Job ID = 2001719 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 26,546,209 reads read : 26,546,209 reads written : 26,546,209 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: 00:00:02 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:05:09 26546209 reads; of these: 26546209 (100.00%) were unpaired; of these: 537962 (2.03%) aligned 0 times 23427663 (88.25%) aligned exactly 1 time 2580584 (9.72%) aligned >1 times 97.97% overall alignment rate Time searching: 00:05:15 Overall time: 00:05:17 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] 13377751 / 26008247 = 0.5144 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 09:54:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.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 09:54:21: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:54:21: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:54:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.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 09:54:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:54:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:54:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.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 09:54:23: #1 read tag files... INFO @ Fri, 05 Jul 2019 09:54:23: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 09:54:29: 1000000 INFO @ Fri, 05 Jul 2019 09:54:29: 1000000 INFO @ Fri, 05 Jul 2019 09:54:30: 1000000 INFO @ Fri, 05 Jul 2019 09:54:36: 2000000 INFO @ Fri, 05 Jul 2019 09:54:36: 2000000 INFO @ Fri, 05 Jul 2019 09:54:37: 2000000 INFO @ Fri, 05 Jul 2019 09:54:43: 3000000 INFO @ Fri, 05 Jul 2019 09:54:43: 3000000 INFO @ Fri, 05 Jul 2019 09:54:44: 3000000 INFO @ Fri, 05 Jul 2019 09:54:50: 4000000 INFO @ Fri, 05 Jul 2019 09:54:51: 4000000 INFO @ Fri, 05 Jul 2019 09:54:51: 4000000 INFO @ Fri, 05 Jul 2019 09:54:57: 5000000 INFO @ Fri, 05 Jul 2019 09:54:58: 5000000 INFO @ Fri, 05 Jul 2019 09:54:58: 5000000 INFO @ Fri, 05 Jul 2019 09:55:04: 6000000 INFO @ Fri, 05 Jul 2019 09:55:05: 6000000 INFO @ Fri, 05 Jul 2019 09:55:05: 6000000 INFO @ Fri, 05 Jul 2019 09:55:11: 7000000 INFO @ Fri, 05 Jul 2019 09:55:12: 7000000 INFO @ Fri, 05 Jul 2019 09:55:12: 7000000 INFO @ Fri, 05 Jul 2019 09:55:18: 8000000 INFO @ Fri, 05 Jul 2019 09:55:19: 8000000 INFO @ Fri, 05 Jul 2019 09:55:19: 8000000 INFO @ Fri, 05 Jul 2019 09:55:25: 9000000 INFO @ Fri, 05 Jul 2019 09:55:25: 9000000 INFO @ Fri, 05 Jul 2019 09:55:26: 9000000 INFO @ Fri, 05 Jul 2019 09:55:32: 10000000 INFO @ Fri, 05 Jul 2019 09:55:32: 10000000 INFO @ Fri, 05 Jul 2019 09:55:33: 10000000 INFO @ Fri, 05 Jul 2019 09:55:39: 11000000 INFO @ Fri, 05 Jul 2019 09:55:39: 11000000 INFO @ Fri, 05 Jul 2019 09:55:40: 11000000 INFO @ Fri, 05 Jul 2019 09:55:46: 12000000 INFO @ Fri, 05 Jul 2019 09:55:47: 12000000 INFO @ Fri, 05 Jul 2019 09:55:47: 12000000 INFO @ Fri, 05 Jul 2019 09:55:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:55:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:55:51: #1 total tags in treatment: 12630496 INFO @ Fri, 05 Jul 2019 09:55:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:55:51: #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 09:55:51: #1 tags after filtering in treatment: 12630226 INFO @ Fri, 05 Jul 2019 09:55:51: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:55:51: #1 finished! INFO @ Fri, 05 Jul 2019 09:55:51: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:55:51: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:55:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:55:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:55:51: #1 total tags in treatment: 12630496 INFO @ Fri, 05 Jul 2019 09:55:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:55:51: #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 09:55:51: #1 tag size is determined as 36 bps INFO @ Fri, 05 Jul 2019 09:55:51: #1 tag size = 36 INFO @ Fri, 05 Jul 2019 09:55:51: #1 