Job ID = 9158154 sra ファイルのダウンロード中... Completed: 294338K bytes transferred in 5 seconds (463100K 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 7030548 spots for /home/okishinya/chipatlas/results/dm3/SRX1056712/SRR2060646.sra Written 7030548 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: 00:13:22 7030548 reads; of these: 7030548 (100.00%) were paired; of these: 2572745 (36.59%) aligned concordantly 0 times 3223132 (45.84%) aligned concordantly exactly 1 time 1234671 (17.56%) aligned concordantly >1 times ---- 2572745 pairs aligned concordantly 0 times; of these: 72492 (2.82%) aligned discordantly 1 time ---- 2500253 pairs aligned 0 times concordantly or discordantly; of these: 5000506 mates make up the pairs; of these: 4631656 (92.62%) aligned 0 times 207558 (4.15%) aligned exactly 1 time 161292 (3.23%) aligned >1 times 67.06% overall alignment rate Time searching: 00:13:22 Overall time: 00:13:22 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] 1159234 / 4527966 = 0.2560 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 15:43:43: # Command line: callpeak -t SRX1056712.bam -f BAM -g dm -n SRX1056712.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056712.10 # format = BAM # ChIP-seq file = ['SRX1056712.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 15:43:43: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:43:43: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:43:43: # Command line: callpeak -t SRX1056712.bam -f BAM -g dm -n SRX1056712.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056712.05 # format = BAM # ChIP-seq file = ['SRX1056712.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 15:43:43: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:43:43: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:43:43: # Command line: callpeak -t SRX1056712.bam -f BAM -g dm -n SRX1056712.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056712.20 # format = BAM # ChIP-seq file = ['SRX1056712.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 15:43:43: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:43:43: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:43:49: 1000000 INFO @ Tue, 27 Jun 2017 15:43:49: 1000000 INFO @ Tue, 27 Jun 2017 15:43:51: 1000000 INFO @ Tue, 27 Jun 2017 15:43:55: 2000000 INFO @ Tue, 27 Jun 2017 15:43:55: 2000000 INFO @ Tue, 27 Jun 2017 15:43:58: 2000000 INFO @ Tue, 27 Jun 2017 15:44:02: 3000000 INFO @ Tue, 27 Jun 2017 15:44:02: 3000000 INFO @ Tue, 27 Jun 2017 15:44:06: 3000000 INFO @ Tue, 27 Jun 2017 15:44:08: 4000000 INFO @ Tue, 27 Jun 2017 15:44:08: 4000000 INFO @ Tue, 27 Jun 2017 15:44:13: 4000000 INFO @ Tue, 27 Jun 2017 15:44:14: 5000000 INFO @ Tue, 27 Jun 2017 15:44:14: 5000000 INFO @ Tue, 27 Jun 2017 15:44:20: 6000000 INFO @ Tue, 27 Jun 2017 15:44:20: 6000000 INFO @ Tue, 27 Jun 2017 15:44:21: 5000000 INFO @ Tue, 27 Jun 2017 15:44:26: 7000000 INFO @ Tue, 27 Jun 2017 15:44:26: 7000000 INFO @ Tue, 27 Jun 2017 15:44:27: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:44:27: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:44:27: #1 total tags in treatment: 3308086 INFO @ Tue, 27 Jun 2017 15:44:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:44:27: #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 15:44:27: #1 tags after filtering in treatment: 3130444 INFO @ Tue, 27 Jun 2017 15:44:27: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 27 Jun 2017 15:44:27: #1 finished! INFO @ Tue, 27 Jun 2017 15:44:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:44:27: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:44:27: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:44:27: #1 total tags in treatment: 3308086 INFO @ Tue, 27 Jun 2017 15:44:27: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:44:27: #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 15:44:27: #1 tags after filtering in treatment: 3130444 INFO @ Tue, 27 Jun 2017 15:44:27: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 27 Jun 2017 15:44:27: #1 finished! INFO @ Tue, 27 Jun 2017 