Job ID = 10480709 sra ファイルのダウンロード中... Completed: 465127K bytes transferred in 40 seconds (95015K 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 15073686 spots for /home/okishinya/chipatlas/results/dm3/SRX3068980/SRR5907456.sra Written 15073686 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: 00:04:41 15073686 reads; of these: 15073686 (100.00%) were unpaired; of these: 1096612 (7.28%) aligned 0 times 11839283 (78.54%) aligned exactly 1 time 2137791 (14.18%) aligned >1 times 92.72% overall alignment rate Time searching: 00:04:41 Overall time: 00:04:41 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] 4901310 / 13977074 = 0.3507 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 07:50:22: # Command line: callpeak -t SRX3068980.bam -f BAM -g dm -n SRX3068980.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3068980.20 # format = BAM # ChIP-seq file = ['SRX3068980.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 07:50:22: # Command line: callpeak -t SRX3068980.bam -f BAM -g dm -n SRX3068980.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3068980.10 # format = BAM # ChIP-seq file = ['SRX3068980.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 07:50:22: # Command line: callpeak -t SRX3068980.bam -f BAM -g dm -n SRX3068980.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3068980.05 # format = BAM # ChIP-seq file = ['SRX3068980.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 07:50:22: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:50:22: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:50:22: #1 read tag files... INFO @ Fri, 16 Mar 2018 07:50:22: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:50:22: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:50:22: #1 read treatment tags... INFO @ Fri, 16 Mar 2018 07:50:30: 1000000 INFO @ Fri, 16 Mar 2018 07:50:30: 1000000 INFO @ Fri, 16 Mar 2018 07:50:30: 1000000 INFO @ Fri, 16 Mar 2018 07:50:38: 2000000 INFO @ Fri, 16 Mar 2018 07:50:38: 2000000 INFO @ Fri, 16 Mar 2018 07:50:38: 2000000 INFO @ Fri, 16 Mar 2018 07:50:45: 3000000 INFO @ Fri, 16 Mar 2018 07:50:45: 3000000 INFO @ Fri, 16 Mar 2018 07:50:45: 3000000 INFO @ Fri, 16 Mar 2018 07:50:53: 4000000 INFO @ Fri, 16 Mar 2018 07:50:53: 4000000 INFO @ Fri, 16 Mar 2018 07:50:53: 4000000 INFO @ Fri, 16 Mar 2018 07:51:00: 5000000 INFO @ Fri, 16 Mar 2018 07:51:00: 5000000 INFO @ Fri, 16 Mar 2018 07:51:01: 5000000 INFO @ Fri, 16 Mar 2018 07:51:08: 6000000 INFO @ Fri, 16 Mar 2018 07:51:08: 6000000 INFO @ Fri, 16 Mar 2018 07:51:08: 6000000 INFO @ Fri, 16 Mar 2018 07:51:16: 7000000 INFO @ Fri, 16 Mar 2018 07:51:16: 7000000 INFO @ Fri, 16 Mar 2018 07:51:16: 7000000 INFO @ Fri, 16 Mar 2018 07:51:23: 8000000 INFO @ Fri, 16 Mar 2018 07:51:23: 8000000 INFO @ Fri, 16 Mar 2018 07:51:23: 8000000 INFO @ Fri, 16 Mar 2018 07:51:31: 9000000 INFO @ Fri, 16 Mar 2018 07:51:31: 9000000 INFO @ Fri, 16 Mar 2018 07:51:31: 9000000 INFO @ Fri, 16 Mar 2018 07:51:32: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:51:32: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:51:32: #1 total tags in treatment: 9075764 INFO @ Fri, 16 Mar 2018 07:51:32: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:51:32: #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 07:51:32: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:51:32: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:51:32: #1 total tags in treatment: 9075764 INFO @ Fri, 16 Mar 2018 07:51:32: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:51:32: #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 07:51:32: #1 tag size is determined as 51 bps INFO @ Fri, 16 Mar 2018 07:51:32: #1 tag size = 51 INFO @ Fri, 16 Mar 2018 07:51:32: #1 total tags in treatment: 9075764 INFO @ Fri, 16 Mar 2018 07:51:32: #1 user defined the maximum tags... INFO @ Fri, 16 Mar 2018 07:51:32: #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 07:51:32: #1 tags after filtering in treatment: 9075764 INFO @ Fri, 16 Mar 2018 07:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:51:32: #1 finished! INFO @ Fri, 16 Mar 2018 