Job ID = 2640576 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,011,806 reads read : 42,023,612 reads written : 21,011,806 reads 0-length : 21,011,806 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:10 21011806 reads; of these: 21011806 (100.00%) were unpaired; of these: 1917187 (9.12%) aligned 0 times 15657087 (74.52%) aligned exactly 1 time 3437532 (16.36%) aligned >1 times 90.88% overall alignment rate Time searching: 00:13:13 Overall time: 00:13:13 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] 2330626 / 19094619 = 0.1221 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Sat, 24 Aug 2019 18:11:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.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 18:11:05: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:11:05: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:11:15: 1000000 INFO @ Sat, 24 Aug 2019 18:11:25: 2000000 INFO @ Sat, 24 Aug 2019 18:11:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.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 18:11:35: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:11:35: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:11:35: 3000000 INFO @ Sat, 24 Aug 2019 18:11:43: 1000000 INFO @ Sat, 24 Aug 2019 18:11:45: 4000000 INFO @ Sat, 24 Aug 2019 18:11:52: 2000000 INFO @ Sat, 24 Aug 2019 18:11:55: 5000000 INFO @ Sat, 24 Aug 2019 18:12:00: 3000000 BedGraph に変換中... INFO @ Sat, 24 Aug 2019 18:12:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.bam -f BAM -g 2.15e9 -n /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.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 18:12:05: #1 read tag files... INFO @ Sat, 24 Aug 2019 18:12:05: #1 read treatment tags... INFO @ Sat, 24 Aug 2019 18:12:05: 6000000 INFO @ Sat, 24 Aug 2019 18:12:09: 4000000 INFO @ Sat, 24 Aug 2019 18:12:12: 1000000 INFO @ Sat, 24 Aug 2019 18:12:16: 7000000 INFO @ Sat, 24 Aug 2019 18:12:17: 5000000 INFO @ Sat, 24 Aug 2019 18:12:20: 2000000 INFO @ Sat, 24 Aug 2019 18:12:26: 6000000 INFO @ Sat, 24 Aug 2019 18:12:26: 8000000 INFO @ Sat, 24 Aug 2019 18:12:28: 3000000 INFO @ Sat, 24 Aug 2019 18:12:34: 7000000 INFO @ Sat, 24 Aug 2019 18:12:35: 4000000 INFO @ Sat, 24 Aug 2019 18:12:36: 9000000 INFO @ Sat, 24 Aug 2019 18:12:43: 5000000 INFO @ Sat, 24 Aug 2019 18:12:43: 8000000 INFO @ Sat, 24 Aug 2019 18:12:46: 10000000 INFO @ Sat, 24 Aug 2019 18:12:50: 6000000 INFO @ Sat, 24 Aug 2019 18:12:51: 9000000 INFO @ Sat, 24 Aug 2019 18:12:56: 11000000 INFO @ Sat, 24 Aug 2019 18:12:58: 7000000 INFO @ Sat, 24 Aug 2019 18:12:59: 10000000 INFO @ Sat, 24 Aug 2019 18:13:06: 12000000 INFO @ Sat, 24 Aug 2019 18:13:06: 8000000 INFO @ Sat, 24 Aug 2019 18:13:08: 11000000 INFO @ Sat, 24 Aug 2019 18:13:14: 9000000 INFO @ Sat, 24 Aug 2019 18:13:16: 13000000 INFO @ Sat, 24 Aug 2019 18:13:16: 12000000 INFO @ Sat, 24 Aug 2019 18:13:21: 10000000 INFO @ Sat, 24 Aug 2019 18:13:25: 13000000 INFO @ Sat, 24 Aug 2019 18:13:26: 14000000 INFO @ Sat, 24 Aug 2019 18:13:29: 11000000 INFO @ Sat, 24 Aug 2019 18:13:33: 14000000 INFO @ Sat, 24 Aug 2019 18:13:36: 12000000 INFO @ Sat, 24 Aug 2019 18:13:36: 15000000 INFO @ Sat, 24 Aug 2019 18:13:41: 15000000 INFO @ Sat, 24 Aug 2019 18:13:44: 13000000 INFO @ Sat, 24 Aug 2019 18:13:46: 16000000 INFO @ Sat, 24 Aug 2019 18:13:50: 16000000 INFO @ Sat, 24 Aug 2019 18:13:51: 14000000 INFO @ Sat, 24 Aug 2019 18:13:54: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:13:54: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:13:54: #1 total tags in treatment: 16763993 INFO @ Sat, 24 Aug 2019 18:13:54: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:13:54: #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 18:13:55: #1 tags after filtering in treatment: 16763783 INFO @ Sat, 24 Aug 2019 18:13:55: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:13:55: #1 finished! INFO @ Sat, 24 Aug 2019 18:13:55: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:13:55: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:13:56: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:13:56: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:13:56: #1 total tags in treatment: 16763993 INFO @ Sat, 24 Aug 2019 18:13:56: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:13:56: #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 18:13:57: #1 tags after filtering in treatment: 16763783 INFO @ Sat, 24 Aug 2019 18:13:57: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:13:57: #1 finished! INFO @ Sat, 24 Aug 2019 18:13:57: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:13:57: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:13:59: 15000000 INFO @ Sat, 24 Aug 2019 18:14:00: #2 number of paired peaks: 80866 INFO @ Sat, 24 Aug 2019 18:14:00: start model_add_line... INFO @ Sat, 24 Aug 2019 18:14:00: start X-correlation... INFO @ Sat, 24 Aug 2019 18:14:00: end of X-cor INFO @ Sat, 24 Aug 2019 18:14:00: #2 finished! INFO @ Sat, 24 Aug 2019 18:14:00: #2 predicted fragment length is 173 bps INFO @ Sat, 24 Aug 2019 18:14:00: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 24 Aug 2019 18:14:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.05_model.r INFO @ Sat, 24 Aug 2019 18:14:00: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:14:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:14:02: #2 number of paired peaks: 80866 INFO @ Sat, 24 Aug 2019 18:14:02: start model_add_line... INFO @ Sat, 24 Aug 2019 18:14:02: start X-correlation... INFO @ Sat, 24 Aug 2019 18:14:02: end of X-cor INFO @ Sat, 24 Aug 2019 18:14:02: #2 finished! INFO @ Sat, 24 Aug 2019 18:14:02: #2 predicted fragment length is 173 bps INFO @ Sat, 24 Aug 2019 18:14:02: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 24 Aug 2019 18:14:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.10_model.r INFO @ Sat, 24 Aug 2019 18:14:02: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:14:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:14:06: 16000000 INFO @ Sat, 24 Aug 2019 18:14:12: #1 tag size is determined as 51 bps INFO @ Sat, 24 Aug 2019 18:14:12: #1 tag size = 51 INFO @ Sat, 24 Aug 2019 18:14:12: #1 total tags in treatment: 16763993 INFO @ Sat, 24 Aug 2019 18:14:12: #1 user defined the maximum tags... INFO @ Sat, 24 Aug 2019 18:14:12: #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 18:14:13: #1 tags after filtering in treatment: 16763783 INFO @ Sat, 24 Aug 2019 18:14:13: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 24 Aug 2019 18:14:13: #1 finished! INFO @ Sat, 24 Aug 2019 18:14:13: #2 Build Peak Model... INFO @ Sat, 24 Aug 2019 18:14:13: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 24 Aug 2019 18:14:18: #2 number of paired peaks: 80866 INFO @ Sat, 24 Aug 2019 18:14:18: start model_add_line... INFO @ Sat, 24 Aug 2019 18:14:18: start X-correlation... INFO @ Sat, 24 Aug 2019 18:14:18: end of X-cor INFO @ Sat, 24 Aug 2019 18:14:18: #2 finished! INFO @ Sat, 24 Aug 2019 18:14:18: #2 predicted fragment length is 173 bps INFO @ Sat, 24 Aug 2019 18:14:18: #2 alternative fragment length(s) may be 173 bps INFO @ Sat, 24 Aug 2019 18:14:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.20_model.r INFO @ Sat, 24 Aug 2019 18:14:18: #3 Call peaks... INFO @ Sat, 24 Aug 2019 18:14:18: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 24 Aug 2019 18:14:58: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:15:00: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:15:16: #3 Call peaks for each chromosome... INFO @ Sat, 24 Aug 2019 18:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.05_peaks.xls INFO @ Sat, 24 Aug 2019 18:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.05_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.05_summits.bed INFO @ Sat, 24 Aug 2019 18:15:28: Done! pass1 - making usageList (92 chroms): 5 millis pass2 - checking and writing primary data (18379 records, 4 fields): 28 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:15:29: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.10_peaks.xls INFO @ Sat, 24 Aug 2019 18:15:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.10_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:15:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.10_summits.bed INFO @ Sat, 24 Aug 2019 18:15:30: Done! pass1 - making usageList (75 chroms): 7 millis pass2 - checking and writing primary data (13009 records, 4 fields): 26 millis CompletedMACS2peakCalling INFO @ Sat, 24 Aug 2019 18:15:45: #4 Write output xls file... /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.20_peaks.xls INFO @ Sat, 24 Aug 2019 18:15:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.20_peaks.narrowPeak INFO @ Sat, 24 Aug 2019 18:15:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/rn6/SRX5375019/SRX5375019.20_summits.bed INFO @ Sat, 24 Aug 2019 18:15:46: Done! pass1 - making usageList (51 chroms): 2 millis pass2 - checking and writing primary data (7512 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。