Job ID = 9159850 sra ファイルのダウンロード中... Completed: 1017065K bytes transferred in 13 seconds (635681K 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 16635187 spots for /home/okishinya/chipatlas/results/dm3/SRX749037/SRR1636765.sra Written 16635187 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: 00:30:43 16635187 reads; of these: 16635187 (100.00%) were paired; of these: 1017484 (6.12%) aligned concordantly 0 times 13438287 (80.78%) aligned concordantly exactly 1 time 2179416 (13.10%) aligned concordantly >1 times ---- 1017484 pairs aligned concordantly 0 times; of these: 18879 (1.86%) aligned discordantly 1 time ---- 998605 pairs aligned 0 times concordantly or discordantly; of these: 1997210 mates make up the pairs; of these: 1422182 (71.21%) aligned 0 times 484009 (24.23%) aligned exactly 1 time 91019 (4.56%) aligned >1 times 95.73% overall alignment rate Time searching: 00:30:43 Overall time: 00:30:43 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 16 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] 5449841 / 15629258 = 0.3487 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 00:58:35: # Command line: callpeak -t SRX749037.bam -f BAM -g dm -n SRX749037.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749037.10 # format = BAM # ChIP-seq file = ['SRX749037.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 00:58:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:35: # Command line: callpeak -t SRX749037.bam -f BAM -g dm -n SRX749037.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749037.20 # format = BAM # ChIP-seq file = ['SRX749037.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 00:58:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:35: # Command line: callpeak -t SRX749037.bam -f BAM -g dm -n SRX749037.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749037.05 # format = BAM # ChIP-seq file = ['SRX749037.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 00:58:35: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:58:35: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:58:41: 1000000 INFO @ Wed, 28 Jun 2017 00:58:42: 1000000 INFO @ Wed, 28 Jun 2017 00:58:42: 1000000 INFO @ Wed, 28 Jun 2017 00:58:48: 2000000 INFO @ Wed, 28 Jun 2017 00:58:48: 2000000 INFO @ Wed, 28 Jun 2017 00:58:48: 2000000 INFO @ Wed, 28 Jun 2017 00:58:54: 3000000 INFO @ Wed, 28 Jun 2017 00:58:55: 3000000 INFO @ Wed, 28 Jun 2017 00:58:55: 3000000 INFO @ Wed, 28 Jun 2017 00:59:00: 4000000 INFO @ Wed, 28 Jun 2017 00:59:01: 4000000 INFO @ Wed, 28 Jun 2017 00:59:01: 4000000 INFO @ Wed, 28 Jun 2017 00:59:06: 5000000 INFO @ Wed, 28 Jun 2017 00:59:08: 5000000 INFO @ Wed, 28 Jun 2017 00:59:08: 5000000 INFO @ Wed, 28 Jun 2017 00:59:12: 6000000 INFO @ Wed, 28 Jun 2017 00:59:14: 6000000 INFO @ Wed, 28 Jun 2017 00:59:14: 6000000 INFO @ Wed, 28 Jun 2017 00:59:18: 7000000 INFO @ Wed, 28 Jun 2017 00:59:20: 7000000 INFO @ Wed, 28 Jun 2017 00:59:20: 7000000 INFO @ Wed, 28 Jun 2017 00:59:24: 8000000 INFO @ Wed, 28 Jun 2017 00:59:27: 8000000 INFO @ Wed, 28 Jun 2017 00:59:27: 8000000 INFO @ Wed, 28 Jun 2017 00:59:30: 9000000 INFO @ Wed, 28 Jun 2017 00:59:33: 9000000 INFO @ Wed, 28 Jun 2017 00:59:33: 9000000 INFO @ Wed, 28 Jun 2017 00:59:36: 10000000 INFO @ Wed, 28 Jun 2017 00:59:39: 10000000 INFO @ Wed, 28 Jun 2017 00:59:39: 10000000 INFO @ Wed, 28 Jun 2017 00:59:43: 11000000 INFO @ Wed, 28 Jun 2017 00:59:47: 11000000 INFO @ Wed, 28 Jun 2017 00:59:47: 11000000 INFO @ Wed, 28 Jun 2017 00:59:52: 12000000 INFO @ Wed, 28 Jun 2017 00:59:54: 12000000 INFO @ Wed, 28 Jun 2017 00:59:54: 12000000 INFO @ Wed, 28 Jun 2017 01:00:00: 13000000 INFO @ Wed, 28 Jun 2017 01:00:01: 13000000 INFO @ Wed, 28 Jun 2017 01:00:01: 13000000 INFO @ Wed, 28 Jun 2017 01:00:08: 14000000 INFO @ Wed, 28 Jun 2017 01:00:08: 14000000 INFO @ Wed, 28 Jun 2017 01:00:08: 14000000 INFO @ Wed, 28 Jun 2017 01:00:15: 15000000 INFO @ Wed, 28 Jun 2017 01:00:15: 15000000 INFO @ Wed, 28 Jun 2017 01:00:16: 15000000 INFO @ Wed, 28 Jun 2017 01:00:22: 16000000 INFO @ Wed, 28 Jun 2017 01:00:22: 16000000 INFO @ Wed, 28 Jun 2017 01:00:25: 16000000 INFO @ Wed, 28 Jun 2017 01:00:29: 17000000 INFO @ Wed, 28 Jun 2017 01:00:29: 17000000 INFO @ Wed, 28 Jun 2017 01:00:33: 17000000 INFO @ Wed, 28 Jun 2017 01:00:37: 18000000 INFO @ Wed, 28 Jun 2017 01:00:37: 18000000 INFO @ Wed, 28 Jun 2017 01:00:41: 18000000 INFO @ Wed, 28 Jun 2017 01:00:44: 19000000 INFO @ Wed, 28 Jun 2017 01:00:44: 19000000 INFO @ Wed, 28 Jun 2017 01:00:49: 19000000 INFO @ Wed, 28 Jun 2017 01:00:51: 20000000 INFO @ Wed, 28 Jun 2017 01:00:51: 20000000 INFO @ Wed, 28 Jun 2017 01:00:57: 20000000 INFO @ Wed, 28 Jun 2017 01:00:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:00:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:00:57: #1 total tags in treatment: 10171916 INFO @ Wed, 28 Jun 2017 01:00:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:00:57: #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 