Job ID = 9158162 sra ファイルのダウンロード中... Completed: 184193K bytes transferred in 4 seconds (312105K bits/sec), in 1 file, 2 directories. sra ファイルのダウンロードが完了しました。 Read layout: PAIRED fastq に変換中... Written 4674983 spots for /home/okishinya/chipatlas/results/dm3/SRX1056719/SRR2060653.sra Written 4674983 spots total rm: cannot remove `[DSE]RR*.fastq': そのようなファイルやディレクトリはありません 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: 00:12:59 4674983 reads; of these: 4674983 (100.00%) were paired; of these: 592607 (12.68%) aligned concordantly 0 times 2644461 (56.57%) aligned concordantly exactly 1 time 1437915 (30.76%) aligned concordantly >1 times ---- 592607 pairs aligned concordantly 0 times; of these: 66872 (11.28%) aligned discordantly 1 time ---- 525735 pairs aligned 0 times concordantly or discordantly; of these: 1051470 mates make up the pairs; of these: 694629 (66.06%) aligned 0 times 208924 (19.87%) aligned exactly 1 time 147917 (14.07%) aligned >1 times 92.57% overall alignment rate Time searching: 00:12:59 Overall time: 00:12:59 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_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] 112730 / 4143028 = 0.0272 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 @ Tue, 27 Jun 2017 15:45:56: # Command line: callpeak -t SRX1056719.bam -f BAM -g dm -n SRX1056719.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056719.10 # format = BAM # ChIP-seq file = ['SRX1056719.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 @ Tue, 27 Jun 2017 15:45:56: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:45:56: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:45:56: # Command line: callpeak -t SRX1056719.bam -f BAM -g dm -n SRX1056719.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056719.05 # format = BAM # ChIP-seq file = ['SRX1056719.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 @ Tue, 27 Jun 2017 15:45:56: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:45:56: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:45:56: # Command line: callpeak -t SRX1056719.bam -f BAM -g dm -n SRX1056719.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056719.20 # format = BAM # ChIP-seq file = ['SRX1056719.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 @ Tue, 27 Jun 2017 15:45:56: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:45:56: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:46:02: 1000000 INFO @ Tue, 27 Jun 2017 15:46:03: 1000000 INFO @ Tue, 27 Jun 2017 15:46:03: 1000000 INFO @ Tue, 27 Jun 2017 15:46:08: 2000000 INFO @ Tue, 27 Jun 2017 15:46:09: 2000000 INFO @ Tue, 27 Jun 2017 15:46:09: 2000000 INFO @ Tue, 27 Jun 2017 15:46:14: 3000000 INFO @ Tue, 27 Jun 2017 15:46:16: 3000000 INFO @ Tue, 27 Jun 2017 15:46:16: 3000000 INFO @ Tue, 27 Jun 2017 15:46:20: 4000000 INFO @ Tue, 27 Jun 2017 15:46:23: 4000000 INFO @ Tue, 27 Jun 2017 15:46:23: 4000000 INFO @ Tue, 27 Jun 2017 15:46:26: 5000000 INFO @ Tue, 27 Jun 2017 15:46:29: 5000000 INFO @ Tue, 27 Jun 2017 15:46:29: 5000000 INFO @ Tue, 27 Jun 2017 15:46:32: 6000000 INFO @ Tue, 27 Jun 2017 15:46:36: 6000000 INFO @ Tue, 27 Jun 2017 15:46:36: 6000000 INFO @ Tue, 27 Jun 2017 15:46:38: 7000000 INFO @ Tue, 27 Jun 2017 15:46:43: 7000000 INFO @ Tue, 27 Jun 2017 15:46:43: 7000000 INFO @ Tue, 27 Jun 2017 15:46:43: 8000000 INFO @ Tue, 27 Jun 2017 15:46:46: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:46:46: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:46:46: #1 total tags in treatment: 3971304 INFO @ Tue, 27 Jun 2017 15:46:46: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:46:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:46:46: #1 tags after filtering in treatment: 3664035 INFO @ Tue, 27 Jun 2017 15:46:46: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 27 Jun 2017 15:46:46: #1 finished! INFO @ Tue, 27 Jun 2017 15:46:46: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:46:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:46:46: #2 number of paired peaks: 1103 INFO @ Tue, 27 Jun 2017 15:46:46: start model_add_line... INFO @ Tue, 27 Jun 2017 15:46:46: start X-correlation... INFO @ Tue, 27 Jun 2017 15:46:46: end of X-cor INFO @ Tue, 27 Jun 2017 15:46:46: #2 finished! INFO @ Tue, 27 Jun 2017 15:46:46: #2 predicted fragment length