Job ID = 2001566 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,484,699 reads read : 24,484,699 reads written : 24,484,699 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: 00:05:37 24484699 reads; of these: 24484699 (100.00%) were unpaired; of these: 607413 (2.48%) aligned 0 times 20778211 (84.86%) aligned exactly 1 time 3099075 (12.66%) aligned >1 times 97.52% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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] 8514322 / 23877286 = 0.3566 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 05:14:41: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.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 05:14:41: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:14:41: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:14:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.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 05:14:42: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:14:42: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:14:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.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 05:14:43: #1 read tag files... INFO @ Fri, 05 Jul 2019 05:14:43: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 05:14:50: 1000000 INFO @ Fri, 05 Jul 2019 05:14:50: 1000000 INFO @ Fri, 05 Jul 2019 05:14:51: 1000000 INFO @ Fri, 05 Jul 2019 05:14:57: 2000000 INFO @ Fri, 05 Jul 2019 05:14:58: 2000000 INFO @ Fri, 05 Jul 2019 05:14:59: 2000000 INFO @ Fri, 05 Jul 2019 05:15:04: 3000000 INFO @ Fri, 05 Jul 2019 05:15:06: 3000000 INFO @ Fri, 05 Jul 2019 05:15:07: 3000000 INFO @ Fri, 05 Jul 2019 05:15:11: 4000000 INFO @ Fri, 05 Jul 2019 05:15:15: 4000000 INFO @ Fri, 05 Jul 2019 05:15:15: 4000000 INFO @ Fri, 05 Jul 2019 05:15:17: 5000000 INFO @ Fri, 05 Jul 2019 05:15:23: 5000000 INFO @ Fri, 05 Jul 2019 05:15:23: 5000000 INFO @ Fri, 05 Jul 2019 05:15:24: 6000000 INFO @ Fri, 05 Jul 2019 05:15:31: 7000000 INFO @ Fri, 05 Jul 2019 05:15:31: 6000000 INFO @ Fri, 05 Jul 2019 05:15:32: 6000000 INFO @ Fri, 05 Jul 2019 05:15:37: 8000000 INFO @ Fri, 05 Jul 2019 05:15:39: 7000000 INFO @ Fri, 05 Jul 2019 05:15:40: 7000000 INFO @ Fri, 05 Jul 2019 05:15:44: 9000000 INFO @ Fri, 05 Jul 2019 05:15:48: 8000000 INFO @ Fri, 05 Jul 2019 05:15:48: 8000000 INFO @ Fri, 05 Jul 2019 05:15:51: 10000000 INFO @ Fri, 05 Jul 2019 05:15:56: 9000000 INFO @ Fri, 05 Jul 2019 05:15:56: 9000000 INFO @ Fri, 05 Jul 2019 05:15:58: 11000000 INFO @ Fri, 05 Jul 2019 05:16:04: 10000000 INFO @ Fri, 05 Jul 2019 05:16:05: 10000000 INFO @ Fri, 05 Jul 2019 05:16:05: 12000000 INFO @ Fri, 05 Jul 2019 05:16:12: 13000000 INFO @ Fri, 05 Jul 2019 05:16:13: 11000000 INFO @ Fri, 05 Jul 2019 05:16:14: 11000000 INFO @ Fri, 05 Jul 2019 05:16:19: 14000000 INFO @ Fri, 05 Jul 2019 05:16:21: 12000000 INFO @ Fri, 05 Jul 2019 05:16:22: 12000000 INFO @ Fri, 05 Jul 2019 05:16:26: 15000000 INFO @ Fri, 05 Jul 2019 05:16:28: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:16:28: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:16:28: #1 total tags in treatment: 15362964 INFO @ Fri, 05 Jul 2019 05:16:28: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:16:28: #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 05:16:29: #1 tags after filtering in treatment: 15362712 INFO @ Fri, 05 Jul 2019 05:16:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:16:29: #1 finished! INFO @ Fri, 05 Jul 2019 05:16:29: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:16:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:16:29: 13000000 INFO @ Fri, 05 Jul 2019 05:16:30: 13000000 INFO @ Fri, 05 Jul 2019 05:16:33: #2 number of paired peaks: 47717 INFO @ Fri, 05 Jul 2019 05:16:33: start model_add_line... INFO @ Fri, 05 Jul 2019 05:16:33: start X-correlation... INFO @ Fri, 05 Jul 2019 05:16:33: end of X-cor INFO @ Fri, 05 Jul 2019 05:16:33: #2 finished! INFO @ Fri, 05 Jul 2019 05:16:33: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 05:16:33: #2 alternative fragment length(s) may be 3,142 bps INFO @ Fri, 05 Jul 2019 05:16:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.20_model.r INFO @ Fri, 05 Jul 2019 05:16:33: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:16:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:16:37: 