Job ID = 10480705 sra ファイルのダウンロード中... Completed: 296195K bytes transferred in 29 seconds (81800K 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 9648594 spots for /home/okishinya/chipatlas/results/dm3/SRX3068976/SRR5907452.sra Written 9648594 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: 00:02:53 9648594 reads; of these: 9648594 (100.00%) were unpaired; of these: 1184761 (12.28%) aligned 0 times 7115865 (73.75%) aligned exactly 1 time 1347968 (13.97%) aligned >1 times 87.72% overall alignment rate Time searching: 00:02:53 Overall time: 00:02:53 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] 2682656 / 8463833 = 0.3170 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 07:46:06: # Command line: callpeak -t SRX3068976.bam -f BAM -g dm -n SRX3068976.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068976.20 # format = BAM # ChIP-seq file = ['SRX3068976.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 07:46:06: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:46:06: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:46:06: # Command line: callpeak -t SRX3068976.bam -f BAM -g dm -n SRX3068976.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068976.05 # format = BAM # ChIP-seq file = ['SRX3068976.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 07:46:06: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:46:06: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:46:06: # Command line: callpeak -t SRX3068976.bam -f BAM -g dm -n SRX3068976.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068976.10 # format = BAM # ChIP-seq file = ['SRX3068976.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 07:46:06: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:46:06: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:46:12: 1000000 INFO @ Fri, 16 Mar 2018 07:46:12: 1000000 INFO @ Fri, 16 Mar 2018 07:46:12: 1000000 INFO @ Fri, 16 Mar 2018 07:46:18: 2000000 INFO @ Fri, 16 Mar 2018 07:46:19: 2000000 INFO @ Fri, 16 Mar 2018 07:46:19: 2000000 INFO @ Fri, 16 Mar 2018 07:46:25: 3000000 INFO @ Fri, 16 Mar 2018 07:46:25: 3000000 INFO @ Fri, 16 Mar 2018 07:46:26: 3000000 INFO @ Fri, 16 Mar 2018 07:46:32: 4000000 INFO @ Fri, 16 Mar 2018 07:46:32: 4000000 INFO @ Fri, 16 Mar 2018 07:46:32: 4000000 INFO @ Fri, 16 Mar 2018 07:46:38: 5000000 INFO @ Fri, 16 Mar 2018 07:46:39: 5000000 INFO @ Fri, 16 Mar 2018 07:46:39: 5000000 INFO @ Fri, 16 Mar 2018 07:46:43: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:46:43: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:46:43: #1 total tags in treatment: 5781177 INFO @ Fri, 16 Mar 2018 07:46:43: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:46:43: #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 07:46:43: #1 tags after filtering in treatment: 5781177 INFO @ Fri, 16 Mar 2018 07:46:43: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:46:43: #1 finished! INFO @ Fri, 16 Mar 2018 07:46:43: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:46:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:46:44: #2 number of paired peaks: 1641 INFO @ Fri, 16 Mar 2018 07:46:44: start model_add_line... INFO @ Fri, 16 Mar 2018 07:46:44: start X-correlation... INFO @ Fri, 16 Mar 2018 07:46:44: end of X-cor INFO @ Fri, 16 Mar 2018 07:46:44: #2 finished! INFO @ Fri, 16 Mar 2018 07:46:44: #2 predicted fragment length is 172 bps INFO @ Fri, 16 Mar 2018 07:46:44: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 16 Mar 2018 07:46:44: #2.2 Generate R script for model : SRX3068976.05_model.r INFO @ Fri, 16 Mar 2018 07:46:44: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:46:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:46:44: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:46:44: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:46:44: #1 total tags in treatment: 5781177 INFO @ Fri, 16 Mar 2018 07:46:44: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:46:44: #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 07:46:44: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:46:44: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:46:44: #1 total tags in treatment: 5781177 INFO @ Fri, 16 Mar 2018 07:46:44: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:46:44: #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 07:46:44: #1 tags after filtering in treatment: 5781177 INFO @ Fri, 16 Mar 2018 07:46:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:46:44: #1 finished! INFO @ Fri, 16 Mar 2018 07:46:44: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:46:44: #1 tags after filtering in treatment: 5781177 INFO @ Fri, 16 Mar 2018 07:46:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:46:44: #1 finished! INFO @ Fri, 16 Mar 2018 07:46:44: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:46:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:46:45: #2 number of paired peaks: 1641 INFO @ Fri, 16 Mar 2018 07:46:45: start model_add_line... INFO @ Fri, 16 Mar 2018 07:46:45: #2 number of paired peaks: 1641 INFO @ Fri, 16 Mar 2018 07:46:45: start model_add_line... INFO @ Fri, 16 Mar 2018 07:46:45: start X-correlation... INFO @ Fri, 16 Mar 2018 07:46:45: end of X-cor INFO @ Fri, 16 Mar 2018 07:46:45: #2 finished! INFO @ Fri, 16 Mar 2018 07:46:45: #2 predicted fragment length is 172 bps INFO @ Fri, 16 Mar 2018 07:46:45: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 16 Mar 2018 07:46:45: #2.2 Generate R script for model : SRX3068976.10_model.r INFO @ Fri, 16 Mar 2018 07:46:45: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:46:45: start X-correlation... INFO @ Fri, 16 Mar 2018 07:46:45: end of X-cor INFO @ Fri, 16 Mar 2018 07:46:45: #2 finished! INFO @ Fri, 16 Mar 2018 07:46:45: #2 predicted fragment length is 172 bps INFO @ Fri, 16 Mar 2018 07:46:45: #2 alternative fragment length(s) may be 172 bps INFO @ Fri, 16 Mar 2018 07:46:45: #2.2 Generate R script for model : SRX3068976.20_model.r INFO @ Fri, 16 Mar 2018 07:46:45: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:46:45: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:46:58: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:00: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:00: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:47:06: #4 Write output xls file... SRX3068976.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:07: #4 Write peak in narrowPeak format file... SRX3068976.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:07: #4 Write summits bed file... SRX3068976.05_summits.bed INFO @ Fri, 16 Mar 2018 07:47:07: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5610 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:47:07: #4 Write output xls file... SRX3068976.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:07: #4 Write peak in narrowPeak format file... SRX3068976.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:07: #4 Write summits bed file... SRX3068976.20_summits.bed INFO @ Fri, 16 Mar 2018 07:47:07: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (1457 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:47:08: #4 Write output xls file... SRX3068976.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:47:08: #4 Write peak in narrowPeak format file... SRX3068976.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:47:08: #4 Write summits bed file... SRX3068976.10_summits.bed INFO @ Fri, 16 Mar 2018 07:47:08: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (3191 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。