01:00:57: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:00:57: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:00:57: #1 total tags in treatment: 10171916 INFO @ Wed, 28 Jun 2017 01:00:57: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:00:57: #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 01:00:58: #1 tags after filtering in treatment: 5704611 INFO @ Wed, 28 Jun 2017 01:00:58: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 28 Jun 2017 01:00:58: #1 finished! INFO @ Wed, 28 Jun 2017 01:00:58: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:00:58: #1 tags after filtering in treatment: 5704611 INFO @ Wed, 28 Jun 2017 01:00:58: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 28 Jun 2017 01:00:58: #1 finished! INFO @ Wed, 28 Jun 2017 01:00:58: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:00:58: #2 number of paired peaks: 6200 INFO @ Wed, 28 Jun 2017 01:00:58: start model_add_line... INFO @ Wed, 28 Jun 2017 01:00:58: #2 number of paired peaks: 6200 INFO @ Wed, 28 Jun 2017 01:00:58: start model_add_line... INFO @ Wed, 28 Jun 2017 01:00:59: start X-correlation... INFO @ Wed, 28 Jun 2017 01:00:59: end of X-cor INFO @ Wed, 28 Jun 2017 01:00:59: #2 finished! INFO @ Wed, 28 Jun 2017 01:00:59: #2 predicted fragment length is 150 bps INFO @ Wed, 28 Jun 2017 01:00:59: #2 alternative fragment length(s) may be 150 bps INFO @ Wed, 28 Jun 2017 01:00:59: #2.2 Generate R script for model : SRX749037.20_model.r INFO @ Wed, 28 Jun 2017 01:00:59: start X-correlation... INFO @ Wed, 28 Jun 2017 01:00:59: end of X-cor INFO @ Wed, 28 Jun 2017 01:00:59: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:00:59: #2 finished! INFO @ Wed, 28 Jun 2017 01:00:59: #2 predicted fragment length is 150 bps INFO @ Wed, 28 Jun 2017 01:00:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:00:59: #2 alternative fragment length(s) may be 150 bps INFO @ Wed, 28 Jun 2017 01:00:59: #2.2 Generate R script for model : SRX749037.10_model.r INFO @ Wed, 28 Jun 2017 01:00:59: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:00:59: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:01:05: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 01:01:05: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 01:01:05: #1 total tags in treatment: 10171916 INFO @ Wed, 28 Jun 2017 01:01:05: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:01:05: #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 01:01:05: #1 tags after filtering in treatment: 5704611 INFO @ Wed, 28 Jun 2017 01:01:05: #1 Redundant rate of treatment: 0.44 INFO @ Wed, 28 Jun 2017 01:01:05: #1 finished! INFO @ Wed, 28 Jun 2017 01:01:05: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:01:05: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:01:06: #2 number of paired peaks: 6200 INFO @ Wed, 28 Jun 2017 01:01:06: start model_add_line... INFO @ Wed, 28 Jun 2017 01:01:06: start X-correlation... INFO @ Wed, 28 Jun 2017 01:01:06: end of X-cor INFO @ Wed, 28 Jun 2017 01:01:06: #2 finished! INFO @ Wed, 28 Jun 2017 01:01:06: #2 predicted fragment length is 150 bps INFO @ Wed, 28 Jun 2017 01:01:06: #2 alternative fragment length(s) may be 150 bps INFO @ Wed, 28 Jun 2017 01:01:06: #2.2 Generate R script for model : SRX749037.05_model.r INFO @ Wed, 28 Jun 2017 01:01:06: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:01:06: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:01:14: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:01:15: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:01:22: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:01:24: #4 Write output xls file... SRX749037.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:01:24: #4 Write peak in narrowPeak format file... SRX749037.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:01:24: #4 Write output xls file... SRX749037.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:01:24: #4 Write summits bed file... SRX749037.20_summits.bed INFO @ Wed, 28 Jun 2017 01:01:24: Done! INFO @ Wed, 28 Jun 2017 01:01:24: #4 Write peak in narrowPeak format file... SRX749037.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:01:24: #4 Write summits bed file... SRX749037.10_summits.bed pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (7141 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:01:24: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8882 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:01:32: #4 Write output xls file... SRX749037.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:01:32: #4 Write peak in narrowPeak format file... SRX749037.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:01:32: #4 Write summits bed file... SRX749037.05_summits.bed INFO @ Wed, 28 Jun 2017 01:01:32: Done! pass1 - making usageList (15 chroms): 3 millis pass2 - checking and writing primary data (10704 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。