is 143 bps INFO @ Tue, 27 Jun 2017 15:46:46: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 27 Jun 2017 15:46:46: #2.2 Generate R script for model : SRX1056719.10_model.r INFO @ Tue, 27 Jun 2017 15:46:46: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:46:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:46:50: 8000000 INFO @ Tue, 27 Jun 2017 15:46:50: 8000000 INFO @ Tue, 27 Jun 2017 15:46:52: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:46:52: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:46:52: #1 total tags in treatment: 3971304 INFO @ Tue, 27 Jun 2017 15:46:52: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:46:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:46:52: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:46:52: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:46:52: #1 total tags in treatment: 3971304 INFO @ Tue, 27 Jun 2017 15:46:52: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:46:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:46:52: #1 tags after filtering in treatment: 3664035 INFO @ Tue, 27 Jun 2017 15:46:52: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 27 Jun 2017 15:46:52: #1 finished! INFO @ Tue, 27 Jun 2017 15:46:52: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:46:52: #1 tags after filtering in treatment: 3664035 INFO @ Tue, 27 Jun 2017 15:46:52: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 27 Jun 2017 15:46:52: #1 finished! INFO @ Tue, 27 Jun 2017 15:46:52: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:46:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:46:53: #2 number of paired peaks: 1103 INFO @ Tue, 27 Jun 2017 15:46:53: start model_add_line... INFO @ Tue, 27 Jun 2017 15:46:53: #2 number of paired peaks: 1103 INFO @ Tue, 27 Jun 2017 15:46:53: start model_add_line... INFO @ Tue, 27 Jun 2017 15:46:53: start X-correlation... INFO @ Tue, 27 Jun 2017 15:46:53: end of X-cor INFO @ Tue, 27 Jun 2017 15:46:53: #2 finished! INFO @ Tue, 27 Jun 2017 15:46:53: #2 predicted fragment length is 143 bps INFO @ Tue, 27 Jun 2017 15:46:53: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 27 Jun 2017 15:46:53: #2.2 Generate R script for model : SRX1056719.05_model.r INFO @ Tue, 27 Jun 2017 15:46:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:46:53: start X-correlation... INFO @ Tue, 27 Jun 2017 15:46:53: end of X-cor INFO @ Tue, 27 Jun 2017 15:46:53: #2 finished! INFO @ Tue, 27 Jun 2017 15:46:53: #2 predicted fragment length is 143 bps INFO @ Tue, 27 Jun 2017 15:46:53: #2 alternative fragment length(s) may be 143 bps INFO @ Tue, 27 Jun 2017 15:46:53: #2.2 Generate R script for model : SRX1056719.20_model.r INFO @ Tue, 27 Jun 2017 15:46:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:46:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:46:56: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:47:01: #4 Write output xls file... SRX1056719.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:47:01: #4 Write peak in narrowPeak format file... SRX1056719.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:47:01: #4 Write summits bed file... SRX1056719.10_summits.bed INFO @ Tue, 27 Jun 2017 15:47:01: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1090 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:47:02: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:47:03: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:47:07: #4 Write output xls file... SRX1056719.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:47:07: #4 Write peak in narrowPeak format file... SRX1056719.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:47:07: #4 Write summits bed file... SRX1056719.05_summits.bed INFO @ Tue, 27 Jun 2017 15:47:07: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (1569 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:47:08: #4 Write output xls file... SRX1056719.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:47:08: #4 Write peak in narrowPeak format file... SRX1056719.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:47:08: #4 Write summits bed file... SRX1056719.20_summits.bed INFO @ Tue, 27 Jun 2017 15:47:08: Done! pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (680 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。