Job ID = 2002184 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 28,444,779 reads read : 28,444,779 reads written : 28,444,779 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR235770.sra.cache’: 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: 00:00:00 Multiseed full-index search: 00:12:13 28444779 reads; of these: 28444779 (100.00%) were unpaired; of these: 4610939 (16.21%) aligned 0 times 16692772 (58.68%) aligned exactly 1 time 7141068 (25.11%) aligned >1 times 83.79% overall alignment rate Time searching: 00:12:14 Overall time: 00:12:14 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 8 files... [bam_rmdupse_core] 409397 / 23833840 = 0.0172 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 11:25:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.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 11:25:18: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:25:18: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:25:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.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 11:25:19: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:25:19: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:25:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.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 11:25:20: #1 read tag files... INFO @ Fri, 05 Jul 2019 11:25:20: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 11:25:25: 1000000 INFO @ Fri, 05 Jul 2019 11:25:27: 1000000 INFO @ Fri, 05 Jul 2019 11:25:28: 1000000 INFO @ Fri, 05 Jul 2019 11:25:32: 2000000 INFO @ Fri, 05 Jul 2019 11:25:34: 2000000 INFO @ Fri, 05 Jul 2019 11:25:35: 2000000 INFO @ Fri, 05 Jul 2019 11:25:39: 3000000 INFO @ Fri, 05 Jul 2019 11:25:42: 3000000 INFO @ Fri, 05 Jul 2019 11:25:43: 3000000 INFO @ Fri, 05 Jul 2019 11:25:46: 4000000 INFO @ Fri, 05 Jul 2019 11:25:50: 4000000 INFO @ Fri, 05 Jul 2019 11:25:50: 4000000 INFO @ Fri, 05 Jul 2019 11:25:53: 5000000 INFO @ Fri, 05 Jul 2019 11:26:01: 6000000 INFO @ Fri, 05 Jul 2019 11:26:02: 5000000 INFO @ Fri, 05 Jul 2019 11:26:02: 5000000 INFO @ Fri, 05 Jul 2019 11:26:08: 7000000 INFO @ Fri, 05 Jul 2019 11:26:10: 6000000 INFO @ Fri, 05 Jul 2019 11:26:10: 6000000 INFO @ Fri, 05 Jul 2019 11:26:15: 8000000 INFO @ Fri, 05 Jul 2019 11:26:18: 7000000 INFO @ Fri, 05 Jul 2019 11:26:19: 7000000 INFO @ Fri, 05 Jul 2019 11:26:22: 9000000 INFO @ Fri, 05 Jul 2019 11:26:25: 8000000 INFO @ Fri, 05 Jul 2019 11:26:28: 8000000 INFO @ Fri, 05 Jul 2019 11:26:29: 10000000 INFO @ Fri, 05 Jul 2019 11:26:33: 9000000 INFO @ Fri, 05 Jul 2019 11:26:35: 11000000 INFO @ Fri, 05 Jul 2019 11:26:36: 9000000 INFO @ Fri, 05 Jul 2019 11:26:40: 10000000 INFO @ Fri, 05 Jul 2019 11:26:42: 12000000 INFO @ Fri, 05 Jul 2019 11:26:45: 10000000 INFO @ Fri, 05 Jul 2019 11:26:48: 11000000 INFO @ Fri, 05 Jul 2019 11:26:49: 13000000 INFO @ Fri, 05 Jul 2019 11:26:53: 11000000 INFO @ Fri, 05 Jul 2019 11:26:55: 12000000 INFO @ Fri, 05 Jul 2019 11:26:56: 14000000 INFO @ Fri, 05 Jul 2019 11:27:02: 12000000 INFO @ Fri, 05 Jul 2019 11:27:03: 13000000 INFO @ Fri, 05 Jul 2019 11:27:03: 15000000 INFO @ Fri, 05 Jul 2019 11:27:10: 16000000 INFO @ Fri, 05 Jul 2019 11:27:11: 14000000 INFO @ Fri, 05 Jul 2019 11:27:11: 13000000 INFO @ Fri, 05 Jul 2019 11:27:17: 17000000 INFO @ Fri, 05 Jul 2019 11:27:18: 15000000 INFO @ Fri, 05 Jul 2019 11:27:20: 14000000 INFO @ Fri, 05 Jul 2019 11:27:25: 18000000 INFO @ Fri, 05 Jul 2019 11:27:26: 16000000 INFO @ Fri, 05 Jul 2019 11:27:29: 15000000 INFO @ Fri, 05 Jul 2019 11:27:32: 19000000 INFO @ Fri, 05 Jul 2019 11:27:33: 17000000 INFO @ Fri, 05 Jul 2019 11:27:37: 16000000 INFO @ Fri, 05 Jul 2019 11:27:39: 20000000 INFO @ Fri, 05 Jul 2019 11:27:41: 18000000 INFO @ Fri, 05 Jul 2019 11:27:46: 21000000 INFO @ Fri, 05 Jul 2019 11:27:46: 17000000 INFO @ Fri, 05 Jul 2019 11:27:49: 19000000 INFO @ Fri, 05 Jul 2019 11:27:53: 22000000 INFO @ Fri, 05 Jul 2019 11:27:55: 18000000 INFO @ Fri, 05 Jul 2019 11:27:56: 20000000 INFO @ Fri, 05 Jul 2019 11:28:01: 23000000 INFO @ Fri, 05 Jul 2019 11:28:04: 19000000 INFO @ Fri, 05 Jul 2019 11:28:04: 21000000 INFO @ Fri, 05 Jul 2019 11:28:05: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:28:05: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:28:05: #1 total tags in treatment: 23424443 INFO @ Fri, 05 Jul 2019 11:28:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:28:05: #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 11:28:06: #1 tags after filtering in treatment: 23424327 INFO @ Fri, 05 Jul 2019 11:28:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:28:06: #1 finished! INFO @ Fri, 05 Jul 2019 11:28:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:28:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:28:09: #2 number of paired peaks: 5899 INFO @ Fri, 05 Jul 2019 11:28:09: start model_add_line... INFO @ Fri, 05 Jul 2019 11:28:09: start X-correlation... INFO @ Fri, 05 Jul 2019 11:28:09: end of X-cor INFO @ Fri, 05 Jul 2019 11:28:09: #2 finished! INFO @ Fri, 05 Jul 2019 11:28:09: #2 predicted fragment length is 37 bps INFO @ Fri, 05 Jul 2019 11:28:09: #2 alternative fragment length(s) may be 37 bps INFO @ Fri, 