Job ID = 1295645 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 22,906,103 reads read : 45,812,206 reads written : 45,812,206 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: 00:59:27 22906103 reads; of these: 22906103 (100.00%) were paired; of these: 1787882 (7.81%) aligned concordantly 0 times 15615093 (68.17%) aligned concordantly exactly 1 time 5503128 (24.02%) aligned concordantly >1 times ---- 1787882 pairs aligned concordantly 0 times; of these: 191790 (10.73%) aligned discordantly 1 time ---- 1596092 pairs aligned 0 times concordantly or discordantly; of these: 3192184 mates make up the pairs; of these: 1583498 (49.61%) aligned 0 times 932368 (29.21%) aligned exactly 1 time 676318 (21.19%) aligned >1 times 96.54% overall alignment rate Time searching: 00:59:27 Overall time: 00:59:27 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 20 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] 13828222 / 21230993 = 0.6513 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 16:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.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 16:22:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:22:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.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 16:22:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:22:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:22:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.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 16:22:03: #1 read tag files... INFO @ Mon, 03 Jun 2019 16:22:03: #1 read treatment tags... INFO @ Mon, 03 Jun 2019 16:22:11: 1000000 INFO @ Mon, 03 Jun 2019 16:22:13: 1000000 INFO @ Mon, 03 Jun 2019 16:22:15: 1000000 INFO @ Mon, 03 Jun 2019 16:22:20: 2000000 INFO @ Mon, 03 Jun 2019 16:22:22: 2000000 INFO @ Mon, 03 Jun 2019 16:22:27: 2000000 INFO @ Mon, 03 Jun 2019 16:22:28: 3000000 INFO @ Mon, 03 Jun 2019 16:22:32: 3000000 INFO @ Mon, 03 Jun 2019 16:22:36: 4000000 INFO @ Mon, 03 Jun 2019 16:22:40: 3000000 INFO @ Mon, 03 Jun 2019 16:22:41: 4000000 INFO @ Mon, 03 Jun 2019 16:22:44: 5000000 INFO @ Mon, 03 Jun 2019 16:22:51: 5000000 INFO @ Mon, 03 Jun 2019 16:22:52: 4000000 INFO @ Mon, 03 Jun 2019 16:22:53: 6000000 INFO @ Mon, 03 Jun 2019 16:23:00: 6000000 INFO @ Mon, 03 Jun 2019 16:23:01: 7000000 INFO @ Mon, 03 Jun 2019 16:23:05: 5000000 INFO @ Mon, 03 Jun 2019 16:23:09: 8000000 INFO @ Mon, 03 Jun 2019 16:23:09: 7000000 INFO @ Mon, 03 Jun 2019 16:23:17: 9000000 INFO @ Mon, 03 Jun 2019 16:23:18: 6000000 INFO @ Mon, 03 Jun 2019 16:23:19: 8000000 INFO @ Mon, 03 Jun 2019 16:23:25: 10000000 INFO @ Mon, 03 Jun 2019 16:23:28: 9000000 INFO @ Mon, 03 Jun 2019 16:23:31: 7000000 INFO @ Mon, 03 Jun 2019 16:23:33: 11000000 INFO @ Mon, 03 Jun 2019 16:23:37: 10000000 INFO @ Mon, 03 Jun 2019 16:23:41: 12000000 INFO @ Mon, 03 Jun 2019 16:23:43: 8000000 INFO @ Mon, 03 Jun 2019 16:23:47: 11000000 INFO @ Mon, 03 Jun 2019 16:23:49: 13000000 INFO @ Mon, 03 Jun 2019 16:23:56: 9000000 INFO @ Mon, 03 Jun 2019 16:23:56: 12000000 INFO @ Mon, 03 Jun 2019 16:23:57: 14000000 INFO @ Mon, 03 Jun 2019 16:24:05: 15000000 INFO @ Mon, 03 Jun 2019 16:24:05: 13000000 INFO @ Mon, 03 Jun 2019 16:24:08: 10000000 INFO @ Mon, 03 Jun 2019 16:24:13: 16000000 INFO @ Mon, 03 Jun 2019 16:24:15: 14000000 INFO @ Mon, 03 Jun 2019 16:24:18: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:24:18: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:24:18: #1 total tags in treatment: 7362084 INFO @ Mon, 03 Jun 2019 16:24:18: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:24:18: #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 16:24:18: #1 tags after filtering in treatment: 6138386 INFO @ Mon, 03 Jun 2019 16:24:18: #1 Redundant rate of treatment: 0.17 INFO @ Mon, 03 Jun 2019 16:24:18: #1 finished! INFO @ Mon, 03 Jun 2019 16:24:18: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:24:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:24:19: #2 number of paired peaks: 4190 INFO @ Mon, 03 Jun 2019 16:24:19: start model_add_line... INFO @ Mon, 03 Jun 2019 16:24:19: start X-correlation... INFO @ Mon, 03 Jun 2019 16:24:19: end of X-cor INFO @ Mon, 03 Jun 2019 16:24:19: #2 finished! INFO @ Mon, 03 Jun 2019 16:24:19: #2 predicted fragment length is 220 bps INFO @ Mon, 03 Jun 2019 16:24:19: #2 alternative fragment length(s) may be 220 bps INFO @ Mon, 03 Jun 2019 16:24:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.20_model.r INFO @ Mon, 03 Jun 2019 