30:31: 10000000 INFO @ Fri, 05 Jul 2019 12:30:31: 8000000 INFO @ Fri, 05 Jul 2019 12:30:36: 11000000 INFO @ Fri, 05 Jul 2019 12:30:38: 11000000 INFO @ Fri, 05 Jul 2019 12:30:40: 9000000 INFO @ Fri, 05 Jul 2019 12:30:43: 12000000 INFO @ Fri, 05 Jul 2019 12:30:46: 12000000 INFO @ Fri, 05 Jul 2019 12:30:49: 10000000 INFO @ Fri, 05 Jul 2019 12:30:50: 13000000 INFO @ Fri, 05 Jul 2019 12:30:54: 13000000 INFO @ Fri, 05 Jul 2019 12:30:58: 14000000 INFO @ Fri, 05 Jul 2019 12:30:58: 11000000 INFO @ Fri, 05 Jul 2019 12:31:02: 14000000 INFO @ Fri, 05 Jul 2019 12:31:05: 15000000 INFO @ Fri, 05 Jul 2019 12:31:07: 12000000 INFO @ Fri, 05 Jul 2019 12:31:10: 15000000 INFO @ Fri, 05 Jul 2019 12:31:12: 16000000 INFO @ Fri, 05 Jul 2019 12:31:17: 13000000 INFO @ Fri, 05 Jul 2019 12:31:18: 16000000 INFO @ Fri, 05 Jul 2019 12:31:20: 17000000 INFO @ Fri, 05 Jul 2019 12:31:25: 17000000 INFO @ Fri, 05 Jul 2019 12:31:26: 14000000 INFO @ Fri, 05 Jul 2019 12:31:28: 18000000 INFO @ Fri, 05 Jul 2019 12:31:33: 18000000 INFO @ Fri, 05 Jul 2019 12:31:35: 19000000 INFO @ Fri, 05 Jul 2019 12:31:35: 15000000 INFO @ Fri, 05 Jul 2019 12:31:41: 19000000 INFO @ Fri, 05 Jul 2019 12:31:43: 20000000 INFO @ Fri, 05 Jul 2019 12:31:45: 16000000 INFO @ Fri, 05 Jul 2019 12:31:49: 20000000 INFO @ Fri, 05 Jul 2019 12:31:50: 21000000 INFO @ Fri, 05 Jul 2019 12:31:54: 17000000 INFO @ Fri, 05 Jul 2019 12:31:57: 21000000 INFO @ Fri, 05 Jul 2019 12:31:57: 22000000 INFO @ Fri, 05 Jul 2019 12:32:03: 18000000 INFO @ Fri, 05 Jul 2019 12:32:04: 23000000 INFO @ Fri, 05 Jul 2019 12:32:05: 22000000 INFO @ Fri, 05 Jul 2019 12:32:12: 19000000 INFO @ Fri, 05 Jul 2019 12:32:12: 24000000 INFO @ Fri, 05 Jul 2019 12:32:12: 23000000 INFO @ Fri, 05 Jul 2019 12:32:19: 25000000 INFO @ Fri, 05 Jul 2019 12:32:20: 24000000 INFO @ Fri, 05 Jul 2019 12:32:21: 20000000 INFO @ Fri, 05 Jul 2019 12:32:23: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:32:23: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:32:23: #1 total tags in treatment: 25457951 INFO @ Fri, 05 Jul 2019 12:32:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:32:23: #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 12:32:24: #1 tags after filtering in treatment: 25457843 INFO @ Fri, 05 Jul 2019 12:32:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:32:24: #1 finished! INFO @ Fri, 05 Jul 2019 12:32:24: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:32:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:32:27: #2 number of paired peaks: 6002 INFO @ Fri, 05 Jul 2019 12:32:27: start model_add_line... INFO @ Fri, 05 Jul 2019 12:32:27: start X-correlation... INFO @ Fri, 05 Jul 2019 12:32:27: end of X-cor INFO @ Fri, 05 Jul 2019 12:32:27: #2 finished! INFO @ Fri, 05 Jul 2019 12:32:27: #2 predicted fragment length is 50 bps INFO @ Fri, 05 Jul 2019 12:32:27: #2 alternative fragment length(s) may be 50,221,396 bps INFO @ Fri, 05 Jul 2019 12:32:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.05_model.r WARNING @ Fri, 05 Jul 2019 12:32:27: #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 12:32:27: #2 You may need to consider one of the other alternative d(s): 50,221,396 WARNING @ Fri, 05 Jul 2019 12:32:27: #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 12:32:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:32:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:32:28: 25000000 INFO @ Fri, 05 Jul 2019 12:32:30: 21000000 INFO @ Fri, 05 Jul 2019 12:32:32: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:32:32: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:32:32: #1 total tags in treatment: 25457951 INFO @ Fri, 05 Jul 2019 12:32:32: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:32:32: #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 12:32:33: #1 tags after filtering in treatment: 25457843 INFO @ Fri, 05 Jul 2019 12:32:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:32:33: #1 finished! INFO @ Fri, 05 Jul 2019 12:32:33: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:32:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:32:36: #2 number of