Job ID = 2640410 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 20,784,321 reads read : 20,784,321 reads written : 20,784,321 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR399327.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: 00:00:01 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:04:40 20784321 reads; of these: 20784321 (100.00%) were unpaired; of these: 11260680 (54.18%) aligned 0 times 7007354 (33.71%) aligned exactly 1 time 2516287 (12.11%) aligned >1 times 45.82% overall alignment rate Time searching: 00:04:45 Overall time: 00:04:45 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] 3343844 / 9523641 = 0.3511 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 16:22:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.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 @ Sat, 24 Aug 2019 16:22:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:22:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:22:54: 1000000 INFO @ Sat, 24 Aug 2019 16:23:01: 2000000 INFO @ Sat, 24 Aug 2019 16:23:09: 3000000 INFO @ Sat, 24 Aug 2019 16:23:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.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 @ Sat, 24 Aug 2019 16:23:15: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:23:15: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:23:17: 4000000 INFO @ Sat, 24 Aug 2019 16:23:22: 1000000 INFO @ Sat, 24 Aug 2019 16:23:24: 5000000 INFO @ Sat, 24 Aug 2019 16:23:30: 2000000 INFO @ Sat, 24 Aug 2019 16:23:32: 6000000 INFO @ Sat, 24 Aug 2019 16:23:34: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:23:34: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:23:34: #1 total tags in treatment: 6179797 INFO @ Sat, 24 Aug 2019 16:23:34: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:23:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:23:35: #1 tags after filtering in treatment: 6179562 INFO @ Sat, 24 Aug 2019 16:23:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:23:35: #1 finished! INFO @ Sat, 24 Aug 2019 16:23:35: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:23:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:23:37: #2 number of paired peaks: 27496 INFO @ Sat, 24 Aug 2019 16:23:37: start model_add_line... INFO @ Sat, 24 Aug 2019 16:23:37: start X-correlation... INFO @ Sat, 24 Aug 2019 16:23:37: end of X-cor INFO @ Sat, 24 Aug 2019 16:23:37: #2 finished! INFO @ Sat, 24 Aug 2019 16:23:37: #2 predicted fragment length is 70 bps INFO @ Sat, 24 Aug 2019 16:23:37: #2 alternative fragment length(s) may be 70 bps INFO @ Sat, 24 Aug 2019 16:23:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.05_model.r WARNING @ Sat, 24 Aug 2019 16:23:37: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:23:37: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Sat, 24 Aug 2019 16:23:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 16:23:37: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:23:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:23:38: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 16:23:45: 4000000 INFO @ Sat, 24 Aug 2019 16:23:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.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 @ Sat, 24 Aug 2019 16:23:46: #1 read tag files... INFO @ Sat, 24 Aug 2019 16:23:46: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 16:23:52: 5000000 INFO @ Sat, 24 Aug 2019 16:23:56: 1000000 INFO @ Sat, 24 Aug 2019 16:23:57: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:24:00: 6000000 INFO @ Sat, 24 Aug 2019 16:24:01: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:24:01: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:24:01: #1 total tags in treatment: 6179797 INFO @ Sat, 24 Aug 2019 16:24:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:24:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:24:02: #1 tags after filtering in treatment: 6179562 INFO @ Sat, 24 Aug 2019 16:24:02: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:24:02: #1 finished! INFO @ Sat, 24 Aug 2019 16:24:02: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:24:02: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:24:04: #2 number of paired peaks: 27496 INFO @ Sat, 24 Aug 2019 16:24:04: start model_add_line... INFO @ Sat, 24 Aug 2019 16:24:04: 2000000 INFO @ Sat, 24 Aug 2019 16:24:04: start X-correlation... INFO @ Sat, 24 Aug 2019 16:24:04: end of X-cor INFO @ Sat, 24 Aug 2019 16:24:04: #2 finished! INFO @ Sat, 24 Aug 2019 16:24:04: #2 predicted fragment length is 70 bps INFO @ Sat, 24 Aug 2019 16:24:04: #2 alternative fragment length(s) may be 70 bps INFO @ Sat, 24 Aug 2019 16:24:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.10_model.r WARNING @ Sat, 24 Aug 2019 16:24:04: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:24:04: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Sat, 24 Aug 2019 16:24:04: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 16:24:04: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:24:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:24:07: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.05_peaks.xls INFO @ Sat, 24 Aug 2019 16:24:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:24:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.05_summits.bed INFO @ Sat, 24 Aug 2019 16:24:07: Done! pass1 - making usageList (53 chroms): 4 millis pass2 - checking and writing primary data (1213 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:24:13: 3000000 INFO @ Sat, 24 Aug 2019 16:24:22: 4000000 INFO @ Sat, 24 Aug 2019 16:24:25: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:24:29: 5000000 INFO @ Sat, 24 Aug 2019 16:24:35: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.10_peaks.xls INFO @ Sat, 24 Aug 2019 16:24:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:24:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.10_summits.bed INFO @ Sat, 24 Aug 2019 16:24:35: Done! pass1 - making usageList (41 chroms): 2 millis pass2 - checking and writing primary data (440 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 16:24:38: 6000000 INFO @ Sat, 24 Aug 2019 16:24:39: #1 tag size is determined as 36 bps INFO @ Sat, 24 Aug 2019 16:24:39: #1 tag size = 36 INFO @ Sat, 24 Aug 2019 16:24:39: #1 total tags in treatment: 6179797 INFO @ Sat, 24 Aug 2019 16:24:39: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 16:24:39: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 24 Aug 2019 16:24:40: #1 tags after filtering in treatment: 6179562 INFO @ Sat, 24 Aug 2019 16:24:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 16:24:40: #1 finished! INFO @ Sat, 24 Aug 2019 16:24:40: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 16:24:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 16:24:42: #2 number of paired peaks: 27496 INFO @ Sat, 24 Aug 2019 16:24:42: start model_add_line... INFO @ Sat, 24 Aug 2019 16:24:42: start X-correlation... INFO @ Sat, 24 Aug 2019 16:24:42: end of X-cor INFO @ Sat, 24 Aug 2019 16:24:42: #2 finished! INFO @ Sat, 24 Aug 2019 16:24:42: #2 predicted fragment length is 70 bps INFO @ Sat, 24 Aug 2019 16:24:42: #2 alternative fragment length(s) may be 70 bps INFO @ Sat, 24 Aug 2019 16:24:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.20_model.r WARNING @ Sat, 24 Aug 2019 16:24:42: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 24 Aug 2019 16:24:42: #2 You may need to consider one of the other alternative d(s): 70 WARNING @ Sat, 24 Aug 2019 16:24:42: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 24 Aug 2019 16:24:42: #3 Call peaks... INFO @ Sat, 24 Aug 2019 16:24:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 16:25:04: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 16:25:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.20_peaks.xls INFO @ Sat, 24 Aug 2019 16:25:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 16:25:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX116049/SRX116049.20_summits.bed INFO @ Sat, 24 Aug 2019 16:25:14: Done! pass1 - making usageList (29 chroms): 2 millis pass2 - checking and writing primary data (160 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。