Job ID = 9158160 sra ファイルのダウンロード中... Completed: 316487K bytes transferred in 5 seconds (444249K 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 7554570 spots for /home/okishinya/chipatlas/results/dm3/SRX1056717/SRR2060651.sra Written 7554570 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: 00:17:26 7554570 reads; of these: 7554570 (100.00%) were paired; of these: 1010199 (13.37%) aligned concordantly 0 times 5041801 (66.74%) aligned concordantly exactly 1 time 1502570 (19.89%) aligned concordantly >1 times ---- 1010199 pairs aligned concordantly 0 times; of these: 134113 (13.28%) aligned discordantly 1 time ---- 876086 pairs aligned 0 times concordantly or discordantly; of these: 1752172 mates make up the pairs; of these: 1131919 (64.60%) aligned 0 times 336448 (19.20%) aligned exactly 1 time 283805 (16.20%) aligned >1 times 92.51% overall alignment rate Time searching: 00:17:26 Overall time: 00:17:26 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_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] 665385 / 6675595 = 0.0997 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 15:50:33: # Command line: callpeak -t SRX1056717.bam -f BAM -g dm -n SRX1056717.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1056717.10 # format = BAM # ChIP-seq file = ['SRX1056717.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 15:50:33: # Command line: callpeak -t SRX1056717.bam -f BAM -g dm -n SRX1056717.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1056717.05 # format = BAM # ChIP-seq file = ['SRX1056717.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 15:50:33: # Command line: callpeak -t SRX1056717.bam -f BAM -g dm -n SRX1056717.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1056717.20 # format = BAM # ChIP-seq file = ['SRX1056717.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 15:50:33: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:50:33: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:50:33: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:50:33: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:50:33: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:50:33: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:50:39: 1000000 INFO @ Tue, 27 Jun 2017 15:50:39: 1000000 INFO @ Tue, 27 Jun 2017 15:50:39: 1000000 INFO @ Tue, 27 Jun 2017 15:50:45: 2000000 INFO @ Tue, 27 Jun 2017 15:50:46: 2000000 INFO @ Tue, 27 Jun 2017 15:50:46: 2000000 INFO @ Tue, 27 Jun 2017 15:50:52: 3000000 INFO @ Tue, 27 Jun 2017 15:50:53: 3000000 INFO @ Tue, 27 Jun 2017 15:50:53: 3000000 INFO @ Tue, 27 Jun 2017 15:50:58: 4000000 INFO @ Tue, 27 Jun 2017 15:51:01: 4000000 INFO @ Tue, 27 Jun 2017 15:51:01: 4000000 INFO @ Tue, 27 Jun 2017 15:51:05: 5000000 INFO @ Tue, 27 Jun 2017 15:51:09: 5000000 INFO @ Tue, 27 Jun 2017 15:51:09: 5000000 INFO @ Tue, 27 Jun 2017 15:51:11: 6000000 INFO @ Tue, 27 Jun 2017 15:51:16: 6000000 INFO @ Tue, 27 Jun 2017 15:51:16: 6000000 INFO @ Tue, 27 Jun 2017 15:51:17: 7000000 INFO @ Tue, 27 Jun 2017 15:51:24: 8000000 INFO @ Tue, 27 Jun 2017 15:51:24: 7000000 INFO @ Tue, 27 Jun 2017 15:51:24: 7000000 INFO @ Tue, 27 Jun 2017 15:51:30: 9000000 INFO @ Tue, 27 Jun 2017 15:51:31: 8000000 INFO @ Tue, 27 Jun 2017 15:51:31: 8000000 INFO @ Tue, 27 Jun 2017 15:51:36: 10000000 INFO @ Tue, 27 Jun 2017 15:51:38: 9000000 INFO @ Tue, 27 Jun 2017 15:51:38: 9000000 INFO @ Tue, 27 Jun 2017 15:51:42: 11000000 INFO @ Tue, 27 Jun 2017 15:51:46: 10000000 INFO @ Tue, 27 Jun 2017 15:51:46: 10000000 INFO @ Tue, 27 Jun 2017 15:51:48: 12000000 INFO @ Tue, 27 Jun 2017 15:51:52: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:51:52: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:51:52: #1 total tags in treatment: 5884377 INFO @ Tue, 27 Jun 2017 15:51:52: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:51:52: #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 15:51:52: #1 tags after filtering in treatment: 5399998 INFO @ Tue, 27 Jun 2017 15:51:52: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 27 Jun 2017 15:51:52: #1 finished! INFO @ Tue, 27 Jun 2017 15:51:52: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:51:52: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:51:53: 11000000 INFO @ Tue, 27 Jun 2017 15:51:53: 11000000 INFO @ Tue, 27 Jun 2017 15:51:53: #2 number of paired peaks: 5116 INFO @ Tue, 27 Jun 2017 15:51:53: start model_add_line... INFO @ Tue, 27 Jun 2017 15:51:53: start X-correlation... INFO @ Tue, 27 Jun 2017 15:51:53: end of X-cor INFO @ Tue, 27 Jun 2017 15:51:53: #2 finished! INFO @ Tue, 27 Jun 2017 15:51:53: #2 predicted fragment length is 213 bps INFO @ Tue, 27 Jun 2017 15:51:53: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 27 Jun 2017 15:51:53: #2.2 Generate R script for model : SRX1056717.10_model.r INFO @ Tue, 27 Jun 2017 15:51:53: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:51:53: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:52:00: 12000000 INFO @ Tue, 27 Jun 2017 15:52:00: 12000000 INFO @ Tue, 27 Jun 2017 15:52:05: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:52:05: #1 tag size is determined as 36 bps INFO @ Tue, 27 Jun 2017 15:52:05: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:52:05: #1 tag size = 36 INFO @ Tue, 27 Jun 2017 15:52:05: #1 total tags in treatment: 5884377 INFO @ Tue, 27 Jun 2017 15:52:05: #1 total tags in treatment: 5884377 INFO @ Tue, 27 Jun 2017 15:52:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:52:05: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:52:05: #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 15:52:05: #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 15:52:05: #1 tags after filtering in treatment: 5399998 INFO @ Tue, 27 Jun 2017 15:52:05: #1 tags after filtering in treatment: 5399998 INFO @ Tue, 27 Jun 2017 15:52:05: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 27 Jun 2017 15:52:05: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 27 Jun 2017 15:52:05: #1 finished! INFO @ Tue, 27 Jun 2017 15:52:05: #1 finished! INFO @ Tue, 27 Jun 2017 15:52:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:52:05: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:52:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:52:05: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:52:06: #2 number of paired peaks: 5116 INFO @ Tue, 27 Jun 2017 15:52:06: start model_add_line... INFO @ Tue, 27 Jun 2017 15:52:06: #2 number of paired peaks: 5116 INFO @ Tue, 27 Jun 2017 15:52:06: start model_add_line... INFO @ Tue, 27 Jun 2017 15:52:06: start X-correlation... INFO @ Tue, 27 Jun 2017 15:52:06: end of X-cor INFO @ Tue, 27 Jun 2017 15:52:06: #2 finished! INFO @ Tue, 27 Jun 2017 15:52:06: #2 predicted fragment length is 213 bps INFO @ Tue, 27 Jun 2017 15:52:06: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 27 Jun 2017 15:52:06: #2.2 Generate R script for model : SRX1056717.20_model.r INFO @ Tue, 27 Jun 2017 15:52:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:52:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:52:06: start X-correlation... INFO @ Tue, 27 Jun 2017 15:52:06: end of X-cor INFO @ Tue, 27 Jun 2017 15:52:06: #2 finished! INFO @ Tue, 27 Jun 2017 15:52:06: #2 predicted fragment length is 213 bps INFO @ Tue, 27 Jun 2017 15:52:06: #2 alternative fragment length(s) may be 213 bps INFO @ Tue, 27 Jun 2017 15:52:06: #2.2 Generate R script for model : SRX1056717.05_model.r INFO @ Tue, 27 Jun 2017 15:52:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:52:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:52:08: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:52:16: #4 Write output xls file... SRX1056717.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:52:16: #4 Write peak in narrowPeak format file... SRX1056717.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:52:16: #4 Write summits bed file... SRX1056717.10_summits.bed INFO @ Tue, 27 Jun 2017 15:52:16: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6856 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:52:22: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:52:22: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:52:30: #4 Write output xls file... SRX1056717.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:52:30: #4 Write peak in narrowPeak format file... SRX1056717.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:52:30: #4 Write summits bed file... SRX1056717.20_summits.bed INFO @ Tue, 27 Jun 2017 15:52:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (3107 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:52:31: #4 Write output xls file... SRX1056717.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:52:31: #4 Write peak in narrowPeak format file... SRX1056717.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:52:31: #4 Write summits bed file... SRX1056717.05_summits.bed INFO @ Tue, 27 Jun 2017 15:52:31: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10802 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。