paired peaks: 6002 INFO @ Fri, 05 Jul 2019 12:32:36: start model_add_line... INFO @ Fri, 05 Jul 2019 12:32:36: start X-correlation... INFO @ Fri, 05 Jul 2019 12:32:36: end of X-cor INFO @ Fri, 05 Jul 2019 12:32:36: #2 finished! INFO @ Fri, 05 Jul 2019 12:32:36: #2 predicted fragment length is 50 bps INFO @ Fri, 05 Jul 2019 12:32:36: #2 alternative fragment length(s) may be 50,221,396 bps INFO @ Fri, 05 Jul 2019 12:32:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.10_model.r WARNING @ Fri, 05 Jul 2019 12:32:36: #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 12:32:36: #2 You may need to consider one of the other alternative d(s): 50,221,396 WARNING @ Fri, 05 Jul 2019 12:32:36: #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 12:32:36: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:32:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:32:38: 22000000 INFO @ Fri, 05 Jul 2019 12:32:47: 23000000 INFO @ Fri, 05 Jul 2019 12:32:56: 24000000 INFO @ Fri, 05 Jul 2019 12:33:05: 25000000 INFO @ Fri, 05 Jul 2019 12:33:10: #1 tag size is determined as 50 bps INFO @ Fri, 05 Jul 2019 12:33:10: #1 tag size = 50 INFO @ Fri, 05 Jul 2019 12:33:10: #1 total tags in treatment: 25457951 INFO @ Fri, 05 Jul 2019 12:33:10: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 12:33:10: #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 12:33:10: #1 tags after filtering in treatment: 25457843 INFO @ Fri, 05 Jul 2019 12:33:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 12:33:10: #1 finished! INFO @ Fri, 05 Jul 2019 12:33:10: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 12:33:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 12:33:13: #2 number of paired peaks: 6002 INFO @ Fri, 05 Jul 2019 12:33:13: start model_add_line... INFO @ Fri, 05 Jul 2019 12:33:14: start X-correlation... INFO @ Fri, 05 Jul 2019 12:33:14: end of X-cor INFO @ Fri, 05 Jul 2019 12:33:14: #2 finished! INFO @ Fri, 05 Jul 2019 12:33:14: #2 predicted fragment length is 50 bps INFO @ Fri, 05 Jul 2019 12:33:14: #2 alternative fragment length(s) may be 50,221,396 bps INFO @ Fri, 05 Jul 2019 12:33:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.20_model.r WARNING @ Fri, 05 Jul 2019 12:33:14: #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 12:33:14: #2 You may need to consider one of the other alternative d(s): 50,221,396 WARNING @ Fri, 05 Jul 2019 12:33:14: #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 12:33:14: #3 Call peaks... INFO @ Fri, 05 Jul 2019 12:33:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 12:33:47: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:33:55: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 12:34:27: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.05_peaks.xls INFO @ Fri, 05 Jul 2019 12:34:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:34:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.05_summits.bed INFO @ Fri, 05 Jul 2019 12:34:27: Done! pass1 - making usageList (49 chroms): 2 millis pass2 - checking and writing primary data (1640 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:34:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.10_peaks.xls INFO @ Fri, 05 Jul 2019 12:34:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:34:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.10_summits.bed INFO @ Fri, 05 Jul 2019 12:34:35: Done! pass1 - making usageList (40 chroms): 2 millis pass2 - checking and writing primary data (955 records, 4 fields): 7 millis INFO @ Fri, 05 Jul 2019 12:34:37: #3 Call peaks for each chromosome... CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 12:35:19: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.20_peaks.xls INFO @ Fri, 05 Jul 2019 12:35:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 12:35:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX530940/ERX530940.20_summits.bed INFO @ Fri, 05 Jul 2019 12:35:19: Done! pass1 - making usageList (33 chroms): 1 millis pass2 - checking and writing primary data (479 records, 4 fields): 49 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。