Job ID = 9158126 sra ファイルのダウンロード中... Completed: 1121944K bytes transferred in 11 seconds (782837K 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 17231191 spots for /home/okishinya/chipatlas/results/dm3/SRX1021223/SRR2013420.sra Written 17231191 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: 00:11:32 17231191 reads; of these: 17231191 (100.00%) were paired; of these: 13480199 (78.23%) aligned concordantly 0 times 2896686 (16.81%) aligned concordantly exactly 1 time 854306 (4.96%) aligned concordantly >1 times ---- 13480199 pairs aligned concordantly 0 times; of these: 6072 (0.05%) aligned discordantly 1 time ---- 13474127 pairs aligned 0 times concordantly or discordantly; of these: 26948254 mates make up the pairs; of these: 26753420 (99.28%) aligned 0 times 156187 (0.58%) aligned exactly 1 time 38647 (0.14%) aligned >1 times 22.37% overall alignment rate Time searching: 00:11:32 Overall time: 00:11:32 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_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] 2732183 / 3752314 = 0.7281 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 @ Tue, 27 Jun 2017 15:26:05: # Command line: callpeak -t SRX1021223.bam -f BAM -g dm -n SRX1021223.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1021223.10 # format = BAM # ChIP-seq file = ['SRX1021223.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 @ Tue, 27 Jun 2017 15:26:05: # Command line: callpeak -t SRX1021223.bam -f BAM -g dm -n SRX1021223.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1021223.05 # format = BAM # ChIP-seq file = ['SRX1021223.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 @ Tue, 27 Jun 2017 15:26:05: # Command line: callpeak -t SRX1021223.bam -f BAM -g dm -n SRX1021223.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1021223.20 # format = BAM # ChIP-seq file = ['SRX1021223.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 @ Tue, 27 Jun 2017 15:26:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:26:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:26:05: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:26:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:26:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:26:05: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:26:12: 1000000 INFO @ Tue, 27 Jun 2017 15:26:12: 1000000 INFO @ Tue, 27 Jun 2017 15:26:12: 1000000 INFO @ Tue, 27 Jun 2017 15:26:19: 2000000 INFO @ Tue, 27 Jun 2017 15:26:20: 2000000 INFO @ Tue, 27 Jun 2017 15:26:20: 2000000 INFO @ Tue, 27 Jun 2017 15:26:21: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 15:26:21: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 15:26:21: #1 total tags in treatment: 1022043 INFO @ Tue, 27 Jun 2017 15:26:21: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:26:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:26:21: #1 tags after filtering in treatment: 886681 INFO @ Tue, 27 Jun 2017 15:26:21: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 27 Jun 2017 15:26:21: #1 finished! INFO @ Tue, 27 Jun 2017 15:26:21: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:26:21: #2 number of paired peaks: 3809 INFO @ Tue, 27 Jun 2017 15:26:21: start model_add_line... INFO @ Tue, 27 Jun 2017 15:26:21: start X-correlation... INFO @ Tue, 27 Jun 2017 15:26:21: end of X-cor INFO @ Tue, 27 Jun 2017 15:26:21: #2 finished! INFO @ Tue, 27 Jun 2017 15:26:21: #2 predicted fragment length is 145 bps INFO @ Tue, 27 Jun 2017 15:26:21: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 27 Jun 2017 15:26:21: #2.2 Generate R script for model : SRX1021223.10_model.r INFO @ Tue, 27 Jun 2017 15:26:21: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:26:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:26:21: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 15:26:21: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 15:26:21: #1 total tags in treatment: 1022043 INFO @ Tue, 27 Jun 2017 15:26:21: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:26:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:26:21: #1 tag size is determined as 50 bps INFO @ Tue, 27 Jun 2017 15:26:21: #1 tag size = 50 INFO @ Tue, 27 Jun 2017 15:26:21: #1 total tags in treatment: 1022043 INFO @ Tue, 27 Jun 2017 15:26:21: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:26:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:26:21: #1 tags after filtering in treatment: 886681 INFO @ Tue, 27 Jun 2017 15:26:21: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 27 Jun 2017 15:26:21: #1 finished! INFO @ Tue, 27 Jun 2017 15:26:21: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:26:21: #1 tags after filtering in treatment: 886681 INFO @ Tue, 27 Jun 2017 15:26:21: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 27 Jun 2017 15:26:21: #1 finished! INFO @ Tue, 27 Jun 2017 15:26:21: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:26:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:26:22: #2 number of paired peaks: 3809 INFO @ Tue, 27 Jun 2017 15:26:22: start model_add_line... INFO @ Tue, 27 Jun 2017 15:26:22: start X-correlation... INFO @ Tue, 27 Jun 2017 15:26:22: end of X-cor INFO @ Tue, 27 Jun 2017 15:26:22: #2 finished! INFO @ Tue, 27 Jun 2017 15:26:22: #2 predicted fragment length is 145 bps INFO @ Tue, 27 Jun 2017 15:26:22: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 27 Jun 2017 15:26:22: #2.2 Generate R script for model : SRX1021223.20_model.r INFO @ Tue, 27 Jun 2017 15:26:22: #2 number of paired peaks: 3809 INFO @ Tue, 27 Jun 2017 15:26:22: start model_add_line... INFO @ Tue, 27 Jun 2017 15:26:22: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:26:22: start X-correlation... INFO @ Tue, 27 Jun 2017 15:26:22: end of X-cor INFO @ Tue, 27 Jun 2017 15:26:22: #2 finished! INFO @ Tue, 27 Jun 2017 15:26:22: #2 predicted fragment length is 145 bps INFO @ Tue, 27 Jun 2017 15:26:22: #2 alternative fragment length(s) may be 145 bps INFO @ Tue, 27 Jun 2017 15:26:22: #2.2 Generate R script for model : SRX1021223.05_model.r INFO @ Tue, 27 Jun 2017 15:26:22: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:26:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:26:23: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:26:24: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:26:24: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:26:25: #4 Write output xls file... SRX1021223.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:26:25: #4 Write peak in narrowPeak format file... SRX1021223.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:26:25: #4 Write summits bed file... SRX1021223.10_summits.bed INFO @ Tue, 27 Jun 2017 15:26:25: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1714 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:26:25: #4 Write output xls file... SRX1021223.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:26:25: #4 Write peak in narrowPeak format file... SRX1021223.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:26:25: #4 Write output xls file... SRX1021223.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:26:25: #4 Write peak in narrowPeak format file... SRX1021223.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:26:25: #4 Write summits bed file... SRX1021223.05_summits.bed INFO @ Tue, 27 Jun 2017 15:26:25: #4 Write summits bed file... SRX1021223.20_summits.bed INFO @ Tue, 27 Jun 2017 15:26:25: Done! INFO @ Tue, 27 Jun 2017 15:26:25: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1302 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (2345 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。