Job ID = 1295245 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,855,678 reads read : 10,855,678 reads written : 10,855,678 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: 00:03:35 10855678 reads; of these: 10855678 (100.00%) were unpaired; of these: 593148 (5.46%) aligned 0 times 8746294 (80.57%) aligned exactly 1 time 1516236 (13.97%) aligned >1 times 94.54% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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] 787584 / 10262530 = 0.0767 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 @ Mon, 03 Jun 2019 13:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.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 @ Mon, 03 Jun 2019 13:05:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:05:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.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 @ Mon, 03 Jun 2019 13:05:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:05:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:05:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.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 @ Mon, 03 Jun 2019 13:05:01: #1 read tag files... INFO @ Mon, 03 Jun 2019 13:05:01: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 13:05:12: 1000000 INFO @ Mon, 03 Jun 2019 13:05:13: 1000000 INFO @ Mon, 03 Jun 2019 13:05:13: 1000000 INFO @ Mon, 03 Jun 2019 13:05:22: 2000000 INFO @ Mon, 03 Jun 2019 13:05:25: 2000000 INFO @ Mon, 03 Jun 2019 13:05:25: 2000000 INFO @ Mon, 03 Jun 2019 13:05:32: 3000000 INFO @ Mon, 03 Jun 2019 13:05:36: 3000000 INFO @ Mon, 03 Jun 2019 13:05:36: 3000000 INFO @ Mon, 03 Jun 2019 13:05:43: 4000000 INFO @ Mon, 03 Jun 2019 13:05:48: 4000000 INFO @ Mon, 03 Jun 2019 13:05:48: 4000000 INFO @ Mon, 03 Jun 2019 13:05:53: 5000000 INFO @ Mon, 03 Jun 2019 13:05:59: 5000000 INFO @ Mon, 03 Jun 2019 13:05:59: 5000000 INFO @ Mon, 03 Jun 2019 13:06:03: 6000000 INFO @ Mon, 03 Jun 2019 13:06:10: 6000000 INFO @ Mon, 03 Jun 2019 13:06:10: 6000000 INFO @ Mon, 03 Jun 2019 13:06:14: 7000000 INFO @ Mon, 03 Jun 2019 13:06:21: 7000000 INFO @ Mon, 03 Jun 2019 13:06:21: 7000000 INFO @ Mon, 03 Jun 2019 13:06:24: 8000000 INFO @ Mon, 03 Jun 2019 13:06:32: 8000000 INFO @ Mon, 03 Jun 2019 13:06:33: 8000000 INFO @ Mon, 03 Jun 2019 13:06:33: 9000000 INFO @ Mon, 03 Jun 2019 13:06:37: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:06:37: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:06:37: #1 total tags in treatment: 9474946 INFO @ Mon, 03 Jun 2019 13:06:37: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:06:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:06:37: #1 tags after filtering in treatment: 9474946 INFO @ Mon, 03 Jun 2019 13:06:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:06:37: #1 finished! INFO @ Mon, 03 Jun 2019 13:06:37: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:06:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:06:38: #2 number of paired peaks: 137 WARNING @ Mon, 03 Jun 2019 13:06:38: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Mon, 03 Jun 2019 13:06:38: start model_add_line... INFO @ Mon, 03 Jun 2019 13:06:38: start X-correlation... INFO @ Mon, 03 Jun 2019 13:06:38: end of X-cor INFO @ Mon, 03 Jun 2019 13:06:38: #2 finished! INFO @ Mon, 03 Jun 2019 13:06:38: #2 predicted fragment length is 154 bps INFO @ Mon, 03 Jun 2019 13:06:38: #2 alternative fragment length(s) may be 154,596 bps INFO @ Mon, 03 Jun 2019 13:06:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.20_model.r INFO @ Mon, 03 Jun 2019 13:06:38: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:06:38: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:06:41: 9000000 INFO @ Mon, 03 Jun 2019 13:06:42: 9000000 INFO @ Mon, 03 Jun 2019 13:06:46: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:06:46: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:06:46: #1 total tags in treatment: 9474946 INFO @ Mon, 03 Jun 2019 13:06:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:06:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:06:47: #1 tags after filtering in treatment: 9474946 INFO @ Mon, 03 Jun 2019 13:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:06:47: #1 finished! INFO @ Mon, 03 Jun 2019 13:06:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:06:47: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 13:06:47: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 13:06:47: #1 total tags in treatment: 9474946 INFO @ Mon, 03 Jun 2019 13:06:47: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 13:06:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 03 Jun 2019 13:06:47: #1 tags after filtering in treatment: 9474946 INFO @ Mon, 03 Jun 2019 13:06:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 13:06:47: #1 finished! INFO @ Mon, 03 Jun 2019 13:06:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 13:06:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 13:06:47: #2 number of paired peaks: 137 WARNING @ Mon, 03 Jun 2019 13:06:47: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Mon, 03 Jun 2019 13:06:47: start model_add_line... INFO @ Mon, 03 Jun 2019 13:06:47: start X-correlation... INFO @ Mon, 03 Jun 2019 13:06:47: end of X-cor INFO @ Mon, 03 Jun 2019 13:06:47: #2 finished! INFO @ Mon, 03 Jun 2019 13:06:47: #2 predicted fragment length is 154 bps INFO @ Mon, 03 Jun 2019 13:06:47: #2 alternative fragment length(s) may be 154,596 bps INFO @ Mon, 03 Jun 2019 13:06:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.10_model.r INFO @ Mon, 03 Jun 2019 13:06:47: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:06:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:06:48: #2 number of paired peaks: 137 WARNING @ Mon, 03 Jun 2019 13:06:48: Fewer paired peaks (137) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 137 pairs to build model! INFO @ Mon, 03 Jun 2019 13:06:48: start model_add_line... INFO @ Mon, 03 Jun 2019 13:06:48: start X-correlation... INFO @ Mon, 03 Jun 2019 13:06:48: end of X-cor INFO @ Mon, 03 Jun 2019 13:06:48: #2 finished! INFO @ Mon, 03 Jun 2019 13:06:48: #2 predicted fragment length is 154 bps INFO @ Mon, 03 Jun 2019 13:06:48: #2 alternative fragment length(s) may be 154,596 bps INFO @ Mon, 03 Jun 2019 13:06:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.05_model.r INFO @ Mon, 03 Jun 2019 13:06:48: #3 Call peaks... INFO @ Mon, 03 Jun 2019 13:06:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 13:07:06: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:07:15: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:07:16: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 13:07:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.20_peaks.xls INFO @ Mon, 03 Jun 2019 13:07:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:07:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.20_summits.bed INFO @ Mon, 03 Jun 2019 13:07:20: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (547 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:07:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.10_peaks.xls INFO @ Mon, 03 Jun 2019 13:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:07:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.10_summits.bed INFO @ Mon, 03 Jun 2019 13:07:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2048 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 13:07:30: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.05_peaks.xls INFO @ Mon, 03 Jun 2019 13:07:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 13:07:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX331407/SRX331407.05_summits.bed INFO @ Mon, 03 Jun 2019 13:07:30: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4145 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。