Job ID = 9159848 sra ファイルのダウンロード中... Completed: 763821K bytes transferred in 10 seconds (591821K 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 13063936 spots for /home/okishinya/chipatlas/results/dm3/SRX749034/SRR1636762.sra Written 13063936 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: 00:33:26 13063936 reads; of these: 13063936 (100.00%) were paired; of these: 1794257 (13.73%) aligned concordantly 0 times 8097431 (61.98%) aligned concordantly exactly 1 time 3172248 (24.28%) aligned concordantly >1 times ---- 1794257 pairs aligned concordantly 0 times; of these: 72712 (4.05%) aligned discordantly 1 time ---- 1721545 pairs aligned 0 times concordantly or discordantly; of these: 3443090 mates make up the pairs; of these: 2934306 (85.22%) aligned 0 times 321797 (9.35%) aligned exactly 1 time 186987 (5.43%) aligned >1 times 88.77% overall alignment rate Time searching: 00:33:26 Overall time: 00:33:26 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] 4613107 / 11330423 = 0.4071 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 00:56:05: # Command line: callpeak -t SRX749034.bam -f BAM -g dm -n SRX749034.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749034.20 # format = BAM # ChIP-seq file = ['SRX749034.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 00:56:05: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:56:05: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:56:05: # Command line: callpeak -t SRX749034.bam -f BAM -g dm -n SRX749034.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749034.10 # format = BAM # ChIP-seq file = ['SRX749034.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 00:56:05: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:56:05: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:56:05: # Command line: callpeak -t SRX749034.bam -f BAM -g dm -n SRX749034.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749034.05 # format = BAM # ChIP-seq file = ['SRX749034.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 00:56:05: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:56:05: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:56:12: 1000000 INFO @ Wed, 28 Jun 2017 00:56:12: 1000000 INFO @ Wed, 28 Jun 2017 00:56:12: 1000000 INFO @ Wed, 28 Jun 2017 00:56:19: 2000000 INFO @ Wed, 28 Jun 2017 00:56:19: 2000000 INFO @ Wed, 28 Jun 2017 00:56:19: 2000000 INFO @ Wed, 28 Jun 2017 00:56:26: 3000000 INFO @ Wed, 28 Jun 2017 00:56:27: 3000000 INFO @ Wed, 28 Jun 2017 00:56:27: 3000000 INFO @ Wed, 28 Jun 2017 00:56:33: 4000000 INFO @ Wed, 28 Jun 2017 00:56:34: 4000000 INFO @ Wed, 28 Jun 2017 00:56:34: 4000000 INFO @ Wed, 28 Jun 2017 00:56:41: 5000000 INFO @ Wed, 28 Jun 2017 00:56:42: 5000000 INFO @ Wed, 28 Jun 2017 00:56:42: 5000000 INFO @ Wed, 28 Jun 2017 00:56:48: 6000000 INFO @ Wed, 28 Jun 2017 00:56:49: 6000000 INFO @ Wed, 28 Jun 2017 00:56:49: 6000000 INFO @ Wed, 28 Jun 2017 00:56:55: 7000000 INFO @ Wed, 28 Jun 2017 00:56:57: 7000000 INFO @ Wed, 28 Jun 2017 00:56:57: 7000000 INFO @ Wed, 28 Jun 2017 00:57:02: 8000000 INFO @ Wed, 28 Jun 2017 00:57:04: 8000000 INFO @ Wed, 28 Jun 2017 00:57:04: 8000000 INFO @ Wed, 28 Jun 2017 00:57:09: 9000000 INFO @ Wed, 28 Jun 2017 00:57:11: 9000000 INFO @ Wed, 28 Jun 2017 00:57:11: 9000000 INFO @ Wed, 28 Jun 2017 00:57:17: 10000000 INFO @ Wed, 28 Jun 2017 00:57:18: 10000000 INFO @ Wed, 28 Jun 2017 00:57:18: 10000000 INFO @ Wed, 28 Jun 2017 00:57:24: 11000000 INFO @ Wed, 28 Jun 2017 00:57:25: 11000000 INFO @ Wed, 28 Jun 2017 00:57:25: 11000000 INFO @ Wed, 28 Jun 2017 00:57:31: 12000000 INFO @ Wed, 28 Jun 2017 00:57:33: 12000000 INFO @ Wed, 28 Jun 2017 00:57:33: 12000000 INFO @ Wed, 28 Jun 2017 00:57:39: 13000000 INFO @ Wed, 28 Jun 2017 00:57:40: 13000000 INFO @ Wed, 28 Jun 2017 00:57:40: 13000000 INFO @ Wed, 28 Jun 2017 00:57:46: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:57:46: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:57:46: #1 total tags in treatment: 6667747 INFO @ Wed, 28 Jun 2017 00:57:46: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:57:46: #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 00:57:46: #1 tags after filtering in treatment: 6323131 INFO @ Wed, 28 Jun 2017 00:57:46: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:57:46: #1 finished! INFO @ Wed, 28 Jun 2017 00:57:46: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:57:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:57:46: #2 number of paired peaks: 