14000000 INFO @ Fri, 05 Jul 2019 05:16:38: 14000000 INFO @ Fri, 05 Jul 2019 05:16:45: 15000000 INFO @ Fri, 05 Jul 2019 05:16:46: 15000000 INFO @ Fri, 05 Jul 2019 05:16:48: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:16:48: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:16:48: #1 total tags in treatment: 15362964 INFO @ Fri, 05 Jul 2019 05:16:48: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:16:48: #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 05:16:48: #1 tags after filtering in treatment: 15362712 INFO @ Fri, 05 Jul 2019 05:16:48: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:16:48: #1 finished! INFO @ Fri, 05 Jul 2019 05:16:48: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:16:50: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 05:16:50: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 05:16:50: #1 total tags in treatment: 15362964 INFO @ Fri, 05 Jul 2019 05:16:50: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 05:16:50: #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 05:16:50: #1 tags after filtering in treatment: 15362712 INFO @ Fri, 05 Jul 2019 05:16:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 05:16:50: #1 finished! INFO @ Fri, 05 Jul 2019 05:16:50: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 05:16:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 05:16:52: #2 number of paired peaks: 47717 INFO @ Fri, 05 Jul 2019 05:16:52: start model_add_line... INFO @ Fri, 05 Jul 2019 05:16:52: start X-correlation... INFO @ Fri, 05 Jul 2019 05:16:52: end of X-cor INFO @ Fri, 05 Jul 2019 05:16:52: #2 finished! INFO @ Fri, 05 Jul 2019 05:16:52: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 05:16:52: #2 alternative fragment length(s) may be 3,142 bps INFO @ Fri, 05 Jul 2019 05:16:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.05_model.r INFO @ Fri, 05 Jul 2019 05:16:52: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:16:52: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:16:54: #2 number of paired peaks: 47717 INFO @ Fri, 05 Jul 2019 05:16:54: start model_add_line... INFO @ Fri, 05 Jul 2019 05:16:54: start X-correlation... INFO @ Fri, 05 Jul 2019 05:16:54: end of X-cor INFO @ Fri, 05 Jul 2019 05:16:54: #2 finished! INFO @ Fri, 05 Jul 2019 05:16:54: #2 predicted fragment length is 142 bps INFO @ Fri, 05 Jul 2019 05:16:54: #2 alternative fragment length(s) may be 3,142 bps INFO @ Fri, 05 Jul 2019 05:16:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.10_model.r INFO @ Fri, 05 Jul 2019 05:16:54: #3 Call peaks... INFO @ Fri, 05 Jul 2019 05:16:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 05:17:22: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:17:41: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:17:44: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 05:17:49: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.20_peaks.xls INFO @ Fri, 05 Jul 2019 05:17:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:17:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.20_summits.bed INFO @ Fri, 05 Jul 2019 05:17:49: Done! pass1 - making usageList (79 chroms): 5 millis pass2 - checking and writing primary data (20905 records, 4 fields): 30 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:18:09: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.05_peaks.xls INFO @ Fri, 05 Jul 2019 05:18:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:18:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.05_summits.bed INFO @ Fri, 05 Jul 2019 05:18:10: Done! pass1 - making usageList (125 chroms): 8 millis pass2 - checking and writing primary data (40183 records, 4 fields): 55 millis CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 05:18:11: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.10_peaks.xls INFO @ Fri, 05 Jul 2019 05:18:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 05:18:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX101909/ERX101909.10_summits.bed INFO @ Fri, 05 Jul 2019 05:18:11: Done! pass1 - making usageList (108 chroms): 8 millis pass2 - checking and writing primary data (31668 records, 4 fields): 44 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。