Job ID = 9159841 sra ファイルのダウンロード中... Completed: 1510843K bytes transferred in 15 seconds (812313K 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 23656456 spots for /home/okishinya/chipatlas/results/dm3/SRX749024/SRR1636752.sra Written 23656456 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: 00:54:51 23656456 reads; of these: 23656456 (100.00%) were paired; of these: 2628904 (11.11%) aligned concordantly 0 times 14841393 (62.74%) aligned concordantly exactly 1 time 6186159 (26.15%) aligned concordantly >1 times ---- 2628904 pairs aligned concordantly 0 times; of these: 19776 (0.75%) aligned discordantly 1 time ---- 2609128 pairs aligned 0 times concordantly or discordantly; of these: 5218256 mates make up the pairs; of these: 4400753 (84.33%) aligned 0 times 540039 (10.35%) aligned exactly 1 time 277464 (5.32%) aligned >1 times 90.70% overall alignment rate Time searching: 00:54:51 Overall time: 00:54:51 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] 15684920 / 21016453 = 0.7463 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 @ Wed, 28 Jun 2017 01:17:56: # Command line: callpeak -t SRX749024.bam -f BAM -g dm -n SRX749024.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749024.20 # format = BAM # ChIP-seq file = ['SRX749024.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 @ Wed, 28 Jun 2017 01:17:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:17:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:17:56: # Command line: callpeak -t SRX749024.bam -f BAM -g dm -n SRX749024.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749024.05 # format = BAM # ChIP-seq file = ['SRX749024.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 @ Wed, 28 Jun 2017 01:17:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:17:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:17:56: # Command line: callpeak -t SRX749024.bam -f BAM -g dm -n SRX749024.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749024.10 # format = BAM # ChIP-seq file = ['SRX749024.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 @ Wed, 28 Jun 2017 01:17:56: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:17:56: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:18:04: 1000000 INFO @ Wed, 28 Jun 2017 01:18:04: 1000000 INFO @ Wed, 28 Jun 2017 01:18:04: 1000000 INFO @ Wed, 28 Jun 2017 01:18:12: 2000000 INFO @ Wed, 28 Jun 2017 01:18:12: 2000000 INFO @ Wed, 28 Jun 2017 01:18:12: 2000000 INFO @ Wed, 28 Jun 2017 01:18:21: 3000000 INFO @ Wed, 28 Jun 2017 01:18:21: 3000000 INFO @ Wed, 28 Jun 2017 01:18:21: 3000000 INFO @ Wed, 28 Jun 2017 01:18:29: 4000000 INFO @ Wed, 28 Jun 2017 01:18:29: 4000000 INFO @ Wed, 28 Jun 2017 01:18:29: 4000000 INFO @ Wed, 28 Jun 2017 01:18:37: 5000000 INFO @ Wed, 28 Jun 2017 01:18:37: 5000000 INFO @ Wed, 28 Jun 2017 01:18:37: 5000000 INFO @ Wed, 28 Jun 2017 01:18:45: 6000000 INFO @ Wed, 28 Jun 2017 01:18:45: 6000000 INFO @ Wed, 28 Jun 2017 01:18:45: 6000000 INFO @ Wed, 28 Jun 2017 01:18:53: 7000000 INFO @ Wed, 28 Jun 2017 01:18:53: 7000000 INFO @ Wed, 28 Jun 2017 01:18:53: 7000000 INFO @ Wed, 28 Jun 2017 01:19:00: 8000000 INFO @ Wed, 28 Jun 2017 01:19:00: 8000000 INFO @ Wed, 28 Jun 2017 01:19:02: 8000000 INFO @ Wed, 28 Jun 2017 01:19:08: 9000000 INFO @ Wed, 28 Jun 2017 01:19:08: 9000000 INFO @ Wed, 28 Jun 2017 01:19:10: 9000000 INFO @ Wed, 28 Jun 2017 01:19:16: 10000000 INFO @ Wed, 28 Jun 2017 01:19:16: 10000000 INFO @ Wed, 28 Jun 2017 01:19:19: 10000000 INFO @ Wed, 28 Jun 2017 01:19:23: 11000000 INFO @ Wed, 28 Jun 2017 01:19:23: 11000000 INFO @ Wed, 28 Jun 2017 01:19:27: 11000000 INFO @ Wed, 28 Jun 2017 01:19:27: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:19:27: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:19:27: #1 total tags in treatment: 5355534 INFO @ Wed, 28 Jun 2017 01:19:27: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:19:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:19:27: #1 tags after filtering in treatment: 4836855 INFO @ Wed, 28 Jun 2017 01:19:27: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 28 Jun 2017 01:19:27: #1 finished! INFO @ Wed, 28 Jun 2017 01:19:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:19:27: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:19:27: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:19:27: #1 total tags in treatment: 5355534 INFO @ Wed, 28 Jun 2017 