Job ID = 9159866 sra ファイルのダウンロード中... Completed: 734278K bytes transferred in 9 seconds (647517K 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 11327322 spots for /home/okishinya/chipatlas/results/dm3/SRX749072/SRR1636800.sra Written 11327322 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: 00:12:44 11327322 reads; of these: 11327322 (100.00%) were paired; of these: 2501736 (22.09%) aligned concordantly 0 times 7895336 (69.70%) aligned concordantly exactly 1 time 930250 (8.21%) aligned concordantly >1 times ---- 2501736 pairs aligned concordantly 0 times; of these: 5015 (0.20%) aligned discordantly 1 time ---- 2496721 pairs aligned 0 times concordantly or discordantly; of these: 4993442 mates make up the pairs; of these: 4872196 (97.57%) aligned 0 times 93741 (1.88%) aligned exactly 1 time 27505 (0.55%) aligned >1 times 78.49% overall alignment rate Time searching: 00:12:44 Overall time: 00:12:44 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] 1177754 / 8827624 = 0.1334 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 00:42:06: # Command line: callpeak -t SRX749072.bam -f BAM -g dm -n SRX749072.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX749072.10 # format = BAM # ChIP-seq file = ['SRX749072.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 00:42:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:42:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:42:06: # Command line: callpeak -t SRX749072.bam -f BAM -g dm -n SRX749072.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX749072.20 # format = BAM # ChIP-seq file = ['SRX749072.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 00:42:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:42:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:42:06: # Command line: callpeak -t SRX749072.bam -f BAM -g dm -n SRX749072.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX749072.05 # format = BAM # ChIP-seq file = ['SRX749072.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 00:42:06: #1 read tag files... INFO @ Wed, 28 Jun 2017 00:42:06: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 00:42:13: 1000000 INFO @ Wed, 28 Jun 2017 00:42:15: 1000000 INFO @ Wed, 28 Jun 2017 00:42:15: 1000000 INFO @ Wed, 28 Jun 2017 00:42:19: 2000000 INFO @ Wed, 28 Jun 2017 00:42:23: 2000000 INFO @ Wed, 28 Jun 2017 00:42:23: 2000000 INFO @ Wed, 28 Jun 2017 00:42:25: 3000000 INFO @ Wed, 28 Jun 2017 00:42:32: 4000000 INFO @ Wed, 28 Jun 2017 00:42:32: 3000000 INFO @ Wed, 28 Jun 2017 00:42:32: 3000000 INFO @ Wed, 28 Jun 2017 00:42:38: 5000000 INFO @ Wed, 28 Jun 2017 00:42:40: 4000000 INFO @ Wed, 28 Jun 2017 00:42:40: 4000000 INFO @ Wed, 28 Jun 2017 00:42:45: 6000000 INFO @ Wed, 28 Jun 2017 00:42:49: 5000000 INFO @ Wed, 28 Jun 2017 00:42:49: 5000000 INFO @ Wed, 28 Jun 2017 00:42:51: 7000000 INFO @ Wed, 28 Jun 2017 00:42:58: 6000000 INFO @ Wed, 28 Jun 2017 00:42:58: 6000000 INFO @ Wed, 28 Jun 2017 00:42:58: 8000000 INFO @ Wed, 28 Jun 2017 00:43:04: 9000000 INFO @ Wed, 28 Jun 2017 00:43:06: 7000000 INFO @ Wed, 28 Jun 2017 00:43:06: 7000000 INFO @ Wed, 28 Jun 2017 00:43:10: 10000000 INFO @ Wed, 28 Jun 2017 00:43:15: 8000000 INFO @ Wed, 28 Jun 2017 00:43:15: 8000000 INFO @ Wed, 28 Jun 2017 00:43:17: 11000000 INFO @ Wed, 28 Jun 2017 00:43:23: 9000000 INFO @ Wed, 28 Jun 2017 00:43:23: 9000000 INFO @ Wed, 28 Jun 2017 00:43:23: 12000000 INFO @ Wed, 28 Jun 2017 00:43:30: 13000000 INFO @ Wed, 28 Jun 2017 00:43:32: 10000000 INFO @ Wed, 28 Jun 2017 00:43:32: 10000000 INFO @ Wed, 28 Jun 2017 00:43:36: 14000000 INFO @ Wed, 28 Jun 2017 00:43:40: 11000000 INFO @ Wed, 28 Jun 2017 00:43:40: 11000000 INFO @ Wed, 28 Jun 2017 00:43:43: 15000000 INFO @ Wed, 28 Jun 2017 00:43:45: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:43:45: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:43:45: #1 total tags in treatment: 7648043 INFO @ Wed, 28 Jun 2017 00:43:45: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:43:45: #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 00:43:46: #1 tags after filtering in treatment: 5444604 INFO @ Wed, 28 Jun 2017 00:43:46: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 00:43:46: #1 finished! INFO @ Wed, 28 Jun 2017 00:43:46: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:43:46: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:43:47: #2 number of paired peaks: 8009 INFO @ Wed, 28 Jun 2017 00:43:47: start model_add_line... INFO @ Wed, 28 Jun 2017 00:43:47: start X-correlation... INFO @ Wed, 28 Jun 2017 00:43:47: end of X-cor INFO @ Wed, 28 Jun 2017 00:43:47: #2 finished! INFO @ Wed, 28 Jun 2017 00:43:47: #2 predicted fragment