Job ID = 9159846 sra ファイルのダウンロード中... Completed: 445452K bytes transferred in 6 seconds (545657K 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 7591306 spots for /home/okishinya/chipatlas/results/dm3/SRX749032/SRR1636760.sra Written 7591306 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: 00:18:03 7591306 reads; of these: 7591306 (100.00%) were paired; of these: 957358 (12.61%) aligned concordantly 0 times 5082550 (66.95%) aligned concordantly exactly 1 time 1551398 (20.44%) aligned concordantly >1 times ---- 957358 pairs aligned concordantly 0 times; of these: 72814 (7.61%) aligned discordantly 1 time ---- 884544 pairs aligned 0 times concordantly or discordantly; of these: 1769088 mates make up the pairs; of these: 1447897 (81.84%) aligned 0 times 211129 (11.93%) aligned exactly 1 time 110062 (6.22%) aligned >1 times 90.46% overall alignment rate Time searching: 00:18:03 Overall time: 00:18:03 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 8 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] 2351204 / 6702937 = 0.3508 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 00:37:30: # Command line: callpeak -t SRX749032.bam -f BAM -g dm -n SRX749032.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749032.20 # format = BAM # ChIP-seq file = ['SRX749032.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 00:37:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:37:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:37:30: # Command line: callpeak -t SRX749032.bam -f BAM -g dm -n SRX749032.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749032.10 # format = BAM # ChIP-seq file = ['SRX749032.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 00:37:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:37:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:37:30: # Command line: callpeak -t SRX749032.bam -f BAM -g dm -n SRX749032.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749032.05 # format = BAM # ChIP-seq file = ['SRX749032.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 00:37:30: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:37:30: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:37:38: 1000000 INFO @ Wed, 28 Jun 2017 00:37:38: 1000000 INFO @ Wed, 28 Jun 2017 00:37:38: 1000000 INFO @ Wed, 28 Jun 2017 00:37:46: 2000000 INFO @ Wed, 28 Jun 2017 00:37:47: 2000000 INFO @ Wed, 28 Jun 2017 00:37:47: 2000000 INFO @ Wed, 28 Jun 2017 00:37:55: 3000000 INFO @ Wed, 28 Jun 2017 00:37:55: 3000000 INFO @ Wed, 28 Jun 2017 00:37:55: 3000000 INFO @ Wed, 28 Jun 2017 00:38:03: 4000000 INFO @ Wed, 28 Jun 2017 00:38:03: 4000000 INFO @ Wed, 28 Jun 2017 00:38:03: 4000000 INFO @ Wed, 28 Jun 2017 00:38:11: 5000000 INFO @ Wed, 28 Jun 2017 00:38:11: 5000000 INFO @ Wed, 28 Jun 2017 00:38:12: 5000000 INFO @ Wed, 28 Jun 2017 00:38:20: 6000000 INFO @ Wed, 28 Jun 2017 00:38:20: 6000000 INFO @ Wed, 28 Jun 2017 00:38:21: 6000000 INFO @ Wed, 28 Jun 2017 00:38:28: 7000000 INFO @ Wed, 28 Jun 2017 00:38:29: 7000000 INFO @ Wed, 28 Jun 2017 00:38:29: 7000000 INFO @ Wed, 28 Jun 2017 00:38:37: 8000000 INFO @ Wed, 28 Jun 2017 00:38:37: 8000000 INFO @ Wed, 28 Jun 2017 00:38:38: 8000000 INFO @ Wed, 28 Jun 2017 00:38:45: 9000000 INFO @ Wed, 28 Jun 2017 00:38:45: 9000000 INFO @ Wed, 28 Jun 2017 00:38:45: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:38:45: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:38:45: #1 total tags in treatment: 4291765 INFO @ Wed, 28 Jun 2017 00:38:45: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:38:45: #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 00:38:45: #1 tags after filtering in treatment: 4070649 INFO @ Wed, 28 Jun 2017 00:38:45: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:38:45: #1 finished! INFO @ Wed, 28 Jun 2017 00:38:45: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:38:45: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:38:45: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:38:45: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:38:45: #1 total tags in treatment: 4291765 INFO @ Wed, 28 Jun 2017 00:38:45: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:38:45: #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 00:38:46: #1 tags after filtering in treatment: 