05 Jul 2019 11:28:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.05_model.r WARNING @ Fri, 05 Jul 2019 11:28:09: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:28:09: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Fri, 05 Jul 2019 11:28:09: #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 11:28:09: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:28:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:28:11: 22000000 INFO @ Fri, 05 Jul 2019 11:28:12: 20000000 INFO @ Fri, 05 Jul 2019 11:28:19: 23000000 INFO @ Fri, 05 Jul 2019 11:28:21: 21000000 INFO @ Fri, 05 Jul 2019 11:28:23: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:28:23: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:28:23: #1 total tags in treatment: 23424443 INFO @ Fri, 05 Jul 2019 11:28:23: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:28:23: #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 11:28:23: #1 tags after filtering in treatment: 23424327 INFO @ Fri, 05 Jul 2019 11:28:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:28:23: #1 finished! INFO @ Fri, 05 Jul 2019 11:28:23: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:28:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:28:26: #2 number of paired peaks: 5899 INFO @ Fri, 05 Jul 2019 11:28:26: start model_add_line... INFO @ Fri, 05 Jul 2019 11:28:26: start X-correlation... INFO @ Fri, 05 Jul 2019 11:28:26: end of X-cor INFO @ Fri, 05 Jul 2019 11:28:26: #2 finished! INFO @ Fri, 05 Jul 2019 11:28:26: #2 predicted fragment length is 37 bps INFO @ Fri, 05 Jul 2019 11:28:26: #2 alternative fragment length(s) may be 37 bps INFO @ Fri, 05 Jul 2019 11:28:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.10_model.r WARNING @ Fri, 05 Jul 2019 11:28:26: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:28:26: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Fri, 05 Jul 2019 11:28:26: #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 11:28:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:28:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:28:30: 22000000 INFO @ Fri, 05 Jul 2019 11:28:38: 23000000 INFO @ Fri, 05 Jul 2019 11:28:42: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 11:28:42: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 11:28:42: #1 total tags in treatment: 23424443 INFO @ Fri, 05 Jul 2019 11:28:42: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 11:28:42: #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 11:28:43: #1 tags after filtering in treatment: 23424327 INFO @ Fri, 05 Jul 2019 11:28:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 11:28:43: #1 finished! INFO @ Fri, 05 Jul 2019 11:28:43: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 11:28:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 11:28:46: #2 number of paired peaks: 5899 INFO @ Fri, 05 Jul 2019 11:28:48: start model_add_line... INFO @ Fri, 05 Jul 2019 11:28:48: start X-correlation... INFO @ Fri, 05 Jul 2019 11:28:48: end of X-cor INFO @ Fri, 05 Jul 2019 11:28:48: #2 finished! INFO @ Fri, 05 Jul 2019 11:28:48: #2 predicted fragment length is 37 bps INFO @ Fri, 05 Jul 2019 11:28:48: #2 alternative fragment length(s) may be 37 bps INFO @ Fri, 05 Jul 2019 11:28:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.20_model.r WARNING @ Fri, 05 Jul 2019 11:28:48: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 05 Jul 2019 11:28:48: #2 You may need to consider one of the other alternative d(s): 37 WARNING @ Fri, 05 Jul 2019 11:28:48: #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 11:28:48: #3 Call peaks... INFO @ Fri, 05 Jul 2019 11:28:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 11:29:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:29:39: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 11:29:57: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.05_peaks.xls INFO @ Fri, 05 Jul 2019 11:29:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:29:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.05_summits.bed INFO @ Fri, 05 Jul 2019 11:30:00: Done! pass1 - making usageList (49 chroms): 2 millis INFO @ Fri, 05 Jul 2019 11:30:01: #3 Call peaks for each chromosome... pass2 - checking and writing primary data (1801 records, 4 fields): 481 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:30:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.10_peaks.xls INFO @ Fri, 05 Jul 2019 11:30:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:30:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.10_summits.bed INFO @ Fri, 05 Jul 2019 11:30:14: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (939 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 11:30:37: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.20_peaks.xls INFO @ Fri, 05 Jul 2019 11:30:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 11:30:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX210293/ERX210293.20_summits.bed INFO @ Fri, 05 Jul 2019 11:30:38: Done! pass1 - making usageList (28 chroms): 2 millis pass2 - checking and writing primary data (349 records, 4 fields): 155 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。