Job ID = 4303131 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 30,529,482 reads read : 30,529,482 reads written : 30,529,482 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1552297.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:08:37 30529482 reads; of these: 30529482 (100.00%) were unpaired; of these: 5780993 (18.94%) aligned 0 times 22283903 (72.99%) aligned exactly 1 time 2464586 (8.07%) aligned >1 times 81.06% overall alignment rate Time searching: 00:08:37 Overall time: 00:08:37 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_sort_core] merging from 12 files... [bam_rmdupse_core] 7833844 / 24748489 = 0.3165 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 01:04:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 12 Dec 2019 01:04:58: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:04:58: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:05:07: 1000000 INFO @ Thu, 12 Dec 2019 01:05:16: 2000000 INFO @ Thu, 12 Dec 2019 01:05:25: 3000000 INFO @ Thu, 12 Dec 2019 01:05:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 12 Dec 2019 01:05:28: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:05:28: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:05:34: 4000000 INFO @ Thu, 12 Dec 2019 01:05:38: 1000000 INFO @ Thu, 12 Dec 2019 01:05:43: 5000000 INFO @ Thu, 12 Dec 2019 01:05:47: 2000000 INFO @ Thu, 12 Dec 2019 01:05:53: 6000000 BedGraph に変換中... INFO @ Thu, 12 Dec 2019 01:05:57: 3000000 INFO @ Thu, 12 Dec 2019 01:05:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 12 Dec 2019 01:05:58: #1 read tag files... INFO @ Thu, 12 Dec 2019 01:05:58: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 01:06:02: 7000000 INFO @ Thu, 12 Dec 2019 01:06:06: 4000000 INFO @ Thu, 12 Dec 2019 01:06:06: 1000000 INFO @ Thu, 12 Dec 2019 01:06:11: 8000000 INFO @ Thu, 12 Dec 2019 01:06:14: 2000000 INFO @ Thu, 12 Dec 2019 01:06:16: 5000000 INFO @ Thu, 12 Dec 2019 01:06:19: 9000000 INFO @ Thu, 12 Dec 2019 01:06:22: 3000000 INFO @ Thu, 12 Dec 2019 01:06:26: 6000000 INFO @ Thu, 12 Dec 2019 01:06:28: 10000000 INFO @ Thu, 12 Dec 2019 01:06:30: 4000000 INFO @ Thu, 12 Dec 2019 01:06:35: 7000000 INFO @ Thu, 12 Dec 2019 01:06:37: 11000000 INFO @ Thu, 12 Dec 2019 01:06:38: 5000000 INFO @ Thu, 12 Dec 2019 01:06:44: 8000000 INFO @ Thu, 12 Dec 2019 01:06:46: 6000000 INFO @ Thu, 12 Dec 2019 01:06:47: 12000000 INFO @ Thu, 12 Dec 2019 01:06:53: 9000000 INFO @ Thu, 12 Dec 2019 01:06:54: 7000000 INFO @ Thu, 12 Dec 2019 01:06:56: 13000000 INFO @ Thu, 12 Dec 2019 01:07:01: 8000000 INFO @ Thu, 12 Dec 2019 01:07:02: 10000000 INFO @ Thu, 12 Dec 2019 01:07:05: 14000000 INFO @ Thu, 12 Dec 2019 01:07:09: 9000000 INFO @ Thu, 12 Dec 2019 01:07:11: 11000000 INFO @ Thu, 12 Dec 2019 01:07:14: 15000000 INFO @ Thu, 12 Dec 2019 01:07:17: 10000000 INFO @ Thu, 12 Dec 2019 01:07:20: 12000000 INFO @ Thu, 12 Dec 2019 01:07:24: 16000000 INFO @ Thu, 12 Dec 2019 01:07:25: 11000000 INFO @ Thu, 12 Dec 2019 01:07:29: 13000000 INFO @ Thu, 12 Dec 2019 01:07:32: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:07:32: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:07:32: #1 total tags in treatment: 16914645 INFO @ Thu, 12 Dec 2019 01:07:32: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:07:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:07:32: 12000000 INFO @ Thu, 12 Dec 2019 01:07:33: #1 tags after filtering in treatment: 16914645 INFO @ Thu, 12 Dec 2019 01:07:33: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:07:33: #1 finished! INFO @ Thu, 12 Dec 2019 01:07:33: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:07:33: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:07:34: #2 number of paired peaks: 1738 INFO @ Thu, 12 Dec 2019 01:07:34: start model_add_line... INFO @ Thu, 12 Dec 2019 01:07:34: start X-correlation... INFO @ Thu, 12 Dec 2019 01:07:34: end of X-cor INFO @ Thu, 12 Dec 2019 01:07:34: #2 finished! INFO @ Thu, 12 Dec 2019 01:07:34: #2 predicted fragment length is 207 bps INFO @ Thu, 12 Dec 2019 01:07:34: #2 alternative fragment length(s) may be 207 bps INFO @ Thu, 12 Dec 2019 01:07:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.05_model.r INFO @ Thu, 12 Dec 2019 01:07:34: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:07:34: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:07:38: 