Job ID = 9159859 sra ファイルのダウンロード中... Completed: 952319K bytes transferred in 10 seconds (723218K 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 15322201 spots for /home/okishinya/chipatlas/results/dm3/SRX749061/SRR1636789.sra Written 15322201 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: 00:21:46 15322201 reads; of these: 15322201 (100.00%) were paired; of these: 1245145 (8.13%) aligned concordantly 0 times 12423137 (81.08%) aligned concordantly exactly 1 time 1653919 (10.79%) aligned concordantly >1 times ---- 1245145 pairs aligned concordantly 0 times; of these: 16375 (1.32%) aligned discordantly 1 time ---- 1228770 pairs aligned 0 times concordantly or discordantly; of these: 2457540 mates make up the pairs; of these: 2070927 (84.27%) aligned 0 times 314382 (12.79%) aligned exactly 1 time 72231 (2.94%) aligned >1 times 93.24% overall alignment rate Time searching: 00:21:46 Overall time: 00:21:46 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] 1696015 / 14086281 = 0.1204 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 00:51:04: # Command line: callpeak -t SRX749061.bam -f BAM -g dm -n SRX749061.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749061.20 # format = BAM # ChIP-seq file = ['SRX749061.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 00:51:04: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:51:04: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:51:04: # Command line: callpeak -t SRX749061.bam -f BAM -g dm -n SRX749061.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749061.10 # format = BAM # ChIP-seq file = ['SRX749061.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 00:51:04: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:51:04: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:51:04: # Command line: callpeak -t SRX749061.bam -f BAM -g dm -n SRX749061.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749061.05 # format = BAM # ChIP-seq file = ['SRX749061.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 00:51:04: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:51:04: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:51:10: 1000000 INFO @ Wed, 28 Jun 2017 00:51:10: 1000000 INFO @ Wed, 28 Jun 2017 00:51:10: 1000000 INFO @ Wed, 28 Jun 2017 00:51:17: 2000000 INFO @ Wed, 28 Jun 2017 00:51:17: 2000000 INFO @ Wed, 28 Jun 2017 00:51:17: 2000000 INFO @ Wed, 28 Jun 2017 00:51:23: 3000000 INFO @ Wed, 28 Jun 2017 00:51:23: 3000000 INFO @ Wed, 28 Jun 2017 00:51:24: 3000000 INFO @ Wed, 28 Jun 2017 00:51:29: 4000000 INFO @ Wed, 28 Jun 2017 00:51:30: 4000000 INFO @ Wed, 28 Jun 2017 00:51:30: 4000000 INFO @ Wed, 28 Jun 2017 00:51:36: 5000000 INFO @ Wed, 28 Jun 2017 00:51:36: 5000000 INFO @ Wed, 28 Jun 2017 00:51:37: 5000000 INFO @ Wed, 28 Jun 2017 00:51:42: 6000000 INFO @ Wed, 28 Jun 2017 00:51:43: 6000000 INFO @ Wed, 28 Jun 2017 00:51:44: 6000000 INFO @ Wed, 28 Jun 2017 00:51:49: 7000000 INFO @ Wed, 28 Jun 2017 00:51:49: 7000000 INFO @ Wed, 28 Jun 2017 00:51:51: 7000000 INFO @ Wed, 28 Jun 2017 00:51:55: 8000000 INFO @ Wed, 28 Jun 2017 00:51:56: 8000000 INFO @ Wed, 28 Jun 2017 00:51:57: 8000000 INFO @ Wed, 28 Jun 2017 00:52:02: 9000000 INFO @ Wed, 28 Jun 2017 00:52:02: 9000000 INFO @ Wed, 28 Jun 2017 00:52:04: 9000000 INFO @ Wed, 28 Jun 2017 00:52:09: 10000000 INFO @ Wed, 28 Jun 2017 00:52:09: 10000000 INFO @ Wed, 28 Jun 2017 00:52:11: 10000000 INFO @ Wed, 28 Jun 2017 00:52:15: 11000000 INFO @ Wed, 28 Jun 2017 00:52:16: 11000000 INFO @ Wed, 28 Jun 2017 00:52:18: 11000000 INFO @ Wed, 28 Jun 2017 00:52:22: 