Job ID = 9157941 sra ファイルのダウンロード中... Completed: 304681K bytes transferred in 5 seconds (447166K 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: SINGLE fastq に変換中... Written 10706947 spots for /home/okishinya/chipatlas/results/dm3/SRX2033489/SRR4042504.sra Written 10706947 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: 00:03:20 10706947 reads; of these: 10706947 (100.00%) were unpaired; of these: 786513 (7.35%) aligned 0 times 7463592 (69.71%) aligned exactly 1 time 2456842 (22.95%) aligned >1 times 92.65% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 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_rmdupse_core] 3885487 / 9920434 = 0.3917 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 14:16:34: # Command line: callpeak -t SRX2033489.bam -f BAM -g dm -n SRX2033489.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2033489.20 # format = BAM # ChIP-seq file = ['SRX2033489.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 14:16:34: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:16:34: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:16:34: # Command line: callpeak -t SRX2033489.bam -f BAM -g dm -n SRX2033489.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2033489.05 # format = BAM # ChIP-seq file = ['SRX2033489.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 14:16:34: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:16:34: # Command line: callpeak -t SRX2033489.bam -f BAM -g dm -n SRX2033489.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2033489.10 # format = BAM # ChIP-seq file = ['SRX2033489.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 14:16:34: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:16:34: #1 read tag files... INFO @ Tue, 27 Jun 2017 14:16:34: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 14:16:42: 1000000 INFO @ Tue, 27 Jun 2017 14:16:42: 1000000 INFO @ Tue, 27 Jun 2017 14:16:42: 1000000 INFO @ Tue, 27 Jun 2017 14:16:50: 2000000 INFO @ Tue, 27 Jun 2017 14:16:50: 2000000 INFO @ Tue, 27 Jun 2017 14:16:50: 2000000 INFO @ Tue, 27 Jun 2017 14:16:57: 3000000 INFO @ Tue, 27 Jun 2017 14:16:59: 3000000 INFO @ Tue, 27 Jun 2017 14:16:59: 3000000 INFO @ Tue, 27 Jun 2017 14:17:05: 4000000 INFO @ Tue, 27 Jun 2017 14:17:07: 4000000 INFO @ Tue, 27 Jun 2017 14:17:07: 4000000 INFO @ Tue, 27 Jun 2017 14:17:13: 5000000 INFO @ Tue, 27 Jun 2017 14:17:15: 5000000 INFO @ Tue, 27 Jun 2017 14:17:15: 5000000 INFO @ Tue, 27 Jun 2017 14:17:21: 6000000 INFO @ Tue, 27 Jun 2017 14:17:21: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:17:21: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:17:21: #1 total tags in treatment: 6034947 INFO @ Tue, 27 Jun 2017 14:17:21: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:17:21: #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 14:17:21: #1 tags after filtering in treatment: 6034947 INFO @ Tue, 27 Jun 2017 14:17:21: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:17:21: #1 finished! INFO @ Tue, 27 Jun 2017 14:17:21: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:17:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:17:22: #2 number of paired peaks: 4599 INFO @ Tue, 27 Jun 2017 14:17:22: start model_add_line... INFO @ Tue, 27 Jun 2017 14:17:22: start X-correlation... INFO @ Tue, 27 Jun 2017 14:17:22: end of X-cor INFO @ Tue, 27 Jun 2017 14:17:22: #2 finished! INFO @ Tue, 27 Jun 2017 14:17:22: #2 predicted fragment length is 152 bps INFO @ Tue, 27 Jun 2017 14:17:22: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 27 Jun 2017 14:17:22: #2.2 Generate R script for model : SRX2033489.20_model.r INFO @ Tue, 27 Jun 2017 14:17:22: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:17:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:17:24: 6000000 INFO @ Tue, 27 Jun 2017 14:17:24: 6000000 INFO @ Tue, 27 Jun 2017 14:17:24: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:17:24: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:17:24: #1 total tags in treatment: 6034947 INFO @ Tue, 27 Jun 2017 14:17:24: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:17:24: #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 14:17:24: #1 tag size is determined as 51 bps INFO @ Tue, 27 Jun 2017 14:17:24: #1 tag size = 51 INFO @ Tue, 27 Jun 2017 14:17:24: #1 total tags in treatment: 6034947 INFO @ Tue, 27 Jun 2017 14:17:24: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 14:17:24: #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 14:17:24: #1 tags after filtering in treatment: 6034947 INFO @ Tue, 27 Jun 2017 14:17:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:17:24: #1 finished! INFO @ Tue, 27 Jun 2017 14:17:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:17:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:17:24: #1 tags after filtering in treatment: 6034947 INFO @ Tue, 27 Jun 2017 14:17:24: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 14:17:24: #1 finished! INFO @ Tue, 27 Jun 2017 14:17:24: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 14:17:24: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 14:17:25: #2 number of paired peaks: 4599 INFO @ Tue, 27 Jun 2017 14:17:25: start model_add_line... INFO @ Tue, 27 Jun 2017 14:17:25: #2 number of paired peaks: 4599 INFO @ Tue, 27 Jun 2017 14:17:25: start model_add_line... INFO @ Tue, 27 Jun 2017 14:17:25: start X-correlation... INFO @ Tue, 27 Jun 2017 14:17:25: end of X-cor INFO @ Tue, 27 Jun 2017 14:17:25: #2 finished! INFO @ Tue, 27 Jun 2017 14:17:25: #2 predicted fragment length is 152 bps INFO @ Tue, 27 Jun 2017 14:17:25: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 27 Jun 2017 14:17:25: #2.2 Generate R script for model : SRX2033489.05_model.r INFO @ Tue, 27 Jun 2017 14:17:25: start X-correlation... INFO @ Tue, 27 Jun 2017 14:17:25: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:17:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:17:25: end of X-cor INFO @ Tue, 27 Jun 2017 14:17:25: #2 finished! INFO @ Tue, 27 Jun 2017 14:17:25: #2 predicted fragment length is 152 bps INFO @ Tue, 27 Jun 2017 14:17:25: #2 alternative fragment length(s) may be 152 bps INFO @ Tue, 27 Jun 2017 14:17:25: #2.2 Generate R script for model : SRX2033489.10_model.r INFO @ Tue, 27 Jun 2017 14:17:25: #3 Call peaks... INFO @ Tue, 27 Jun 2017 14:17:25: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 14:17:40: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:17:42: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:17:43: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 14:17:49: #4 Write output xls file... SRX2033489.20_peaks.xls INFO @ Tue, 27 Jun 2017 14:17:49: #4 Write peak in narrowPeak format file... SRX2033489.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:17:49: #4 Write summits bed file... SRX2033489.20_summits.bed INFO @ Tue, 27 Jun 2017 14:17:49: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (4935 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:17:53: #4 Write output xls file... SRX2033489.10_peaks.xls INFO @ Tue, 27 Jun 2017 14:17:53: #4 Write peak in narrowPeak format file... SRX2033489.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:17:53: #4 Write summits bed file... SRX2033489.10_summits.bed INFO @ Tue, 27 Jun 2017 14:17:53: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8052 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 14:17:53: #4 Write output xls file... SRX2033489.05_peaks.xls INFO @ Tue, 27 Jun 2017 14:17:53: #4 Write peak in narrowPeak format file... SRX2033489.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 14:17:53: #4 Write summits bed file... SRX2033489.05_summits.bed INFO @ Tue, 27 Jun 2017 14:17:54: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (10770 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。