07:51:32: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:51:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:51:32: #1 tags after filtering in treatment: 9075764 INFO @ Fri, 16 Mar 2018 07:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:51:32: #1 finished! INFO @ Fri, 16 Mar 2018 07:51:32: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:51:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:51:32: #1 tags after filtering in treatment: 9075764 INFO @ Fri, 16 Mar 2018 07:51:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 16 Mar 2018 07:51:32: #1 finished! INFO @ Fri, 16 Mar 2018 07:51:32: #2 Build Peak Model... INFO @ Fri, 16 Mar 2018 07:51:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 16 Mar 2018 07:51:33: #2 number of paired peaks: 1339 INFO @ Fri, 16 Mar 2018 07:51:33: start model_add_line... INFO @ Fri, 16 Mar 2018 07:51:33: #2 number of paired peaks: 1339 INFO @ Fri, 16 Mar 2018 07:51:33: start model_add_line... INFO @ Fri, 16 Mar 2018 07:51:33: #2 number of paired peaks: 1339 INFO @ Fri, 16 Mar 2018 07:51:33: start model_add_line... INFO @ Fri, 16 Mar 2018 07:51:33: start X-correlation... INFO @ Fri, 16 Mar 2018 07:51:33: start X-correlation... INFO @ Fri, 16 Mar 2018 07:51:33: end of X-cor INFO @ Fri, 16 Mar 2018 07:51:33: #2 finished! INFO @ Fri, 16 Mar 2018 07:51:33: #2 predicted fragment length is 212 bps INFO @ Fri, 16 Mar 2018 07:51:33: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 16 Mar 2018 07:51:33: #2.2 Generate R script for model : SRX3068980.10_model.r INFO @ Fri, 16 Mar 2018 07:51:33: end of X-cor INFO @ Fri, 16 Mar 2018 07:51:33: #2 finished! INFO @ Fri, 16 Mar 2018 07:51:33: #2 predicted fragment length is 212 bps INFO @ Fri, 16 Mar 2018 07:51:33: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 16 Mar 2018 07:51:33: #2.2 Generate R script for model : SRX3068980.20_model.r INFO @ Fri, 16 Mar 2018 07:51:33: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:51:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:51:33: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:51:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:51:33: start X-correlation... INFO @ Fri, 16 Mar 2018 07:51:33: end of X-cor INFO @ Fri, 16 Mar 2018 07:51:33: #2 finished! INFO @ Fri, 16 Mar 2018 07:51:33: #2 predicted fragment length is 212 bps INFO @ Fri, 16 Mar 2018 07:51:33: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 16 Mar 2018 07:51:33: #2.2 Generate R script for model : SRX3068980.05_model.r INFO @ Fri, 16 Mar 2018 07:51:33: #3 Call peaks... INFO @ Fri, 16 Mar 2018 07:51:33: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 16 Mar 2018 07:51:54: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:51:55: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:51:55: #3 Call peaks for each chromosome... INFO @ Fri, 16 Mar 2018 07:52:06: #4 Write output xls file... SRX3068980.20_peaks.xls INFO @ Fri, 16 Mar 2018 07:52:06: #4 Write peak in narrowPeak format file... SRX3068980.20_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:52:06: #4 Write summits bed file... SRX3068980.20_summits.bed INFO @ Fri, 16 Mar 2018 07:52:06: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (2808 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:52:07: #4 Write output xls file... SRX3068980.10_peaks.xls INFO @ Fri, 16 Mar 2018 07:52:07: #4 Write peak in narrowPeak format file... SRX3068980.10_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:52:07: #4 Write summits bed file... SRX3068980.10_summits.bed INFO @ Fri, 16 Mar 2018 07:52:07: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (5942 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 16 Mar 2018 07:52:08: #4 Write output xls file... SRX3068980.05_peaks.xls INFO @ Fri, 16 Mar 2018 07:52:08: #4 Write peak in narrowPeak format file... SRX3068980.05_peaks.narrowPeak INFO @ Fri, 16 Mar 2018 07:52:08: #4 Write summits bed file... SRX3068980.05_summits.bed INFO @ Fri, 16 Mar 2018 07:52:08: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (8620 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。