12000000 INFO @ Wed, 28 Jun 2017 00:52:22: 12000000 INFO @ Wed, 28 Jun 2017 00:52:24: 12000000 INFO @ Wed, 28 Jun 2017 00:52:28: 13000000 INFO @ Wed, 28 Jun 2017 00:52:29: 13000000 INFO @ Wed, 28 Jun 2017 00:52:31: 13000000 INFO @ Wed, 28 Jun 2017 00:52:35: 14000000 INFO @ Wed, 28 Jun 2017 00:52:35: 14000000 INFO @ Wed, 28 Jun 2017 00:52:38: 14000000 INFO @ Wed, 28 Jun 2017 00:52:42: 15000000 INFO @ Wed, 28 Jun 2017 00:52:42: 15000000 INFO @ Wed, 28 Jun 2017 00:52:45: 15000000 INFO @ Wed, 28 Jun 2017 00:52:48: 16000000 INFO @ Wed, 28 Jun 2017 00:52:48: 16000000 INFO @ Wed, 28 Jun 2017 00:52:51: 16000000 INFO @ Wed, 28 Jun 2017 00:52:55: 17000000 INFO @ Wed, 28 Jun 2017 00:52:55: 17000000 INFO @ Wed, 28 Jun 2017 00:52:58: 17000000 INFO @ Wed, 28 Jun 2017 00:53:01: 18000000 INFO @ Wed, 28 Jun 2017 00:53:02: 18000000 INFO @ Wed, 28 Jun 2017 00:53:05: 18000000 INFO @ Wed, 28 Jun 2017 00:53:08: 19000000 INFO @ Wed, 28 Jun 2017 00:53:08: 19000000 INFO @ Wed, 28 Jun 2017 00:53:12: 19000000 INFO @ Wed, 28 Jun 2017 00:53:15: 20000000 INFO @ Wed, 28 Jun 2017 00:53:15: 20000000 INFO @ Wed, 28 Jun 2017 00:53:18: 20000000 INFO @ Wed, 28 Jun 2017 00:53:21: 21000000 INFO @ Wed, 28 Jun 2017 00:53:22: 21000000 INFO @ Wed, 28 Jun 2017 00:53:25: 21000000 INFO @ Wed, 28 Jun 2017 00:53:28: 22000000 INFO @ Wed, 28 Jun 2017 00:53:28: 22000000 INFO @ Wed, 28 Jun 2017 00:53:32: 22000000 INFO @ Wed, 28 Jun 2017 00:53:34: 23000000 INFO @ Wed, 28 Jun 2017 00:53:35: 23000000 INFO @ Wed, 28 Jun 2017 00:53:39: 23000000 INFO @ Wed, 28 Jun 2017 00:53:41: 24000000 INFO @ Wed, 28 Jun 2017 00:53:41: 24000000 INFO @ Wed, 28 Jun 2017 00:53:45: 24000000 INFO @ Wed, 28 Jun 2017 00:53:47: 25000000 INFO @ Wed, 28 Jun 2017 00:53:48: 25000000 INFO @ Wed, 28 Jun 2017 00:53:49: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:53:49: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:53:49: #1 total tags in treatment: 12382331 INFO @ Wed, 28 Jun 2017 00:53:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:53:49: #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 00:53:49: #1 tags after filtering in treatment: 8915566 INFO @ Wed, 28 Jun 2017 00:53:49: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 00:53:49: #1 finished! INFO @ Wed, 28 Jun 2017 00:53:49: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:53:49: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:53:49: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:53:49: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:53:49: #1 total tags in treatment: 12382331 INFO @ Wed, 28 Jun 2017 00:53:49: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:53:49: #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 00:53:50: #1 tags after filtering in treatment: 8915566 INFO @ Wed, 28 Jun 2017 00:53:50: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 00:53:50: #1 finished! INFO @ Wed, 28 Jun 2017 00:53:50: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:53:50: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:53:50: #2 number of paired peaks: 3573 INFO @ Wed, 28 Jun 2017 00:53:50: start model_add_line... INFO @ Wed, 28 Jun 2017 00:53:50: start X-correlation... INFO @ Wed, 28 Jun 2017 00:53:50: end of X-cor INFO @ Wed, 28 Jun 2017 00:53:50: #2 finished! INFO @ Wed, 28 Jun 2017 00:53:50: #2 predicted fragment length is 138 bps INFO @ Wed, 28 Jun 2017 00:53:50: #2 alternative fragment length(s) may be 138 bps INFO @ Wed, 28 Jun 2017 00:53:50: #2.2 Generate R script for model : SRX749061.20_model.r INFO @ Wed, 28 Jun 2017 