Job ID = 9158564 sra ファイルのダウンロード中... Completed: 849404K bytes transferred in 7 seconds (910892K 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 13670092 spots for /home/okishinya/chipatlas/results/dm3/SRX1728712/SRR3452729.sra Written 13670092 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: 00:27:30 13670092 reads; of these: 13670092 (100.00%) were paired; of these: 717475 (5.25%) aligned concordantly 0 times 10641490 (77.85%) aligned concordantly exactly 1 time 2311127 (16.91%) aligned concordantly >1 times ---- 717475 pairs aligned concordantly 0 times; of these: 17744 (2.47%) aligned discordantly 1 time ---- 699731 pairs aligned 0 times concordantly or discordantly; of these: 1399462 mates make up the pairs; of these: 1128062 (80.61%) aligned 0 times 200847 (14.35%) aligned exactly 1 time 70553 (5.04%) aligned >1 times 95.87% overall alignment rate Time searching: 00:27:30 Overall time: 00:27:30 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_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] 1888232 / 12959326 = 0.1457 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 18:34:31: # Command line: callpeak -t SRX1728712.bam -f BAM -g dm -n SRX1728712.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1728712.10 # format = BAM # ChIP-seq file = ['SRX1728712.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 18:34:31: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:34:31: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:34:31: # Command line: callpeak -t SRX1728712.bam -f BAM -g dm -n SRX1728712.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1728712.05 # format = BAM # ChIP-seq file = ['SRX1728712.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 18:34:31: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:34:31: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:34:31: # Command line: callpeak -t SRX1728712.bam -f BAM -g dm -n SRX1728712.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1728712.20 # format = BAM # ChIP-seq file = ['SRX1728712.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 18:34:31: #1 read tag files... INFO @ Tue, 27 Jun 2017 18:34:31: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 18:34:40: 1000000 INFO @ Tue, 27 Jun 2017 18:34:40: 1000000 INFO @ Tue, 27 Jun 2017 18:34:40: 1000000 INFO @ Tue, 27 Jun 2017 18:34:49: 2000000 INFO @ Tue, 27 Jun 2017 18:34:49: 2000000 INFO @ Tue, 27 Jun 2017 18:34:49: 2000000 INFO @ Tue, 27 Jun 2017 18:34:58: 3000000 INFO @ Tue, 27 Jun 2017 18:34:59: 3000000 INFO @ Tue, 27 Jun 2017 18:34:59: 3000000 INFO @ Tue, 27 Jun 2017 18:35:07: 4000000 INFO @ Tue, 27 Jun 2017 18:35:08: 4000000 INFO @ Tue, 27 Jun 2017 18:35:08: 4000000 INFO @ Tue, 27 Jun 2017 18:35:15: 5000000 INFO @ Tue, 27 Jun 2017 18:35:17: 5000000 INFO @ Tue, 27 Jun 2017 18:35:17: 5000000 INFO @ Tue, 27 Jun 2017 18:35:21: 6000000 INFO @ Tue, 27 Jun 2017 18:35:25: 6000000 INFO @ Tue, 27 Jun 2017 18:35:25: 6000000 INFO @ Tue, 27 Jun 2017 18:35:28: 7000000 INFO @ Tue, 27 Jun 2017 18:35:34: 7000000 INFO @ Tue, 27 Jun 2017 18:35:34: 7000000 INFO @ Tue, 27 Jun 2017 18:35:35: 8000000 INFO @ Tue, 27 Jun 2017 18:35:41: 9000000 INFO @ Tue, 27 Jun 2017 18:35:42: 8000000 INFO @ Tue, 27 Jun 2017 18:35:42: 8000000 INFO @ Tue, 27 Jun 2017 18:35:48: 10000000 INFO @ Tue, 27 Jun 2017 18:35:51: 9000000 INFO @ Tue, 27 Jun 2017 18:35:51: 9000000 INFO @ Tue, 27 Jun 2017 18:35:54: 11000000 INFO @ Tue, 27 Jun 2017 