Job ID = 10175226 sra ファイルのダウンロード中... Completed: 184357K bytes transferred in 6 seconds (248006K 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 11305060 spots for /home/okishinya/chipatlas/results/dm3/SRX2458929/SRR5140278.sra Written 11305060 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: 00:04:47 11305060 reads; of these: 11305060 (100.00%) were unpaired; of these: 519532 (4.60%) aligned 0 times 7991755 (70.69%) aligned exactly 1 time 2793773 (24.71%) aligned >1 times 95.40% overall alignment rate Time searching: 00:04:47 Overall time: 00:04:47 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] 7045501 / 10785528 = 0.6532 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 11:48:49: # Command line: callpeak -t SRX2458929.bam -f BAM -g dm -n SRX2458929.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2458929.05 # format = BAM # ChIP-seq file = ['SRX2458929.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 11:48:49: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:48:49: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:48:49: # Command line: callpeak -t SRX2458929.bam -f BAM -g dm -n SRX2458929.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2458929.10 # format = BAM # ChIP-seq file = ['SRX2458929.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 11:48:49: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:48:49: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:48:49: # Command line: callpeak -t SRX2458929.bam -f BAM -g dm -n SRX2458929.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2458929.20 # format = BAM # ChIP-seq file = ['SRX2458929.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 11:48:49: #1 read tag files... INFO @ Mon, 06 Nov 2017 11:48:49: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 11:48:57: 1000000 INFO @ Mon, 06 Nov 2017 11:48:57: 1000000 INFO @ Mon, 06 Nov 2017 11:48:57: 1000000 INFO @ Mon, 06 Nov 2017 11:49:04: 2000000 INFO @ Mon, 06 Nov 2017 11:49:04: 2000000 INFO @ Mon, 06 Nov 2017 11:49:05: 2000000 INFO @ Mon, 06 Nov 2017 11:49:11: 3000000 INFO @ Mon, 06 Nov 2017 11:49:12: 3000000 INFO @ Mon, 06 Nov 2017 11:49:12: 3000000 INFO @ Mon, 06 Nov 2017 11:49:16: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:49:16: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:49:16: #1 total tags in treatment: 3740027 INFO @ Mon, 06 Nov 2017 11:49:16: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:49:16: #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 11:49:16: #1 tags after filtering in treatment: 3740027 INFO @ Mon, 06 Nov 2017 11:49:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:49:16: #1 finished! INFO @ Mon, 06 Nov 2017 11:49:16: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:49:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:49:17: #2 number of paired peaks: 1510 INFO @ Mon, 06 Nov 2017 11:49:17: start model_add_line... INFO @ Mon, 06 Nov 2017 11:49:17: start X-correlation... INFO @ Mon, 06 Nov 2017 11:49:17: end of X-cor INFO @ Mon, 06 Nov 2017 11:49:17: #2 finished! INFO @ Mon, 06 Nov 2017 11:49:17: #2 predicted fragment length is 101 bps INFO @ Mon, 06 Nov 2017 11:49:17: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 06 Nov 2017 11:49:17: #2.2 Generate R script for model : SRX2458929.20_model.r INFO @ Mon, 06 Nov 2017 11:49:17: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:49:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:49:17: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:49:17: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:49:17: #1 total tags in treatment: 3740027 INFO @ Mon, 06 Nov 2017 11:49:17: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:49:17: #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 11:49:17: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 11:49:17: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 11:49:17: #1 total tags in treatment: 3740027 INFO @ Mon, 06 Nov 2017 11:49:17: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 11:49:17: #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 11:49:17: #1 tags after filtering in treatment: 3740027 INFO @ Mon, 06 Nov 2017 11:49:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:49:17: #1 finished! INFO @ Mon, 06 Nov 2017 11:49:17: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:49:17: #1 tags after filtering in treatment: 3740027 INFO @ Mon, 06 Nov 2017 11:49:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 11:49:17: #1 finished! INFO @ Mon, 06 Nov 2017 11:49:17: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 11:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 11:49:17: #2 number of paired peaks: 1510 INFO @ Mon, 06 Nov 2017 11:49:17: start model_add_line... INFO @ Mon, 06 Nov 2017 11:49:17: #2 number of paired peaks: 1510 INFO @ Mon, 06 Nov 2017 11:49:17: start model_add_line... INFO @ Mon, 06 Nov 2017 11:49:17: start X-correlation... INFO @ Mon, 06 Nov 2017 11:49:17: end of X-cor INFO @ Mon, 06 Nov 2017 11:49:17: #2 finished! INFO @ Mon, 06 Nov 2017 11:49:17: #2 predicted fragment length is 101 bps INFO @ Mon, 06 Nov 2017 11:49:17: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 06 Nov 2017 11:49:17: #2.2 Generate R script for model : SRX2458929.10_model.r INFO @ Mon, 06 Nov 2017 11:49:17: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:49:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:49:17: start X-correlation... INFO @ Mon, 06 Nov 2017 11:49:17: end of X-cor INFO @ Mon, 06 Nov 2017 11:49:17: #2 finished! INFO @ Mon, 06 Nov 2017 11:49:17: #2 predicted fragment length is 101 bps INFO @ Mon, 06 Nov 2017 11:49:17: #2 alternative fragment length(s) may be 101 bps INFO @ Mon, 06 Nov 2017 11:49:17: #2.2 Generate R script for model : SRX2458929.05_model.r INFO @ Mon, 06 Nov 2017 11:49:17: #3 Call peaks... INFO @ Mon, 06 Nov 2017 11:49:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 11:49:25: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:49:26: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:49:27: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 11:49:30: #4 Write output xls file... SRX2458929.20_peaks.xls INFO @ Mon, 06 Nov 2017 11:49:30: #4 Write peak in narrowPeak format file... SRX2458929.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:49:30: #4 Write summits bed file... SRX2458929.20_summits.bed INFO @ Mon, 06 Nov 2017 11:49:30: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (419 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 11:49:31: #4 Write output xls file... SRX2458929.10_peaks.xls INFO @ Mon, 06 Nov 2017 11:49:31: #4 Write peak in narrowPeak format file... SRX2458929.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:49:32: #4 Write summits bed file... SRX2458929.10_summits.bed INFO @ Mon, 06 Nov 2017 11:49:32: Done! INFO @ Mon, 06 Nov 2017 11:49:32: #4 Write output xls file... SRX2458929.05_peaks.xls INFO @ Mon, 06 Nov 2017 11:49:32: #4 Write peak in narrowPeak format file... SRX2458929.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 11:49:32: #4 Write summits bed file... SRX2458929.05_summits.bed pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1070 records, 4 fields): 3 millis INFO @ Mon, 06 Nov 2017 11:49:32: Done! CompletedMACS2peakCalling pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2035 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。