14000000 INFO @ Thu, 12 Dec 2019 01:07:40: 13000000 INFO @ Thu, 12 Dec 2019 01:07:46: 15000000 INFO @ Thu, 12 Dec 2019 01:07:48: 14000000 INFO @ Thu, 12 Dec 2019 01:07:56: 16000000 INFO @ Thu, 12 Dec 2019 01:07:56: 15000000 INFO @ Thu, 12 Dec 2019 01:08:04: 16000000 INFO @ Thu, 12 Dec 2019 01:08:05: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:08:05: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:08:05: #1 total tags in treatment: 16914645 INFO @ Thu, 12 Dec 2019 01:08:05: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:08:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:08:05: #1 tags after filtering in treatment: 16914645 INFO @ Thu, 12 Dec 2019 01:08:05: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:08:05: #1 finished! INFO @ Thu, 12 Dec 2019 01:08:05: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:08:05: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:08:07: #2 number of paired peaks: 1738 INFO @ Thu, 12 Dec 2019 01:08:07: start model_add_line... INFO @ Thu, 12 Dec 2019 01:08:07: start X-correlation... INFO @ Thu, 12 Dec 2019 01:08:07: end of X-cor INFO @ Thu, 12 Dec 2019 01:08:07: #2 finished! INFO @ Thu, 12 Dec 2019 01:08:07: #2 predicted fragment length is 207 bps INFO @ Thu, 12 Dec 2019 01:08:07: #2 alternative fragment length(s) may be 207 bps INFO @ Thu, 12 Dec 2019 01:08:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.10_model.r INFO @ Thu, 12 Dec 2019 01:08:07: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:08:07: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:08:11: #1 tag size is determined as 50 bps INFO @ Thu, 12 Dec 2019 01:08:11: #1 tag size = 50 INFO @ Thu, 12 Dec 2019 01:08:11: #1 total tags in treatment: 16914645 INFO @ Thu, 12 Dec 2019 01:08:11: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 01:08:11: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 01:08:12: #1 tags after filtering in treatment: 16914645 INFO @ Thu, 12 Dec 2019 01:08:12: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 01:08:12: #1 finished! INFO @ Thu, 12 Dec 2019 01:08:12: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 01:08:12: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 01:08:13: #2 number of paired peaks: 1738 INFO @ Thu, 12 Dec 2019 01:08:13: start model_add_line... INFO @ Thu, 12 Dec 2019 01:08:14: start X-correlation... INFO @ Thu, 12 Dec 2019 01:08:14: end of X-cor INFO @ Thu, 12 Dec 2019 01:08:14: #2 finished! INFO @ Thu, 12 Dec 2019 01:08:14: #2 predicted fragment length is 207 bps INFO @ Thu, 12 Dec 2019 01:08:14: #2 alternative fragment length(s) may be 207 bps INFO @ Thu, 12 Dec 2019 01:08:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.20_model.r INFO @ Thu, 12 Dec 2019 01:08:14: #3 Call peaks... INFO @ Thu, 12 Dec 2019 01:08:14: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 01:08:28: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:08:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.05_peaks.xls INFO @ Thu, 12 Dec 2019 01:08:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:08:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.05_summits.bed INFO @ Thu, 12 Dec 2019 01:08:56: Done! pass1 - making usageList (15 chroms): 6 millis pass2 - checking and writing primary data (11992 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:09:00: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:09:07: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 01:09:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.10_peaks.xls INFO @ Thu, 12 Dec 2019 01:09:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:09:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.10_summits.bed INFO @ Thu, 12 Dec 2019 01:09:28: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (8133 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 01:09:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.20_peaks.xls INFO @ Thu, 12 Dec 2019 01:09:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 01:09:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681828/SRX681828.20_summits.bed INFO @ Thu, 12 Dec 2019 01:09:33: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (4958 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。