1294 INFO @ Wed, 28 Jun 2017 00:57:46: start model_add_line... INFO @ Wed, 28 Jun 2017 00:57:47: start X-correlation... INFO @ Wed, 28 Jun 2017 00:57:47: end of X-cor INFO @ Wed, 28 Jun 2017 00:57:47: #2 finished! INFO @ Wed, 28 Jun 2017 00:57:47: #2 predicted fragment length is 156 bps INFO @ Wed, 28 Jun 2017 00:57:47: #2 alternative fragment length(s) may be 156 bps INFO @ Wed, 28 Jun 2017 00:57:47: #2.2 Generate R script for model : SRX749034.10_model.r INFO @ Wed, 28 Jun 2017 00:57:47: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:57:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:57:47: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:57:47: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:57:47: #1 total tags in treatment: 6667747 INFO @ Wed, 28 Jun 2017 00:57:47: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:57:47: #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 00:57:47: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:57:47: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:57:47: #1 total tags in treatment: 6667747 INFO @ Wed, 28 Jun 2017 00:57:47: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:57:47: #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 00:57:47: #1 tags after filtering in treatment: 6323131 INFO @ Wed, 28 Jun 2017 00:57:47: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:57:47: #1 finished! INFO @ Wed, 28 Jun 2017 00:57:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:57:47: #1 tags after filtering in treatment: 6323131 INFO @ Wed, 28 Jun 2017 00:57:47: #1 Redundant rate of treatment: 0.05 INFO @ Wed, 28 Jun 2017 00:57:47: #1 finished! INFO @ Wed, 28 Jun 2017 00:57:47: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:57:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:57:48: #2 number of paired peaks: 1294 INFO @ Wed, 28 Jun 2017 00:57:48: start model_add_line... INFO @ Wed, 28 Jun 2017 00:57:48: #2 number of paired peaks: 1294 INFO @ Wed, 28 Jun 2017 00:57:48: start model_add_line... INFO @ Wed, 28 Jun 2017 00:57:48: start X-correlation... INFO @ Wed, 28 Jun 2017 00:57:48: end of X-cor INFO @ Wed, 28 Jun 2017 00:57:48: #2 finished! INFO @ Wed, 28 Jun 2017 00:57:48: #2 predicted fragment length is 156 bps INFO @ Wed, 28 Jun 2017 00:57:48: #2 alternative fragment length(s) may be 156 bps INFO @ Wed, 28 Jun 2017 00:57:48: #2.2 Generate R script for model : SRX749034.20_model.r INFO @ Wed, 28 Jun 2017 00:57:48: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:57:48: start X-correlation... INFO @ Wed, 28 Jun 2017 00:57:48: end of X-cor INFO @ Wed, 28 Jun 2017 00:57:48: #2 finished! INFO @ Wed, 28 Jun 2017 00:57:48: #2 predicted fragment length is 156 bps INFO @ Wed, 28 Jun 2017 00:57:48: #2 alternative fragment length(s) may be 156 bps INFO @ Wed, 28 Jun 2017 00:57:48: #2.2 Generate R script for model : SRX749034.05_model.r INFO @ Wed, 28 Jun 2017 00:57:48: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:57:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:58:03: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:58:03: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:58:04: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:58:11: #4 Write output xls file... SRX749034.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:58:11: #4 Write peak in narrowPeak format file... SRX749034.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:58:11: #4 Write summits bed file... SRX749034.05_summits.bed INFO @ Wed, 28 Jun 2017 00:58:11: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (5549 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:58:11: #4 Write output xls file... SRX749034.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:58:12: #4 Write peak in narrowPeak format file... SRX749034.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:58:12: #4 Write summits bed file... SRX749034.10_summits.bed INFO @ Wed, 28 Jun 2017 00:58:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2670 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:58:14: #4 Write output xls file... SRX749034.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:58:14: #4 Write peak in narrowPeak format file... SRX749034.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:58:14: #4 Write summits bed file... SRX749034.20_summits.bed INFO @ Wed, 28 Jun 2017 00:58:14: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1073 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。