4070649 INFO @ Wed, 28 Jun 2017 00:38:46: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:38:46: #1 finished! INFO @ Wed, 28 Jun 2017 00:38:46: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:38:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:38:46: #2 number of paired peaks: 3080 INFO @ Wed, 28 Jun 2017 00:38:46: start model_add_line... INFO @ Wed, 28 Jun 2017 00:38:46: start X-correlation... INFO @ Wed, 28 Jun 2017 00:38:46: end of X-cor INFO @ Wed, 28 Jun 2017 00:38:46: #2 finished! INFO @ Wed, 28 Jun 2017 00:38:46: #2 predicted fragment length is 197 bps INFO @ Wed, 28 Jun 2017 00:38:46: #2 alternative fragment length(s) may be 197 bps INFO @ Wed, 28 Jun 2017 00:38:46: #2.2 Generate R script for model : SRX749032.20_model.r INFO @ Wed, 28 Jun 2017 00:38:46: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:38:46: #2 number of paired peaks: 3080 INFO @ Wed, 28 Jun 2017 00:38:46: start model_add_line... INFO @ Wed, 28 Jun 2017 00:38:46: start X-correlation... INFO @ Wed, 28 Jun 2017 00:38:46: end of X-cor INFO @ Wed, 28 Jun 2017 00:38:46: #2 finished! INFO @ Wed, 28 Jun 2017 00:38:46: #2 predicted fragment length is 197 bps INFO @ Wed, 28 Jun 2017 00:38:46: #2 alternative fragment length(s) may be 197 bps INFO @ Wed, 28 Jun 2017 00:38:46: #2.2 Generate R script for model : SRX749032.10_model.r INFO @ Wed, 28 Jun 2017 00:38:46: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:38:46: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:38:46: 9000000 INFO @ Wed, 28 Jun 2017 00:38:47: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:38:47: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:38:47: #1 total tags in treatment: 4291765 INFO @ Wed, 28 Jun 2017 00:38:47: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:38:47: #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 00:38:47: #1 tags after filtering in treatment: 4070649 INFO @ Wed, 28 Jun 2017 00:38:47: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:38:47: #1 finished! INFO @ Wed, 28 Jun 2017 00:38:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:38:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:38:48: #2 number of paired peaks: 3080 INFO @ Wed, 28 Jun 2017 00:38:48: start model_add_line... INFO @ Wed, 28 Jun 2017 00:38:48: start X-correlation... INFO @ Wed, 28 Jun 2017 00:38:48: end of X-cor INFO @ Wed, 28 Jun 2017 00:38:48: #2 finished! INFO @ Wed, 28 Jun 2017 00:38:48: #2 predicted fragment length is 197 bps INFO @ Wed, 28 Jun 2017 00:38:48: #2 alternative fragment length(s) may be 197 bps INFO @ Wed, 28 Jun 2017 00:38:48: #2.2 Generate R script for model : SRX749032.05_model.r INFO @ Wed, 28 Jun 2017 00:38:48: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:38:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:38:56: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:38:57: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:39:00: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:39:02: #4 Write output xls file... SRX749032.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:39:02: #4 Write peak in narrowPeak format file... SRX749032.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:39:02: #4 Write summits bed file... SRX749032.20_summits.bed INFO @ Wed, 28 Jun 2017 00:39:02: Done! pass1 - making usageList (13 chroms): 3 millis pass2 - checking and writing primary data (2567 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:39:03: #4 Write output xls file... SRX749032.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:39:03: #4 Write peak in narrowPeak format file... SRX749032.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:39:03: #4 Write summits bed file... SRX749032.10_summits.bed INFO @ Wed, 28 Jun 2017 00:39:03: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (3799 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:39:07: #4 Write output xls file... SRX749032.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:39:07: #4 Write peak in narrowPeak format file... SRX749032.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:39:07: #4 Write summits bed file... SRX749032.05_summits.bed INFO @ Wed, 28 Jun 2017 00:39:07: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4910 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。