Job ID = 1293605 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,211,560 reads read : 27,211,560 reads written : 27,211,560 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: 00:10:40 27211560 reads; of these: 27211560 (100.00%) were unpaired; of these: 1159079 (4.26%) aligned 0 times 19190379 (70.52%) aligned exactly 1 time 6862102 (25.22%) aligned >1 times 95.74% overall alignment rate Time searching: 00:10:40 Overall time: 00:10:40 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] 7955743 / 26052481 = 0.3054 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 01:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.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 01:21:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:21:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.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 01:21:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:21:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:21:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.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 01:21:52: #1 read tag files... INFO @ Mon, 03 Jun 2019 01:21:52: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 01:22:01: 1000000 INFO @ Mon, 03 Jun 2019 01:22:02: 1000000 INFO @ Mon, 03 Jun 2019 01:22:03: 1000000 INFO @ Mon, 03 Jun 2019 01:22:09: 2000000 INFO @ Mon, 03 Jun 2019 01:22:12: 2000000 INFO @ Mon, 03 Jun 2019 01:22:13: 2000000 INFO @ Mon, 03 Jun 2019 01:22:17: 3000000 INFO @ Mon, 03 Jun 2019 01:22:22: 3000000 INFO @ Mon, 03 Jun 2019 01:22:23: 3000000 INFO @ Mon, 03 Jun 2019 01:22:25: 4000000 INFO @ Mon, 03 Jun 2019 01:22:32: 4000000 INFO @ Mon, 03 Jun 2019 01:22:32: 4000000 INFO @ Mon, 03 Jun 2019 01:22:33: 5000000 INFO @ Mon, 03 Jun 2019 01:22:41: 6000000 INFO @ Mon, 03 Jun 2019 01:22:42: 5000000 INFO @ Mon, 03 Jun 2019 01:22:42: 5000000 INFO @ Mon, 03 Jun 2019 01:22:50: 7000000 INFO @ Mon, 03 Jun 2019 01:22:51: 6000000 INFO @ Mon, 03 Jun 2019 01:22:52: 6000000 INFO @ Mon, 03 Jun 2019 01:22:58: 8000000 INFO @ Mon, 03 Jun 2019 01:23:00: 7000000 INFO @ Mon, 03 Jun 2019 01:23:02: 7000000 INFO @ Mon, 03 Jun 2019 01:23:06: 9000000 INFO @ Mon, 03 Jun 2019 01:23:09: 8000000 INFO @ Mon, 03 Jun 2019 01:23:12: 8000000 INFO @ Mon, 03 Jun 2019 01:23:14: 10000000 INFO @ Mon, 03 Jun 2019 01:23:18: 9000000 INFO @ Mon, 03 Jun 2019 01:23:22: 11000000 INFO @ Mon, 03 Jun 2019 01:23:22: 9000000 INFO @ Mon, 03 Jun 2019 01:23:28: 10000000 INFO @ Mon, 03 Jun 2019 01:23:30: 12000000 INFO @ Mon, 03 Jun 2019 01:23:32: 10000000 INFO @ Mon, 03 Jun 2019 01:23:38: 11000000 INFO @ Mon, 03 Jun 2019 01:23:38: 13000000 INFO @ Mon, 03 Jun 2019 01:23:42: 11000000 INFO @ Mon, 03 Jun 2019 01:23:46: 14000000 INFO @ Mon, 03 Jun 2019 01:23:47: 12000000 INFO @ Mon, 03 Jun 2019 01:23:52: 12000000 INFO @ Mon, 03 Jun 2019 01:23:54: 15000000 INFO @ Mon, 03 Jun 2019 01:23:57: 13000000 INFO @ Mon, 03 Jun 2019 01:24:02: 16000000 INFO @ Mon, 03 Jun 2019 01:24:02: 13000000 INFO @ Mon, 03 Jun 2019 01:24:07: 14000000 INFO @ Mon, 03 Jun 2019 01:24:10: 17000000 INFO @ Mon, 03 Jun 2019 01:24:12: 14000000 INFO @ Mon, 03 Jun 2019 01:24:16: 15000000 INFO @ Mon, 03 Jun 2019 01:24:18: 18000000 INFO @ Mon, 03 Jun 2019 01:24:19: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:24:19: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:24:19: #1 total tags in treatment: 18096738 INFO @ Mon, 03 Jun 2019 01:24:19: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:24:19: #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 01:24:19: #1 tags after filtering in treatment: 18096738 INFO @ Mon, 03 Jun 2019 01:24:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:24:19: #1 finished! INFO @ Mon, 03 Jun 2019 01:24:19: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:24:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:24:21: #2 number of paired peaks: 238 WARNING @ Mon, 03 Jun 2019 01:24:21: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Mon, 03 Jun 2019 01:24:21: start model_add_line... INFO @ Mon, 03 Jun 2019 01:24:21: start X-correlation... INFO @ Mon, 03 Jun 2019 01:24:21: end of X-cor INFO @ Mon, 03 Jun 2019 01:24:21: #2 finished! INFO @ Mon, 03 Jun 2019 01:24:21: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 01:24:21: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 01:24:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.10_model.r INFO @ Mon, 03 Jun 2019 