15:44:27: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:44:27: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:44:27: #2 number of paired peaks: 2662 INFO @ Tue, 27 Jun 2017 15:44:27: start model_add_line... INFO @ Tue, 27 Jun 2017 15:44:27: start X-correlation... INFO @ Tue, 27 Jun 2017 15:44:27: end of X-cor INFO @ Tue, 27 Jun 2017 15:44:27: #2 finished! INFO @ Tue, 27 Jun 2017 15:44:27: #2 predicted fragment length is 191 bps INFO @ Tue, 27 Jun 2017 15:44:27: #2 alternative fragment length(s) may be 191 bps INFO @ Tue, 27 Jun 2017 15:44:27: #2.2 Generate R script for model : SRX1056712.05_model.r INFO @ Tue, 27 Jun 2017 15:44:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:44:27: #2 number of paired peaks: 2662 INFO @ Tue, 27 Jun 2017 15:44:27: start model_add_line... INFO @ Tue, 27 Jun 2017 15:44:27: start X-correlation... INFO @ Tue, 27 Jun 2017 15:44:27: end of X-cor INFO @ Tue, 27 Jun 2017 15:44:27: #2 finished! INFO @ Tue, 27 Jun 2017 15:44:27: #2 predicted fragment length is 191 bps INFO @ Tue, 27 Jun 2017 15:44:27: #2 alternative fragment length(s) may be 191 bps INFO @ Tue, 27 Jun 2017 15:44:27: #2.2 Generate R script for model : SRX1056712.10_model.r INFO @ Tue, 27 Jun 2017 15:44:27: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:44:27: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:44:28: 6000000 INFO @ Tue, 27 Jun 2017 15:44:35: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:44:36: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:44:36: 7000000 INFO @ Tue, 27 Jun 2017 15:44:37: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:44:37: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:44:37: #1 total tags in treatment: 3308086 INFO @ Tue, 27 Jun 2017 15:44:37: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:44:37: #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 15:44:37: #1 tags after filtering in treatment: 3130444 INFO @ Tue, 27 Jun 2017 15:44:37: #1 Redundant rate of treatment: 0.05 INFO @ Tue, 27 Jun 2017 15:44:37: #1 finished! INFO @ Tue, 27 Jun 2017 15:44:37: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:44:37: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:44:37: #2 number of paired peaks: 2662 INFO @ Tue, 27 Jun 2017 15:44:37: start model_add_line... INFO @ Tue, 27 Jun 2017 15:44:37: start X-correlation... INFO @ Tue, 27 Jun 2017 15:44:37: end of X-cor INFO @ Tue, 27 Jun 2017 15:44:37: #2 finished! INFO @ Tue, 27 Jun 2017 15:44:37: #2 predicted fragment length is 191 bps INFO @ Tue, 27 Jun 2017 15:44:37: #2 alternative fragment length(s) may be 191 bps INFO @ Tue, 27 Jun 2017 15:44:37: #2.2 Generate R script for model : SRX1056712.20_model.r INFO @ Tue, 27 Jun 2017 15:44:37: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:44:37: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:44:40: #4 Write output xls file... SRX1056712.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:44:40: #4 Write peak in narrowPeak format file... SRX1056712.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:44:40: #4 Write summits bed file... SRX1056712.05_summits.bed INFO @ Tue, 27 Jun 2017 15:44:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5712 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:44:40: #4 Write output xls file... SRX1056712.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:44:40: #4 Write peak in narrowPeak format file... SRX1056712.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:44:40: #4 Write summits bed file... SRX1056712.10_summits.bed INFO @ Tue, 27 Jun 2017 15:44:41: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (2529 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:44:46: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:44:51: #4 Write output xls file... SRX1056712.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:44:51: #4 Write peak in narrowPeak format file... SRX1056712.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:44:51: #4 Write summits bed file... SRX1056712.20_summits.bed INFO @ Tue, 27 Jun 2017 15:44:51: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (816 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。