00:53:50: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:53:50: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:53:51: #2 number of paired peaks: 3573 INFO @ Wed, 28 Jun 2017 00:53:51: start model_add_line... INFO @ Wed, 28 Jun 2017 00:53:51: start X-correlation... INFO @ Wed, 28 Jun 2017 00:53:51: end of X-cor INFO @ Wed, 28 Jun 2017 00:53:51: #2 finished! INFO @ Wed, 28 Jun 2017 00:53:51: #2 predicted fragment length is 138 bps INFO @ Wed, 28 Jun 2017 00:53:51: #2 alternative fragment length(s) may be 138 bps INFO @ Wed, 28 Jun 2017 00:53:51: #2.2 Generate R script for model : SRX749061.10_model.r INFO @ Wed, 28 Jun 2017 00:53:51: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:53:51: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:53:52: 25000000 INFO @ Wed, 28 Jun 2017 00:53:53: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:53:53: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:53:53: #1 total tags in treatment: 12382331 INFO @ Wed, 28 Jun 2017 00:53:53: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:53:53: #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 00:53:53: #1 tags after filtering in treatment: 8915566 INFO @ Wed, 28 Jun 2017 00:53:53: #1 Redundant rate of treatment: 0.28 INFO @ Wed, 28 Jun 2017 00:53:53: #1 finished! INFO @ Wed, 28 Jun 2017 00:53:53: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:53:53: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:53:54: #2 number of paired peaks: 3573 INFO @ Wed, 28 Jun 2017 00:53:54: start model_add_line... INFO @ Wed, 28 Jun 2017 00:53:54: start X-correlation... INFO @ Wed, 28 Jun 2017 00:53:54: end of X-cor INFO @ Wed, 28 Jun 2017 00:53:54: #2 finished! INFO @ Wed, 28 Jun 2017 00:53:54: #2 predicted fragment length is 138 bps INFO @ Wed, 28 Jun 2017 00:53:54: #2 alternative fragment length(s) may be 138 bps INFO @ Wed, 28 Jun 2017 00:53:54: #2.2 Generate R script for model : SRX749061.05_model.r INFO @ Wed, 28 Jun 2017 00:53:54: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:53:54: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:54:15: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:54:16: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:54:17: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:54:27: #4 Write output xls file... SRX749061.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:54:27: #4 Write peak in narrowPeak format file... SRX749061.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:54:27: #4 Write summits bed file... SRX749061.20_summits.bed INFO @ Wed, 28 Jun 2017 00:54:28: Done! pass1 - making usageList (14 chroms): 7 millis pass2 - checking and writing primary data (5506 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:54:29: #4 Write output xls file... SRX749061.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:54:29: #4 Write peak in narrowPeak format file... SRX749061.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:54:29: #4 Write summits bed file... SRX749061.10_summits.bed INFO @ Wed, 28 Jun 2017 00:54:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8003 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:54:30: #4 Write output xls file... SRX749061.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:54:30: #4 Write peak in narrowPeak format file... SRX749061.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:54:30: #4 Write summits bed file... SRX749061.05_summits.bed INFO @ Wed, 28 Jun 2017 00:54:30: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (11236 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。