Job ID = 1299520 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 25,409,137 reads read : 50,818,274 reads written : 50,818,274 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: 00:46:14 25409137 reads; of these: 25409137 (100.00%) were paired; of these: 8221611 (32.36%) aligned concordantly 0 times 12729060 (50.10%) aligned concordantly exactly 1 time 4458466 (17.55%) aligned concordantly >1 times ---- 8221611 pairs aligned concordantly 0 times; of these: 72938 (0.89%) aligned discordantly 1 time ---- 8148673 pairs aligned 0 times concordantly or discordantly; of these: 16297346 mates make up the pairs; of these: 15764321 (96.73%) aligned 0 times 372155 (2.28%) aligned exactly 1 time 160870 (0.99%) aligned >1 times 68.98% overall alignment rate Time searching: 00:46:14 Overall time: 00:46:14 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 16 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 14286506 / 17248595 = 0.8283 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 19:33:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.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 19:33:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:33:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:33:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.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 19:33:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:33:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:33:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.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 19:33:00: #1 read tag files... INFO @ Mon, 03 Jun 2019 19:33:00: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 19:33:07: 1000000 INFO @ Mon, 03 Jun 2019 19:33:07: 1000000 INFO @ Mon, 03 Jun 2019 19:33:09: 1000000 INFO @ Mon, 03 Jun 2019 19:33:14: 2000000 INFO @ Mon, 03 Jun 2019 19:33:14: 2000000 INFO @ Mon, 03 Jun 2019 19:33:17: 2000000 INFO @ Mon, 03 Jun 2019 19:33:21: 3000000 INFO @ Mon, 03 Jun 2019 19:33:21: 3000000 INFO @ Mon, 03 Jun 2019 19:33:26: 3000000 INFO @ Mon, 03 Jun 2019 19:33:28: 4000000 INFO @ Mon, 03 Jun 2019 19:33:30: 4000000 INFO @ Mon, 03 Jun 2019 19:33:35: 5000000 INFO @ Mon, 03 Jun 2019 19:33:37: 4000000 INFO @ Mon, 03 Jun 2019 19:33:39: 5000000 INFO @ Mon, 03 Jun 2019 19:33:45: 6000000 INFO @ Mon, 03 Jun 2019 19:33:45: 6000000 INFO @ Mon, 03 Jun 2019 19:33:48: 5000000 INFO @ Mon, 03 Jun 2019 19:33:48: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:33:48: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:33:48: #1 total tags in treatment: 2953575 INFO @ Mon, 03 Jun 2019 19:33:48: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:33:48: #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 19:33:48: #1 tags after filtering in treatment: 2639755 INFO @ Mon, 03 Jun 2019 19:33:48: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 19:33:48: #1 finished! INFO @ Mon, 03 Jun 2019 19:33:48: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:33:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:33:49: #2 number of paired peaks: 4102 INFO @ Mon, 03 Jun 2019 19:33:49: start model_add_line... INFO @ Mon, 03 Jun 2019 19:33:49: start X-correlation... INFO @ Mon, 03 Jun 2019 19:33:49: end of X-cor INFO @ Mon, 03 Jun 2019 19:33:49: #2 finished! INFO @ Mon, 03 Jun 2019 19:33:49: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 19:33:49: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 19:33:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.05_model.r INFO @ Mon, 03 Jun 2019 19:33:49: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:33:49: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:33:50: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:33:50: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:33:50: #1 total tags in treatment: 2953575 INFO @ Mon, 03 Jun 2019 19:33:50: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:33:50: #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 19:33:50: #1 tags after filtering in treatment: 2639755 INFO @ Mon, 03 Jun 2019 19:33:50: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 19:33:50: #1 finished! INFO @ Mon, 03 Jun 2019 19:33:50: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:33:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:33:50: #2 number of paired peaks: 4102 INFO @ Mon, 03 Jun 2019 19:33:50: start model_add_line... INFO @ Mon, 03 Jun 2019 19:33:50: start X-correlation... INFO @ Mon, 03 Jun 2019 19:33:50: end of X-cor INFO @ Mon, 03 Jun 2019 19:33:50: #2 finished! INFO @ Mon, 03 Jun 2019 19:33:50: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 19:33:50: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 19:33:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.10_model.r INFO @ Mon, 03 Jun 2019 19:33:50: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:33:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:33:56: 6000000 INFO @ Mon, 03 Jun 2019 19:33:57: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:33:59: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:34:01: #1 tag size is determined as 50 bps INFO @ Mon, 03 Jun 2019 19:34:01: #1 tag size = 50 INFO @ Mon, 03 Jun 2019 19:34:01: #1 total tags in treatment: 2953575 INFO @ Mon, 03 Jun 2019 19:34:01: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 19:34:01: #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 19:34:01: #1 tags after filtering in treatment: 2639755 INFO @ Mon, 03 Jun 2019 19:34:01: #1 Redundant rate of treatment: 0.11 INFO @ Mon, 03 Jun 2019 19:34:01: #1 finished! INFO @ Mon, 03 Jun 2019 19:34:01: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 19:34:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 19:34:01: #2 number of paired peaks: 4102 INFO @ Mon, 03 Jun 2019 19:34:01: start model_add_line... INFO @ Mon, 03 Jun 2019 19:34:01: start X-correlation... INFO @ Mon, 03 Jun 2019 19:34:01: end of X-cor INFO @ Mon, 03 Jun 2019 19:34:01: #2 finished! INFO @ Mon, 03 Jun 2019 19:34:01: #2 predicted fragment length is 131 bps INFO @ Mon, 03 Jun 2019 19:34:01: #2 alternative fragment length(s) may be 131 bps INFO @ Mon, 03 Jun 2019 19:34:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.20_model.r INFO @ Mon, 03 Jun 2019 19:34:01: #3 Call peaks... INFO @ Mon, 03 Jun 2019 19:34:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 19:34:02: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.05_peaks.xls INFO @ Mon, 03 Jun 2019 19:34:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:34:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.05_summits.bed INFO @ Mon, 03 Jun 2019 19:34:02: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (3834 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:34:04: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.10_peaks.xls INFO @ Mon, 03 Jun 2019 19:34:04: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:34:04: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.10_summits.bed INFO @ Mon, 03 Jun 2019 19:34:04: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1460 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 19:34:10: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 19:34:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.20_peaks.xls INFO @ Mon, 03 Jun 2019 19:34:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 19:34:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474587/SRX474587.20_summits.bed INFO @ Mon, 03 Jun 2019 19:34:14: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (634 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。