Job ID = 1293281 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,359,977 reads read : 18,359,977 reads written : 18,359,977 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:22 18359977 reads; of these: 18359977 (100.00%) were unpaired; of these: 577109 (3.14%) aligned 0 times 16379115 (89.21%) aligned exactly 1 time 1403753 (7.65%) aligned >1 times 96.86% overall alignment rate Time searching: 00:03:22 Overall time: 00:03:22 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 8 files... [bam_rmdupse_core] 11460184 / 17782868 = 0.6445 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 @ Sun, 02 Jun 2019 22:52:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.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 @ Sun, 02 Jun 2019 22:52:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:52:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:52:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.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 @ Sun, 02 Jun 2019 22:52:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:52:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:52:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.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 @ Sun, 02 Jun 2019 22:52:12: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:52:12: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:52:19: 1000000 INFO @ Sun, 02 Jun 2019 22:52:19: 1000000 INFO @ Sun, 02 Jun 2019 22:52:19: 1000000 INFO @ Sun, 02 Jun 2019 22:52:25: 2000000 INFO @ Sun, 02 Jun 2019 22:52:26: 2000000 INFO @ Sun, 02 Jun 2019 22:52:26: 2000000 INFO @ Sun, 02 Jun 2019 22:52:31: 3000000 INFO @ Sun, 02 Jun 2019 22:52:33: 3000000 INFO @ Sun, 02 Jun 2019 22:52:33: 3000000 INFO @ Sun, 02 Jun 2019 22:52:38: 4000000 INFO @ Sun, 02 Jun 2019 22:52:40: 4000000 INFO @ Sun, 02 Jun 2019 22:52:40: 4000000 INFO @ Sun, 02 Jun 2019 22:52:44: 5000000 INFO @ Sun, 02 Jun 2019 22:52:47: 5000000 INFO @ Sun, 02 Jun 2019 22:52:47: 5000000 INFO @ Sun, 02 Jun 2019 22:52:51: 6000000 INFO @ Sun, 02 Jun 2019 22:52:53: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:52:53: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:52:53: #1 total tags in treatment: 6322684 INFO @ Sun, 02 Jun 2019 22:52:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:52:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:52:53: #1 tags after filtering in treatment: 6322684 INFO @ Sun, 02 Jun 2019 22:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:52:53: #1 finished! INFO @ Sun, 02 Jun 2019 22:52:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:52:53: 6000000 INFO @ Sun, 02 Jun 2019 22:52:54: 6000000 INFO @ Sun, 02 Jun 2019 22:52:54: #2 number of paired peaks: 9036 INFO @ Sun, 02 Jun 2019 22:52:54: start model_add_line... INFO @ Sun, 02 Jun 2019 22:52:54: start X-correlation... INFO @ Sun, 02 Jun 2019 22:52:54: end of X-cor INFO @ Sun, 02 Jun 2019 22:52:54: #2 finished! INFO @ Sun, 02 Jun 2019 22:52:54: #2 predicted fragment length is 157 bps INFO @ Sun, 02 Jun 2019 22:52:54: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 02 Jun 2019 22:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.10_model.r INFO @ Sun, 02 Jun 2019 22:52:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:52:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:52:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:52:56: #1 total tags in treatment: 6322684 INFO @ Sun, 02 Jun 2019 22:52:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:52:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:52:56: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:52:56: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:52:56: #1 total tags in treatment: 6322684 INFO @ Sun, 02 Jun 2019 22:52:56: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:52:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 22:52:56: #1 tags after filtering in treatment: 6322684 INFO @ Sun, 02 Jun 2019 22:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:52:56: #1 finished! INFO @ Sun, 02 Jun 2019 22:52:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:52:56: #1 tags after filtering in treatment: 6322684 INFO @ Sun, 02 Jun 2019 22:52:56: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:52:56: #1 finished! INFO @ Sun, 02 Jun 2019 22:52:56: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:52:56: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:52:57: #2 number of paired peaks: 9036 INFO @ Sun, 02 Jun 2019 22:52:57: start model_add_line... INFO @ Sun, 02 Jun 2019 22:52:57: #2 number of paired peaks: 9036 INFO @ Sun, 02 Jun 2019 22:52:57: start model_add_line... INFO @ Sun, 02 Jun 2019 22:52:57: start X-correlation... INFO @ Sun, 02 Jun 2019 22:52:57: end of X-cor INFO @ Sun, 02 Jun 2019 22:52:57: #2 finished! INFO @ Sun, 02 Jun 2019 22:52:57: #2 predicted fragment length is 157 bps INFO @ Sun, 02 Jun 2019 22:52:57: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 02 Jun 2019 22:52:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.05_model.r INFO @ Sun, 02 Jun 2019 22:52:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:52:57: start X-correlation... INFO @ Sun, 02 Jun 2019 22:52:57: end of X-cor INFO @ Sun, 02 Jun 2019 22:52:57: #2 finished! INFO @ Sun, 02 Jun 2019 22:52:57: #2 predicted fragment length is 157 bps INFO @ Sun, 02 Jun 2019 22:52:57: #2 alternative fragment length(s) may be 157 bps INFO @ Sun, 02 Jun 2019 22:52:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.20_model.r INFO @ Sun, 02 Jun 2019 22:52:57: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:52:57: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:53:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:53:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:53:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:53:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:53:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:53:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.10_summits.bed INFO @ Sun, 02 Jun 2019 22:53:27: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (4367 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:53:29: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:53:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:53:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.05_summits.bed INFO @ Sun, 02 Jun 2019 22:53:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7956 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:53:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:53:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:53:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/ERX011417/ERX011417.20_summits.bed INFO @ Sun, 02 Jun 2019 22:53:30: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1788 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。