length is 136 bps INFO @ Wed, 28 Jun 2017 00:43:47: #2 alternative fragment length(s) may be 136 bps INFO @ Wed, 28 Jun 2017 00:43:47: #2.2 Generate R script for model : SRX749072.10_model.r INFO @ Wed, 28 Jun 2017 00:43:47: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:43:47: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:43:49: 12000000 INFO @ Wed, 28 Jun 2017 00:43:49: 12000000 INFO @ Wed, 28 Jun 2017 00:43:58: 13000000 INFO @ Wed, 28 Jun 2017 00:43:58: 13000000 INFO @ Wed, 28 Jun 2017 00:44:03: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:44:07: 14000000 INFO @ Wed, 28 Jun 2017 00:44:07: 14000000 INFO @ Wed, 28 Jun 2017 00:44:11: #4 Write output xls file... SRX749072.10_peaks.xls INFO @ Wed, 28 Jun 2017 00:44:11: #4 Write peak in narrowPeak format file... SRX749072.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:44:11: #4 Write summits bed file... SRX749072.10_summits.bed INFO @ Wed, 28 Jun 2017 00:44:11: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (7817 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:44:15: 15000000 INFO @ Wed, 28 Jun 2017 00:44:16: 15000000 INFO @ Wed, 28 Jun 2017 00:44:18: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:44:18: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:44:18: #1 total tags in treatment: 7648043 INFO @ Wed, 28 Jun 2017 00:44:18: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:44:18: #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 00:44:18: #1 tags after filtering in treatment: 5444604 INFO @ Wed, 28 Jun 2017 00:44:18: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 00:44:18: #1 finished! INFO @ Wed, 28 Jun 2017 00:44:18: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:44:18: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:44:19: #2 number of paired peaks: 8009 INFO @ Wed, 28 Jun 2017 00:44:19: start model_add_line... INFO @ Wed, 28 Jun 2017 00:44:19: #1 tag size is determined as 50 bps INFO @ Wed, 28 Jun 2017 00:44:19: #1 tag size = 50 INFO @ Wed, 28 Jun 2017 00:44:19: #1 total tags in treatment: 7648043 INFO @ Wed, 28 Jun 2017 00:44:19: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 00:44:19: #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 00:44:19: start X-correlation... INFO @ Wed, 28 Jun 2017 00:44:19: end of X-cor INFO @ Wed, 28 Jun 2017 00:44:19: #2 finished! INFO @ Wed, 28 Jun 2017 00:44:19: #2 predicted fragment length is 136 bps INFO @ Wed, 28 Jun 2017 00:44:19: #2 alternative fragment length(s) may be 136 bps INFO @ Wed, 28 Jun 2017 00:44:19: #2.2 Generate R script for model : SRX749072.20_model.r INFO @ Wed, 28 Jun 2017 00:44:19: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:44:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:44:19: #1 tags after filtering in treatment: 5444604 INFO @ Wed, 28 Jun 2017 00:44:19: #1 Redundant rate of treatment: 0.29 INFO @ Wed, 28 Jun 2017 00:44:19: #1 finished! INFO @ Wed, 28 Jun 2017 00:44:19: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 00:44:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 00:44:20: #2 number of paired peaks: 8009 INFO @ Wed, 28 Jun 2017 00:44:20: start model_add_line... INFO @ Wed, 28 Jun 2017 00:44:20: start X-correlation... INFO @ Wed, 28 Jun 2017 00:44:20: end of X-cor INFO @ Wed, 28 Jun 2017 00:44:20: #2 finished! INFO @ Wed, 28 Jun 2017 00:44:20: #2 predicted fragment length is 136 bps INFO @ Wed, 28 Jun 2017 00:44:20: #2 alternative fragment length(s) may be 136 bps INFO @ Wed, 28 Jun 2017 00:44:20: #2.2 Generate R script for model : SRX749072.05_model.r INFO @ Wed, 28 Jun 2017 00:44:20: #3 Call peaks... INFO @ Wed, 28 Jun 2017 00:44:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 00:44:36: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:44:39: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 00:44:45: #4 Write output xls file... SRX749072.20_peaks.xls INFO @ Wed, 28 Jun 2017 00:44:45: #4 Write peak in narrowPeak format file... SRX749072.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:44:45: #4 Write summits bed file... SRX749072.20_summits.bed INFO @ Wed, 28 Jun 2017 00:44:45: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (5030 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 00:44:50: #4 Write output xls file... SRX749072.05_peaks.xls INFO @ Wed, 28 Jun 2017 00:44:50: #4 Write peak in narrowPeak format file... SRX749072.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 00:44:50: #4 Write summits bed file... SRX749072.05_summits.bed INFO @ Wed, 28 Jun 2017 00:44:50: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (11284 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。