01:24:21: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:24:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:24:22: 15000000 INFO @ Mon, 03 Jun 2019 01:24:26: 16000000 INFO @ Mon, 03 Jun 2019 01:24:32: 16000000 INFO @ Mon, 03 Jun 2019 01:24:36: 17000000 INFO @ Mon, 03 Jun 2019 01:24:42: 17000000 INFO @ Mon, 03 Jun 2019 01:24:45: 18000000 INFO @ Mon, 03 Jun 2019 01:24:46: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:24:46: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:24:46: #1 total tags in treatment: 18096738 INFO @ Mon, 03 Jun 2019 01:24:46: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:24:46: #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 01:24:47: #1 tags after filtering in treatment: 18096738 INFO @ Mon, 03 Jun 2019 01:24:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:24:47: #1 finished! INFO @ Mon, 03 Jun 2019 01:24:47: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:24:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:24:48: #2 number of paired peaks: 238 WARNING @ Mon, 03 Jun 2019 01:24:48: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Mon, 03 Jun 2019 01:24:48: start model_add_line... INFO @ Mon, 03 Jun 2019 01:24:49: start X-correlation... INFO @ Mon, 03 Jun 2019 01:24:49: end of X-cor INFO @ Mon, 03 Jun 2019 01:24:49: #2 finished! INFO @ Mon, 03 Jun 2019 01:24:49: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 01:24:49: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 01:24:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.05_model.r INFO @ Mon, 03 Jun 2019 01:24:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:24:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:24:52: 18000000 INFO @ Mon, 03 Jun 2019 01:24:53: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 01:24:53: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 01:24:53: #1 total tags in treatment: 18096738 INFO @ Mon, 03 Jun 2019 01:24:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 01:24:53: #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 01:24:53: #1 tags after filtering in treatment: 18096738 INFO @ Mon, 03 Jun 2019 01:24:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 01:24:53: #1 finished! INFO @ Mon, 03 Jun 2019 01:24:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 01:24:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 01:24:55: #2 number of paired peaks: 238 WARNING @ Mon, 03 Jun 2019 01:24:55: Fewer paired peaks (238) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 238 pairs to build model! INFO @ Mon, 03 Jun 2019 01:24:55: start model_add_line... INFO @ Mon, 03 Jun 2019 01:24:55: start X-correlation... INFO @ Mon, 03 Jun 2019 01:24:55: end of X-cor INFO @ Mon, 03 Jun 2019 01:24:55: #2 finished! INFO @ Mon, 03 Jun 2019 01:24:55: #2 predicted fragment length is 118 bps INFO @ Mon, 03 Jun 2019 01:24:55: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 03 Jun 2019 01:24:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.20_model.r INFO @ Mon, 03 Jun 2019 01:24:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 01:24:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 01:25:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:25:33: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.10_peaks.xls INFO @ Mon, 03 Jun 2019 01:25:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:25:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.10_summits.bed INFO @ Mon, 03 Jun 2019 01:25:33: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (3913 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:25:37: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:25:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 01:26:01: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.05_peaks.xls INFO @ Mon, 03 Jun 2019 01:26:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:26:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.05_summits.bed INFO @ Mon, 03 Jun 2019 01:26:01: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6784 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 01:26:07: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.20_peaks.xls INFO @ Mon, 03 Jun 2019 01:26:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 01:26:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX1032389/SRX1032389.20_summits.bed INFO @ Mon, 03 Jun 2019 01:26:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2024 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。