Job ID = 10175306 sra ファイルのダウンロード中... Completed: 133904K bytes transferred in 5 seconds (192800K bits/sec), in 1 file. 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 8165316 spots for /home/okishinya/chipatlas/results/dm3/SRX3170979/SRR6019826.sra Written 8165316 spots total rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:02:17 8165316 reads; of these: 8165316 (100.00%) were unpaired; of these: 271916 (3.33%) aligned 0 times 6615115 (81.01%) aligned exactly 1 time 1278285 (15.66%) aligned >1 times 96.67% overall alignment rate Time searching: 00:02:17 Overall time: 00:02:17 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_rmdupse_core] 1962116 / 7893400 = 0.2486 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 @ Mon, 06 Nov 2017 12:26:20: # Command line: callpeak -t SRX3170979.bam -f BAM -g dm -n SRX3170979.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3170979.10 # format = BAM # ChIP-seq file = ['SRX3170979.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 @ Mon, 06 Nov 2017 12:26:20: # Command line: callpeak -t SRX3170979.bam -f BAM -g dm -n SRX3170979.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3170979.05 # format = BAM # ChIP-seq file = ['SRX3170979.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 @ Mon, 06 Nov 2017 12:26:20: # Command line: callpeak -t SRX3170979.bam -f BAM -g dm -n SRX3170979.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3170979.20 # format = BAM # ChIP-seq file = ['SRX3170979.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 @ Mon, 06 Nov 2017 12:26:20: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:26:20: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:26:20: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:26:20: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:26:20: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:26:20: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:26:27: 1000000 INFO @ Mon, 06 Nov 2017 12:26:27: 1000000 INFO @ Mon, 06 Nov 2017 12:26:27: 1000000 INFO @ Mon, 06 Nov 2017 12:26:33: 2000000 INFO @ Mon, 06 Nov 2017 12:26:33: 2000000 INFO @ Mon, 06 Nov 2017 12:26:33: 2000000 INFO @ Mon, 06 Nov 2017 12:26:40: 3000000 INFO @ Mon, 06 Nov 2017 12:26:40: 3000000 INFO @ Mon, 06 Nov 2017 12:26:40: 3000000 INFO @ Mon, 06 Nov 2017 12:26:46: 4000000 INFO @ Mon, 06 Nov 2017 12:26:47: 4000000 INFO @ Mon, 06 Nov 2017 12:26:47: 4000000 INFO @ Mon, 06 Nov 2017 12:26:53: 5000000 INFO @ Mon, 06 Nov 2017 12:26:53: 5000000 INFO @ Mon, 06 Nov 2017 12:26:54: 5000000 INFO @ Mon, 06 Nov 2017 12:26:59: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:26:59: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:26:59: #1 total tags in treatment: 5931284 INFO @ Mon, 06 Nov 2017 12:26:59: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:26:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:26:59: #1 tags after filtering in treatment: 5931284 INFO @ Mon, 06 Nov 2017 12:26:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:26:59: #1 finished! INFO @ Mon, 06 Nov 2017 12:26:59: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:26:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:26:59: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:26:59: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:26:59: #1 total tags in treatment: 5931284 INFO @ Mon, 06 Nov 2017 12:26:59: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:26:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:27:00: #1 tags after filtering in treatment: 5931284 INFO @ Mon, 06 Nov 2017 12:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:27:00: #1 finished! INFO @ Mon, 06 Nov 2017 12:27:00: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:27:00: #2 number of paired peaks: 7909 INFO @ Mon, 06 Nov 2017 12:27:00: start model_add_line... INFO @ Mon, 06 Nov 2017 12:27:00: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:27:00: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:27:00: #1 total tags in treatment: 5931284 INFO @ Mon, 06 Nov 2017 12:27:00: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:27:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:27:00: start X-correlation... INFO @ Mon, 06 Nov 2017 12:27:00: #1 tags after filtering in treatment: 5931284 INFO @ Mon, 06 Nov 2017 12:27:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:27:00: #1 finished! INFO @ Mon, 06 Nov 2017 12:27:00: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:27:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:27:00: end of X-cor INFO @ Mon, 06 Nov 2017 12:27:00: #2 finished! INFO @ Mon, 06 Nov 2017 12:27:00: #2 predicted fragment length is 171 bps INFO @ Mon, 06 Nov 2017 12:27:00: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 06 Nov 2017 12:27:00: #2.2 Generate R script for model : SRX3170979.10_model.r INFO @ Mon, 06 Nov 2017 12:27:00: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:27:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:27:01: #2 number of paired peaks: 7909 INFO @ Mon, 06 Nov 2017 12:27:01: start model_add_line... INFO @ Mon, 06 Nov 2017 12:27:01: start X-correlation... INFO @ Mon, 06 Nov 2017 12:27:01: end of X-cor INFO @ Mon, 06 Nov 2017 12:27:01: #2 finished! INFO @ Mon, 06 Nov 2017 12:27:01: #2 predicted fragment length is 171 bps INFO @ Mon, 06 Nov 2017 12:27:01: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 06 Nov 2017 12:27:01: #2.2 Generate R script for model : SRX3170979.05_model.r INFO @ Mon, 06 Nov 2017 12:27:01: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:27:01: #2 number of paired peaks: 7909 INFO @ Mon, 06 Nov 2017 12:27:01: start model_add_line... INFO @ Mon, 06 Nov 2017 12:27:01: start X-correlation... INFO @ Mon, 06 Nov 2017 12:27:01: end of X-cor INFO @ Mon, 06 Nov 2017 12:27:01: #2 finished! INFO @ Mon, 06 Nov 2017 12:27:01: #2 predicted fragment length is 171 bps INFO @ Mon, 06 Nov 2017 12:27:01: #2 alternative fragment length(s) may be 171 bps INFO @ Mon, 06 Nov 2017 12:27:01: #2.2 Generate R script for model : SRX3170979.20_model.r INFO @ Mon, 06 Nov 2017 12:27:01: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:27:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:27:18: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:27:19: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:27:19: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:27:27: #4 Write output xls file... SRX3170979.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:27:27: #4 Write peak in narrowPeak format file... SRX3170979.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:27:27: #4 Write summits bed file... SRX3170979.10_summits.bed INFO @ Mon, 06 Nov 2017 12:27:27: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (4307 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:27:27: #4 Write output xls file... SRX3170979.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:27:27: #4 Write peak in narrowPeak format file... SRX3170979.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:27:28: #4 Write summits bed file... SRX3170979.20_summits.bed INFO @ Mon, 06 Nov 2017 12:27:28: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (1432 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:27:28: #4 Write output xls file... SRX3170979.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:27:28: #4 Write peak in narrowPeak format file... SRX3170979.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:27:28: #4 Write summits bed file... SRX3170979.05_summits.bed INFO @ Mon, 06 Nov 2017 12:27:29: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (8347 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。