18:35:59: 10000000 INFO @ Tue, 27 Jun 2017 18:35:59: 10000000 INFO @ Tue, 27 Jun 2017 18:36:01: 12000000 INFO @ Tue, 27 Jun 2017 18:36:07: 11000000 INFO @ Tue, 27 Jun 2017 18:36:07: 11000000 INFO @ Tue, 27 Jun 2017 18:36:07: 13000000 INFO @ Tue, 27 Jun 2017 18:36:14: 14000000 INFO @ Tue, 27 Jun 2017 18:36:15: 12000000 INFO @ Tue, 27 Jun 2017 18:36:15: 12000000 INFO @ Tue, 27 Jun 2017 18:36:21: 15000000 INFO @ Tue, 27 Jun 2017 18:36:22: 13000000 INFO @ Tue, 27 Jun 2017 18:36:23: 13000000 INFO @ Tue, 27 Jun 2017 18:36:28: 16000000 INFO @ Tue, 27 Jun 2017 18:36:29: 14000000 INFO @ Tue, 27 Jun 2017 18:36:31: 14000000 INFO @ Tue, 27 Jun 2017 18:36:35: 17000000 INFO @ Tue, 27 Jun 2017 18:36:36: 15000000 INFO @ Tue, 27 Jun 2017 18:36:38: 15000000 INFO @ Tue, 27 Jun 2017 18:36:42: 18000000 INFO @ Tue, 27 Jun 2017 18:36:43: 16000000 INFO @ Tue, 27 Jun 2017 18:36:46: 16000000 INFO @ Tue, 27 Jun 2017 18:36:49: 19000000 INFO @ Tue, 27 Jun 2017 18:36:51: 17000000 INFO @ Tue, 27 Jun 2017 18:36:54: 17000000 INFO @ Tue, 27 Jun 2017 18:36:56: 20000000 INFO @ Tue, 27 Jun 2017 18:36:58: 18000000 INFO @ Tue, 27 Jun 2017 18:37:02: 18000000 INFO @ Tue, 27 Jun 2017 18:37:03: 21000000 INFO @ Tue, 27 Jun 2017 18:37:05: 19000000 INFO @ Tue, 27 Jun 2017 18:37:10: 19000000 INFO @ Tue, 27 Jun 2017 18:37:10: 22000000 INFO @ Tue, 27 Jun 2017 18:37:12: 20000000 INFO @ Tue, 27 Jun 2017 18:37:13: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 18:37:13: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 18:37:13: #1 total tags in treatment: 11065940 INFO @ Tue, 27 Jun 2017 18:37:13: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:37:13: #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 18:37:14: #1 tags after filtering in treatment: 5590001 INFO @ Tue, 27 Jun 2017 18:37:14: #1 Redundant rate of treatment: 0.49 INFO @ Tue, 27 Jun 2017 18:37:14: #1 finished! INFO @ Tue, 27 Jun 2017 18:37:14: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:37:14: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:37:15: #2 number of paired peaks: 6904 INFO @ Tue, 27 Jun 2017 18:37:15: start model_add_line... INFO @ Tue, 27 Jun 2017 18:37:15: start X-correlation... INFO @ Tue, 27 Jun 2017 18:37:15: end of X-cor INFO @ Tue, 27 Jun 2017 18:37:15: #2 finished! INFO @ Tue, 27 Jun 2017 18:37:15: #2 predicted fragment length is 146 bps INFO @ Tue, 27 Jun 2017 18:37:15: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 27 Jun 2017 18:37:15: #2.2 Generate R script for model : SRX1728712.10_model.r INFO @ Tue, 27 Jun 2017 18:37:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:37:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:37:17: 20000000 INFO @ Tue, 27 Jun 2017 18:37:18: 21000000 INFO @ Tue, 27 Jun 2017 18:37:25: 22000000 INFO @ Tue, 27 Jun 2017 18:37:25: 21000000 INFO @ Tue, 27 Jun 2017 18:37:27: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 18:37:27: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 18:37:27: #1 total tags in treatment: 11065940 INFO @ Tue, 27 Jun 2017 18:37:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:37:27: #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 18:37:28: #1 tags after filtering in treatment: 5590001 INFO @ Tue, 27 Jun 2017 18:37:28: #1 Redundant rate of treatment: 0.49 INFO @ Tue, 27 Jun 2017 18:37:28: #1 finished! INFO @ Tue, 27 Jun 2017 18:37:28: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:37:28: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:37:29: #2 number of paired peaks: 6904 INFO @ Tue, 27 Jun 2017 18:37:29: start model_add_line... INFO @ Tue, 27 Jun 2017 18:37:29: start X-correlation... INFO @ Tue, 27 Jun 2017 18:37:29: end of X-cor INFO @ Tue, 27 Jun 2017 18:37:29: #2 finished! INFO @ Tue, 27 Jun 2017 18:37:29: #2 predicted fragment length is 146 bps INFO @ Tue, 27 Jun 2017 18:37:29: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 27 Jun 2017 18:37:29: #2.2 Generate R script for model : SRX1728712.05_model.r INFO @ Tue, 27 Jun 2017 18:37:29: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:37:29: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:37:32: 22000000 INFO @ Tue, 27 Jun 2017 18:37:34: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:37:36: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 18:37:36: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 18:37:36: #1 total tags in treatment: 11065940 INFO @ Tue, 27 Jun 2017 18:37:36: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 18:37:36: #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 18:37:36: #1 tags after filtering in treatment: 5590001 INFO @ Tue, 27 Jun 2017 18:37:36: #1 Redundant rate of treatment: 0.49 INFO @ Tue, 27 Jun 2017 18:37:36: #1 finished! INFO @ Tue, 27 Jun 2017 18:37:36: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 18:37:36: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 18:37:37: #2 number of paired peaks: 6904 INFO @ Tue, 27 Jun 2017 18:37:37: start model_add_line... INFO @ Tue, 27 Jun 2017 18:37:37: start X-correlation... INFO @ Tue, 27 Jun 2017 18:37:37: end of X-cor INFO @ Tue, 27 Jun 2017 18:37:37: #2 finished! INFO @ Tue, 27 Jun 2017 18:37:37: #2 predicted fragment length is 146 bps INFO @ Tue, 27 Jun 2017 18:37:37: #2 alternative fragment length(s) may be 146 bps INFO @ Tue, 27 Jun 2017 18:37:37: #2.2 Generate R script for model : SRX1728712.20_model.r INFO @ Tue, 27 Jun 2017 18:37:37: #3 Call peaks... INFO @ Tue, 27 Jun 2017 18:37:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 18:37:42: #4 Write output xls file... SRX1728712.10_peaks.xls INFO @ Tue, 27 Jun 2017 18:37:42: #4 Write peak in narrowPeak format file... SRX1728712.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:37:42: #4 Write summits bed file... SRX1728712.10_summits.bed INFO @ Tue, 27 Jun 2017 18:37:42: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7627 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:37:48: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:37:56: #4 Write output xls file... SRX1728712.05_peaks.xls INFO @ Tue, 27 Jun 2017 18:37:56: #4 Write peak in narrowPeak format file... SRX1728712.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:37:56: #4 Write summits bed file... SRX1728712.05_summits.bed INFO @ Tue, 27 Jun 2017 18:37:56: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (9091 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 18:37:58: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 18:38:07: #4 Write output xls file... SRX1728712.20_peaks.xls INFO @ Tue, 27 Jun 2017 18:38:07: #4 Write peak in narrowPeak format file... SRX1728712.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 18:38:07: #4 Write summits bed file... SRX1728712.20_summits.bed INFO @ Tue, 27 Jun 2017 18:38:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (6142 records, 4 fields): 10 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。