01:19:27: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:19:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:19:27: #1 tags after filtering in treatment: 4836855 INFO @ Wed, 28 Jun 2017 01:19:27: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 28 Jun 2017 01:19:27: #1 finished! INFO @ Wed, 28 Jun 2017 01:19:27: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:19:27: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:19:28: #2 number of paired peaks: 4867 INFO @ Wed, 28 Jun 2017 01:19:28: start model_add_line... INFO @ Wed, 28 Jun 2017 01:19:28: start X-correlation... INFO @ Wed, 28 Jun 2017 01:19:28: end of X-cor INFO @ Wed, 28 Jun 2017 01:19:28: #2 finished! INFO @ Wed, 28 Jun 2017 01:19:28: #2 predicted fragment length is 180 bps INFO @ Wed, 28 Jun 2017 01:19:28: #2 alternative fragment length(s) may be 180 bps INFO @ Wed, 28 Jun 2017 01:19:28: #2.2 Generate R script for model : SRX749024.20_model.r INFO @ Wed, 28 Jun 2017 01:19:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:19:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:19:28: #2 number of paired peaks: 4867 INFO @ Wed, 28 Jun 2017 01:19:28: start model_add_line... INFO @ Wed, 28 Jun 2017 01:19:28: start X-correlation... INFO @ Wed, 28 Jun 2017 01:19:28: end of X-cor INFO @ Wed, 28 Jun 2017 01:19:28: #2 finished! INFO @ Wed, 28 Jun 2017 01:19:28: #2 predicted fragment length is 180 bps INFO @ Wed, 28 Jun 2017 01:19:28: #2 alternative fragment length(s) may be 180 bps INFO @ Wed, 28 Jun 2017 01:19:28: #2.2 Generate R script for model : SRX749024.05_model.r INFO @ Wed, 28 Jun 2017 01:19:28: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:19:28: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:19:31: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:19:31: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:19:31: #1 total tags in treatment: 5355534 INFO @ Wed, 28 Jun 2017 01:19:31: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:19:31: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:19:31: #1 tags after filtering in treatment: 4836855 INFO @ Wed, 28 Jun 2017 01:19:31: #1 Redundant rate of treatment: 0.10 INFO @ Wed, 28 Jun 2017 01:19:31: #1 finished! INFO @ Wed, 28 Jun 2017 01:19:31: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:19:31: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:19:32: #2 number of paired peaks: 4867 INFO @ Wed, 28 Jun 2017 01:19:32: start model_add_line... INFO @ Wed, 28 Jun 2017 01:19:32: start X-correlation... INFO @ Wed, 28 Jun 2017 01:19:32: end of X-cor INFO @ Wed, 28 Jun 2017 01:19:32: #2 finished! INFO @ Wed, 28 Jun 2017 01:19:32: #2 predicted fragment length is 180 bps INFO @ Wed, 28 Jun 2017 01:19:32: #2 alternative fragment length(s) may be 180 bps INFO @ Wed, 28 Jun 2017 01:19:32: #2.2 Generate R script for model : SRX749024.10_model.r INFO @ Wed, 28 Jun 2017 01:19:32: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:19:32: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:19:42: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:19:42: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:19:46: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:19:49: #4 Write output xls file... SRX749024.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:19:49: #4 Write peak in narrowPeak format file... SRX749024.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:19:49: #4 Write summits bed file... SRX749024.20_summits.bed INFO @ Wed, 28 Jun 2017 01:19:49: Done! INFO @ Wed, 28 Jun 2017 01:19:49: #4 Write output xls file... SRX749024.05_peaks.xls pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2997 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:19:49: #4 Write peak in narrowPeak format file... SRX749024.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:19:50: #4 Write summits bed file... SRX749024.05_summits.bed INFO @ Wed, 28 Jun 2017 01:19:50: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10128 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:19:53: #4 Write output xls file... SRX749024.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:19:54: #4 Write peak in narrowPeak format file... SRX749024.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:19:54: #4 Write summits bed file... SRX749024.10_summits.bed INFO @ Wed, 28 Jun 2017 01:19:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6639 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。