16:24:19: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:24:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:24:21: 11000000 INFO @ Mon, 03 Jun 2019 16:24:24: 15000000 INFO @ Mon, 03 Jun 2019 16:24:33: 16000000 INFO @ Mon, 03 Jun 2019 16:24:34: 12000000 INFO @ Mon, 03 Jun 2019 16:24:38: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:24:38: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:24:38: #1 total tags in treatment: 7362084 INFO @ Mon, 03 Jun 2019 16:24:38: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:24:38: #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 16:24:38: #1 tags after filtering in treatment: 6138386 INFO @ Mon, 03 Jun 2019 16:24:38: #1 Redundant rate of treatment: 0.17 INFO @ Mon, 03 Jun 2019 16:24:38: #1 finished! INFO @ Mon, 03 Jun 2019 16:24:38: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:24:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:24:39: #2 number of paired peaks: 4190 INFO @ Mon, 03 Jun 2019 16:24:39: start model_add_line... INFO @ Mon, 03 Jun 2019 16:24:39: start X-correlation... INFO @ Mon, 03 Jun 2019 16:24:39: end of X-cor INFO @ Mon, 03 Jun 2019 16:24:39: #2 finished! INFO @ Mon, 03 Jun 2019 16:24:39: #2 predicted fragment length is 220 bps INFO @ Mon, 03 Jun 2019 16:24:39: #2 alternative fragment length(s) may be 220 bps INFO @ Mon, 03 Jun 2019 16:24:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.10_model.r INFO @ Mon, 03 Jun 2019 16:24:39: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:24:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 03 Jun 2019 16:24:44: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:24:46: 13000000 INFO @ Mon, 03 Jun 2019 16:24:54: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.20_peaks.xls INFO @ Mon, 03 Jun 2019 16:24:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.20_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:24:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.20_summits.bed INFO @ Mon, 03 Jun 2019 16:24:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (1872 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:24:58: 14000000 INFO @ Mon, 03 Jun 2019 16:25:04: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:25:10: 15000000 INFO @ Mon, 03 Jun 2019 16:25:14: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.10_peaks.xls INFO @ Mon, 03 Jun 2019 16:25:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.10_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:25:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.10_summits.bed INFO @ Mon, 03 Jun 2019 16:25:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3501 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 03 Jun 2019 16:25:21: 16000000 INFO @ Mon, 03 Jun 2019 16:25:28: #1 tag size is determined as 51 bps INFO @ Mon, 03 Jun 2019 16:25:28: #1 tag size = 51 INFO @ Mon, 03 Jun 2019 16:25:28: #1 total tags in treatment: 7362084 INFO @ Mon, 03 Jun 2019 16:25:28: #1 user defined the maximum tags... INFO @ Mon, 03 Jun 2019 16:25:28: #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 16:25:28: #1 tags after filtering in treatment: 6138386 INFO @ Mon, 03 Jun 2019 16:25:28: #1 Redundant rate of treatment: 0.17 INFO @ Mon, 03 Jun 2019 16:25:28: #1 finished! INFO @ Mon, 03 Jun 2019 16:25:28: #2 Build Peak Model... INFO @ Mon, 03 Jun 2019 16:25:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 03 Jun 2019 16:25:29: #2 number of paired peaks: 4190 INFO @ Mon, 03 Jun 2019 16:25:29: start model_add_line... INFO @ Mon, 03 Jun 2019 16:25:29: start X-correlation... INFO @ Mon, 03 Jun 2019 16:25:29: end of X-cor INFO @ Mon, 03 Jun 2019 16:25:29: #2 finished! INFO @ Mon, 03 Jun 2019 16:25:29: #2 predicted fragment length is 220 bps INFO @ Mon, 03 Jun 2019 16:25:29: #2 alternative fragment length(s) may be 220 bps INFO @ Mon, 03 Jun 2019 16:25:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.05_model.r INFO @ Mon, 03 Jun 2019 16:25:29: #3 Call peaks... INFO @ Mon, 03 Jun 2019 16:25:29: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... INFO @ Mon, 03 Jun 2019 16:25:56: #3 Call peaks for each chromosome... INFO @ Mon, 03 Jun 2019 16:26:08: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.05_peaks.xls INFO @ Mon, 03 Jun 2019 16:26:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.05_peaks.narrowPeak INFO @ Mon, 03 Jun 2019 16:26:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX3960603/SRX3960603.05_summits.bed INFO @ Mon, 03 Jun 2019 16:26:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5704 records, 4 fields): 14 millis CompletedMACS2peakCalling BigWig に変換しました。