total tags in treatment: 12630496 INFO @ Fri, 05 Jul 2019 09:55:51: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 09:55:51: #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 09:55:52: #1 tags after filtering in treatment: 12630226 INFO @ Fri, 05 Jul 2019 09:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:55:52: #1 finished! INFO @ Fri, 05 Jul 2019 09:55:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:55:52: #1 tags after filtering in treatment: 12630226 INFO @ Fri, 05 Jul 2019 09:55:52: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 09:55:52: #1 finished! INFO @ Fri, 05 Jul 2019 09:55:52: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 09:55:52: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 09:55:55: #2 number of paired peaks: 56801 INFO @ Fri, 05 Jul 2019 09:55:55: start model_add_line... INFO @ Fri, 05 Jul 2019 09:55:55: start X-correlation... INFO @ Fri, 05 Jul 2019 09:55:55: end of X-cor INFO @ Fri, 05 Jul 2019 09:55:55: #2 finished! INFO @ Fri, 05 Jul 2019 09:55:55: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 09:55:55: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 09:55:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.10_model.r INFO @ Fri, 05 Jul 2019 09:55:55: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:55:55: #2 number of paired peaks: 56801 INFO @ Fri, 05 Jul 2019 09:55:55: start model_add_line... INFO @ Fri, 05 Jul 2019 09:55:55: #2 number of paired peaks: 56801 INFO @ Fri, 05 Jul 2019 09:55:55: start model_add_line... INFO @ Fri, 05 Jul 2019 09:55:56: start X-correlation... INFO @ Fri, 05 Jul 2019 09:55:56: end of X-cor INFO @ Fri, 05 Jul 2019 09:55:56: #2 finished! INFO @ Fri, 05 Jul 2019 09:55:56: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 09:55:56: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 09:55:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.05_model.r INFO @ Fri, 05 Jul 2019 09:55:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:55:56: start X-correlation... INFO @ Fri, 05 Jul 2019 09:55:56: end of X-cor INFO @ Fri, 05 Jul 2019 09:55:56: #2 finished! INFO @ Fri, 05 Jul 2019 09:55:56: #2 predicted fragment length is 129 bps INFO @ Fri, 05 Jul 2019 09:55:56: #2 alternative fragment length(s) may be 4,129 bps INFO @ Fri, 05 Jul 2019 09:55:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.20_model.r INFO @ Fri, 05 Jul 2019 09:55:56: #3 Call peaks... INFO @ Fri, 05 Jul 2019 09:55:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 09:56:33: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:56:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:56:34: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 09:56:55: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.10_peaks.xls INFO @ Fri, 05 Jul 2019 09:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.20_peaks.xls INFO @ Fri, 05 Jul 2019 09:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.10_summits.bed INFO @ Fri, 05 Jul 2019 09:56:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:56:56: Done! INFO @ Fri, 05 Jul 2019 09:56:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.20_summits.bed INFO @ Fri, 05 Jul 2019 09:56:56: Done! INFO @ Fri, 05 Jul 2019 09:56:56: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.05_peaks.xls pass1 - making usageList (81 chroms): 9 millis pass2 - checking and writing primary data (21768 records, 4 fields): 33 millis pass1 - making usageList (114 chroms): 7 millis pass2 - checking and writing primary data (36601 records, 4 fields): 55 millis INFO @ Fri, 05 Jul 2019 09:56:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 09:56:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/ERX102023/ERX102023.05_summits.bed INFO @ Fri, 05 Jul 2019 09:56:57: Done! pass1 - making usageList (143 chroms): 12 millis pass2 - checking and writing primary data (48791 records, 4 fields): 67 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。