Job ID = 2640704 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,976,363 reads read : 23,952,726 reads written : 11,976,363 reads 0-length : 11,976,363 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:10:44 11976363 reads; of these: 11976363 (100.00%) were unpaired; of these: 348462 (2.91%) aligned 0 times 9436780 (78.80%) aligned exactly 1 time 2191121 (18.30%) aligned >1 times 97.09% overall alignment rate Time searching: 00:10:47 Overall time: 00:10:47 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] 3509148 / 11627901 = 0.3018 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:35:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.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 18:35:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:35:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:35:41: 1000000 INFO @ Sat, 24 Aug 2019 18:35:49: 2000000 INFO @ Sat, 24 Aug 2019 18:35:57: 3000000 INFO @ Sat, 24 Aug 2019 18:36:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.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 18:36:03: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:36:03: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:36:05: 4000000 INFO @ Sat, 24 Aug 2019 18:36:10: 1000000 INFO @ Sat, 24 Aug 2019 18:36:13: 5000000 INFO @ Sat, 24 Aug 2019 18:36:18: 2000000 INFO @ Sat, 24 Aug 2019 18:36:20: 6000000 INFO @ Sat, 24 Aug 2019 18:36:25: 3000000 INFO @ Sat, 24 Aug 2019 18:36:28: 7000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:36:32: 4000000 INFO @ Sat, 24 Aug 2019 18:36:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.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 18:36:33: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:36:33: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:36:36: 8000000 INFO @ Sat, 24 Aug 2019 18:36:37: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:36:37: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:36:37: #1 total tags in treatment: 8118753 INFO @ Sat, 24 Aug 2019 18:36:37: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:36:37: #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 18:36:37: #1 tags after filtering in treatment: 8118497 INFO @ Sat, 24 Aug 2019 18:36:37: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:36:37: #1 finished! INFO @ Sat, 24 Aug 2019 18:36:37: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:36:37: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:36:39: 5000000 INFO @ Sat, 24 Aug 2019 18:36:40: 1000000 INFO @ Sat, 24 Aug 2019 18:36:41: #2 number of paired peaks: 76554 INFO @ Sat, 24 Aug 2019 18:36:41: start model_add_line... INFO @ Sat, 24 Aug 2019 18:36:41: start X-correlation... INFO @ Sat, 24 Aug 2019 18:36:41: end of X-cor INFO @ Sat, 24 Aug 2019 18:36:41: #2 finished! INFO @ Sat, 24 Aug 2019 18:36:41: #2 predicted fragment length is 235 bps INFO @ Sat, 24 Aug 2019 18:36:41: #2 alternative fragment length(s) may be 235 bps INFO @ Sat, 24 Aug 2019 18:36:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.05_model.r INFO @ Sat, 24 Aug 2019 18:36:41: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:36:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:36:46: 6000000 INFO @ Sat, 24 Aug 2019 18:36:48: 2000000 INFO @ Sat, 24 Aug 2019 18:36:53: 7000000 INFO @ Sat, 24 Aug 2019 18:36:55: 3000000 INFO @ Sat, 24 Aug 2019 18:37:00: 8000000 INFO @ Sat, 24 Aug 2019 18:37:01: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:37:01: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:37:01: #1 total tags in treatment: 8118753 INFO @ Sat, 24 Aug 2019 18:37:01: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:37:01: #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 18:37:01: #1 tags after filtering in treatment: 8118497 INFO @ Sat, 24 Aug 2019 18:37:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:37:01: #1 finished! INFO @ Sat, 24 Aug 2019 18:37:01: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:37:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:37:02: 4000000 INFO @ Sat, 24 Aug 2019 18:37:05: #2 number of paired peaks: 76554 INFO @ Sat, 24 Aug 2019 18:37:05: start model_add_line... INFO @ Sat, 24 Aug 2019 18:37:05: start X-correlation... INFO @ Sat, 24 Aug 2019 18:37:05: end of X-cor INFO @ Sat, 24 Aug 2019 18:37:05: #2 finished! INFO @ Sat, 24 Aug 2019 18:37:05: #2 predicted fragment length is 235 bps INFO @ Sat, 24 Aug 2019 18:37:05: #2 alternative fragment length(s) may be 235 bps INFO @ Sat, 24 Aug 2019 18:37:05: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.10_model.r INFO @ Sat, 24 Aug 2019 18:37:05: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:37:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:37:07: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:37:09: 5000000 INFO @ Sat, 24 Aug 2019 18:37:16: 6000000 INFO @ Sat, 24 Aug 2019 18:37:20: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:37:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:37:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.05_summits.bed INFO @ Sat, 24 Aug 2019 18:37:20: Done! pass1 - making usageList (37 chroms): 3 millis pass2 - checking and writing primary data (2884 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:37:23: 7000000 INFO @ Sat, 24 Aug 2019 18:37:30: 8000000 INFO @ Sat, 24 Aug 2019 18:37:31: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:37:31: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:37:31: #1 total tags in treatment: 8118753 INFO @ Sat, 24 Aug 2019 18:37:31: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:37:31: #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 18:37:31: #1 tags after filtering in treatment: 8118497 INFO @ Sat, 24 Aug 2019 18:37:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:37:31: #1 finished! INFO @ Sat, 24 Aug 2019 18:37:31: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:37:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:37:31: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:37:34: #2 number of paired peaks: 76554 INFO @ Sat, 24 Aug 2019 18:37:34: start model_add_line... INFO @ Sat, 24 Aug 2019 18:37:34: start X-correlation... INFO @ Sat, 24 Aug 2019 18:37:34: end of X-cor INFO @ Sat, 24 Aug 2019 18:37:34: #2 finished! INFO @ Sat, 24 Aug 2019 18:37:34: #2 predicted fragment length is 235 bps INFO @ Sat, 24 Aug 2019 18:37:34: #2 alternative fragment length(s) may be 235 bps INFO @ Sat, 24 Aug 2019 18:37:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.20_model.r INFO @ Sat, 24 Aug 2019 18:37:34: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:37:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:37:44: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:37:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:37:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.10_summits.bed INFO @ Sat, 24 Aug 2019 18:37:44: Done! pass1 - making usageList (26 chroms): 2 millis pass2 - checking and writing primary data (457 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:38:01: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:38:14: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:38:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:38:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375061/SRX5375061.20_summits.bed INFO @ Sat, 24 Aug 2019 18:38:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (84 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。