Job ID = 10480688 sra ファイルのダウンロード中... Completed: 387698K bytes transferred in 6 seconds (502496K 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 11374515 spots for /home/okishinya/chipatlas/results/dm3/SRX3068959/SRR6490544.sra Written 11374515 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: 00:01:55 11374515 reads; of these: 11374515 (100.00%) were unpaired; of these: 5701818 (50.13%) aligned 0 times 5406745 (47.53%) aligned exactly 1 time 265952 (2.34%) aligned >1 times 49.87% overall alignment rate Time searching: 00:01:55 Overall time: 00:01:55 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] 1718382 / 5672697 = 0.3029 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 @ Fri, 16 Mar 2018 07:39:54: # Command line: callpeak -t SRX3068959.bam -f BAM -g dm -n SRX3068959.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068959.10 # format = BAM # ChIP-seq file = ['SRX3068959.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 @ Fri, 16 Mar 2018 07:39:54: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:54: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:54: # Command line: callpeak -t SRX3068959.bam -f BAM -g dm -n SRX3068959.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068959.05 # format = BAM # ChIP-seq file = ['SRX3068959.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 @ Fri, 16 Mar 2018 07:39:54: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:54: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:39:54: # Command line: callpeak -t SRX3068959.bam -f BAM -g dm -n SRX3068959.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068959.20 # format = BAM # ChIP-seq file = ['SRX3068959.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 @ Fri, 16 Mar 2018 07:39:54: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:39:54: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:40:01: 1000000 INFO @ Fri, 16 Mar 2018 07:40:01: 1000000 INFO @ Fri, 16 Mar 2018 07:40:01: 1000000 INFO @ Fri, 16 Mar 2018 07:40:07: 2000000 INFO @ Fri, 16 Mar 2018 07:40:07: 2000000 INFO @ Fri, 16 Mar 2018 07:40:08: 2000000 INFO @ Fri, 16 Mar 2018 07:40:14: 3000000 INFO @ Fri, 16 Mar 2018 07:40:14: 3000000 INFO @ Fri, 16 Mar 2018 07:40:15: 3000000 INFO @ Fri, 16 Mar 2018 07:40:21: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:40:21: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:40:21: #1 total tags in treatment: 3954315 INFO @ Fri, 16 Mar 2018 07:40:21: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:40:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:40:21: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:40:21: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:40:21: #1 total tags in treatment: 3954315 INFO @ Fri, 16 Mar 2018 07:40:21: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:40:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:40:21: #1 tags after filtering in treatment: 3954315 INFO @ Fri, 16 Mar 2018 07:40:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:40:21: #1 finished! INFO @ Fri, 16 Mar 2018 07:40:21: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:40:21: #1 tags after filtering in treatment: 3954315 INFO @ Fri, 16 Mar 2018 07:40:21: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:40:21: #1 finished! INFO @ Fri, 16 Mar 2018 07:40:21: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:40:21: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:40:21: #2 number of paired peaks: 7294 INFO @ Fri, 16 Mar 2018 07:40:21: start model_add_line... INFO @ Fri, 16 Mar 2018 07:40:21: #2 number of paired peaks: 7294 INFO @ Fri, 16 Mar 2018 07:40:21: start model_add_line... INFO @ Fri, 16 Mar 2018 07:40:21: start X-correlation... INFO @ Fri, 16 Mar 2018 07:40:21: end of X-cor INFO @ Fri, 16 Mar 2018 07:40:21: #2 finished! INFO @ Fri, 16 Mar 2018 07:40:21: #2 predicted fragment length is 153 bps INFO @ Fri, 16 Mar 2018 07:40:21: #2 alternative fragment length(s) may be 153 bps INFO @ Fri, 16 Mar 2018 07:40:21: #2.2 Generate R script for model : SRX3068959.10_model.r INFO @ Fri, 16 Mar 2018 07:40:21: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:40:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:40:22: start X-correlation... INFO @ Fri, 16 Mar 2018 07:40:22: end of X-cor INFO @ Fri, 16 Mar 2018 07:40:22: #2 finished! INFO @ Fri, 16 Mar 2018 07:40:22: #2 predicted fragment length is 153 bps INFO @ Fri, 16 Mar 2018 07:40:22: #2 alternative fragment length(s) may be 153 bps INFO @ Fri, 16 Mar 2018 07:40:22: #2.2 Generate R script for model : SRX3068959.05_model.r INFO @ Fri, 16 Mar 2018 07:40:22: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:40:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:40:22: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:40:22: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:40:22: #1 total tags in treatment: 3954315 INFO @ Fri, 16 Mar 2018 07:40:22: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:40:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 16 Mar 2018 07:40:22: #1 tags after filtering in treatment: 3954315 INFO @ Fri, 16 Mar 2018 07:40:22: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:40:22: #1 finished! INFO @ Fri, 16 Mar 2018 07:40:22: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:40:22: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:40:23: #2 number of paired peaks: 7294 INFO @ Fri, 16 Mar 2018 07:40:23: start model_add_line... INFO @ Fri, 16 Mar 2018 07:40:23: start X-correlation... INFO @ Fri, 16 Mar 2018 07:40:23: end of X-cor INFO @ Fri, 16 Mar 2018 07:40:23: #2 finished! INFO @ Fri, 16 Mar 2018 07:40:23: #2 predicted fragment length is 153 bps INFO @ Fri, 16 Mar 2018 07:40:23: #2 alternative fragment length(s) may be 153 bps INFO @ Fri, 16 Mar 2018 07:40:23: #2.2 Generate R script for model : SRX3068959.20_model.r INFO @ Fri, 16 Mar 2018 07:40:23: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:40:23: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:40:33: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:40:33: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:40:34: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:40:39: #4 Write output xls file... SRX3068959.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:40:39: #4 Write peak in narrowPeak format file... SRX3068959.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:40:39: #4 Write summits bed file... SRX3068959.10_summits.bed INFO @ Fri, 16 Mar 2018 07:40:39: Done! pass1 - making usageList (12 chroms): 2 millis pass2 - checking and writing primary data (6716 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:40:41: #4 Write output xls file... SRX3068959.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:40:41: #4 Write output xls file... SRX3068959.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:40:41: #4 Write peak in narrowPeak format file... SRX3068959.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:40:41: #4 Write summits bed file... SRX3068959.20_summits.bed INFO @ Fri, 16 Mar 2018 07:40:41: #4 Write peak in narrowPeak format file... SRX3068959.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:40:41: Done! INFO @ Fri, 16 Mar 2018 07:40:41: #4 Write summits bed file... SRX3068959.05_summits.bed pass1 - making usageList (10 chroms): 2 millis pass2 - checking and writing primary data (4131 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:40:41: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (9403 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。