Job ID = 1294955 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,256,806 reads read : 15,256,806 reads written : 15,256,806 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: 00:06:42 15256806 reads; of these: 15256806 (100.00%) were unpaired; of these: 740457 (4.85%) aligned 0 times 10115973 (66.30%) aligned exactly 1 time 4400376 (28.84%) aligned >1 times 95.15% overall alignment rate Time searching: 00:06:42 Overall time: 00:06:42 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] 1578706 / 14516349 = 0.1088 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 11:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.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 11:12:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.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 11:12:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.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 11:12:13: #1 read tag files... INFO @ Mon, 03 Jun 2019 11:12:13: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 11:12:21: 1000000 INFO @ Mon, 03 Jun 2019 11:12:24: 1000000 INFO @ Mon, 03 Jun 2019 11:12:25: 1000000 INFO @ Mon, 03 Jun 2019 11:12:29: 2000000 INFO @ Mon, 03 Jun 2019 11:12:34: 2000000 INFO @ Mon, 03 Jun 2019 11:12:36: 2000000 INFO @ Mon, 03 Jun 2019 11:12:37: 3000000 INFO @ Mon, 03 Jun 2019 11:12:44: 3000000 INFO @ Mon, 03 Jun 2019 11:12:45: 4000000 INFO @ Mon, 03 Jun 2019 11:12:46: 3000000 INFO @ Mon, 03 Jun 2019 11:12:52: 5000000 INFO @ Mon, 03 Jun 2019 11:12:54: 4000000 INFO @ Mon, 03 Jun 2019 11:12:56: 4000000 INFO @ Mon, 03 Jun 2019 11:13:00: 6000000 INFO @ Mon, 03 Jun 2019 11:13:04: 5000000 INFO @ Mon, 03 Jun 2019 11:13:07: 5000000 INFO @ Mon, 03 Jun 2019 11:13:08: 7000000 INFO @ Mon, 03 Jun 2019 11:13:15: 6000000 INFO @ Mon, 03 Jun 2019 11:13:17: 8000000 INFO @ Mon, 03 Jun 2019 11:13:18: 6000000 INFO @ Mon, 03 Jun 2019 11:13:24: 9000000 INFO @ Mon, 03 Jun 2019 11:13:25: 7000000 INFO @ Mon, 03 Jun 2019 11:13:27: 7000000 INFO @ Mon, 03 Jun 2019 11:13:32: 10000000 INFO @ Mon, 03 Jun 2019 11:13:35: 8000000 INFO @ Mon, 03 Jun 2019 11:13:37: 8000000 INFO @ Mon, 03 Jun 2019 11:13:39: 11000000 INFO @ Mon, 03 Jun 2019 11:13:45: 9000000 INFO @ Mon, 03 Jun 2019 11:13:46: 12000000 INFO @ Mon, 03 Jun 2019 11:13:46: 9000000 INFO @ Mon, 03 Jun 2019 11:13:53: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:13:53: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:13:53: #1 total tags in treatment: 12937643 INFO @ Mon, 03 Jun 2019 11:13:53: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:13:53: #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 11:13:53: #1 tags after filtering in treatment: 12937643 INFO @ Mon, 03 Jun 2019 11:13:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:13:53: #1 finished! INFO @ Mon, 03 Jun 2019 11:13:53: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:13:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:13:55: #2 number of paired peaks: 1054 INFO @ Mon, 03 Jun 2019 11:13:55: start model_add_line... INFO @ Mon, 03 Jun 2019 11:13:55: start X-correlation... INFO @ Mon, 03 Jun 2019 11:13:55: end of X-cor INFO @ Mon, 03 Jun 2019 11:13:55: #2 finished! INFO @ Mon, 03 Jun 2019 11:13:55: #2 predicted fragment length is 189 bps INFO @ Mon, 03 Jun 2019 11:13:55: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 03 Jun 2019 11:13:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.10_model.r INFO @ Mon, 03 Jun 2019 11:13:55: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:13:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:13:56: 10000000 INFO @ Mon, 03 Jun 2019 11:13:57: 10000000 INFO @ Mon, 03 Jun 2019 11:14:06: 11000000 INFO @ Mon, 03 Jun 2019 11:14:07: 11000000 INFO @ Mon, 03 Jun 2019 11:14:16: 12000000 INFO @ Mon, 03 Jun 2019 11:14:17: 12000000 INFO @ Mon, 03 Jun 2019 11:14:25: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:25: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:25: #1 total tags in treatment: 12937643 INFO @ Mon, 03 Jun 2019 11:14:25: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:25: #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 11:14:26: #1 tags after filtering in treatment: 12937643 INFO @ Mon, 03 Jun 2019 11:14:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:26: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:26: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:26: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 11:14:26: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 11:14:26: #1 total tags in treatment: 12937643 INFO @ Mon, 03 Jun 2019 11:14:26: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 11:14:26: #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 11:14:27: #1 tags after filtering in treatment: 12937643 INFO @ Mon, 03 Jun 2019 11:14:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 03 Jun 2019 11:14:27: #1 finished! INFO @ Mon, 03 Jun 2019 11:14:27: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 11:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 11:14:27: #2 number of paired peaks: 1054 INFO @ Mon, 03 Jun 2019 11:14:27: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:27: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:27: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:27: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:27: #2 predicted fragment length is 189 bps INFO @ Mon, 03 Jun 2019 11:14:27: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 03 Jun 2019 11:14:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.20_model.r INFO @ Mon, 03 Jun 2019 11:14:27: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:28: #2 number of paired peaks: 1054 INFO @ Mon, 03 Jun 2019 11:14:28: start model_add_line... INFO @ Mon, 03 Jun 2019 11:14:28: start X-correlation... INFO @ Mon, 03 Jun 2019 11:14:28: end of X-cor INFO @ Mon, 03 Jun 2019 11:14:28: #2 finished! INFO @ Mon, 03 Jun 2019 11:14:28: #2 predicted fragment length is 189 bps INFO @ Mon, 03 Jun 2019 11:14:28: #2 alternative fragment length(s) may be 189 bps INFO @ Mon, 03 Jun 2019 11:14:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.05_model.r INFO @ Mon, 03 Jun 2019 11:14:28: #3 Call peaks... INFO @ Mon, 03 Jun 2019 11:14:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 11:14:36: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:14:55: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.10_peaks.xls INFO @ Mon, 03 Jun 2019 11:14:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:14:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.10_summits.bed INFO @ Mon, 03 Jun 2019 11:14:55: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3456 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:08: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:09: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 11:15:27: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.20_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.20_summits.bed INFO @ Mon, 03 Jun 2019 11:15:27: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (2247 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 11:15:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.05_peaks.xls INFO @ Mon, 03 Jun 2019 11:15:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 11:15:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX288017/SRX288017.05_summits.bed INFO @ Mon, 03 Jun 2019 11:15:28: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4928 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。