Job ID = 10195000 sra ファイルのダウンロード中... Completed: 306154K bytes transferred in 5 seconds (460475K bits/sec), in 1 file. Completed: 304003K bytes transferred in 5 seconds (461385K 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 16003622 spots for /home/okishinya/chipatlas/results/rn6/SRX831351/SRR1743287.sra Written 16003622 spots total Written 17547664 spots for /home/okishinya/chipatlas/results/rn6/SRX831351/SRR1743286.sra Written 17547664 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 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:10:25 33551286 reads; of these: 33551286 (100.00%) were unpaired; of these: 5695716 (16.98%) aligned 0 times 21713241 (64.72%) aligned exactly 1 time 6142329 (18.31%) aligned >1 times 83.02% overall alignment rate Time searching: 00:10:28 Overall time: 00:10:28 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 22007728 / 27855570 = 0.7901 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, 10 Nov 2017 19:07:17: # Command line: callpeak -t SRX831351.bam -f BAM -g 2.15e9 -n SRX831351.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX831351.05 # format = BAM # ChIP-seq file = ['SRX831351.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 19:07:17: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:07:17: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:07:17: # Command line: callpeak -t SRX831351.bam -f BAM -g 2.15e9 -n SRX831351.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX831351.20 # format = BAM # ChIP-seq file = ['SRX831351.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 19:07:17: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:07:17: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:07:17: # Command line: callpeak -t SRX831351.bam -f BAM -g 2.15e9 -n SRX831351.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX831351.10 # format = BAM # ChIP-seq file = ['SRX831351.bam'] # control file = None # effective genome size = 2.15e+09 # 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, 10 Nov 2017 19:07:17: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:07:17: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:07:23: 1000000 INFO @ Fri, 10 Nov 2017 19:07:23: 1000000 INFO @ Fri, 10 Nov 2017 19:07:23: 1000000 INFO @ Fri, 10 Nov 2017 19:07:29: 2000000 INFO @ Fri, 10 Nov 2017 19:07:29: 2000000 INFO @ Fri, 10 Nov 2017 19:07:29: 2000000 INFO @ Fri, 10 Nov 2017 19:07:35: 3000000 INFO @ Fri, 10 Nov 2017 19:07:35: 3000000 INFO @ Fri, 10 Nov 2017 19:07:35: 3000000 INFO @ Fri, 10 Nov 2017 19:07:41: 4000000 INFO @ Fri, 10 Nov 2017 19:07:41: 4000000 INFO @ Fri, 10 Nov 2017 19:07:41: 4000000 INFO @ Fri, 10 Nov 2017 19:07:47: 5000000 INFO @ Fri, 10 Nov 2017 19:07:47: 5000000 INFO @ Fri, 10 Nov 2017 19:07:47: 5000000 INFO @ Fri, 10 Nov 2017 19:07:52: #1 tag size is determined as 36 bps INFO @ Fri, 10 Nov 2017 19:07:52: #1 tag size = 36 INFO @ Fri, 10 Nov 2017 19:07:52: #1 total tags in treatment: 5847842 INFO @ Fri, 10 Nov 2017 19:07:52: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:07:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 19:07:52: #1 tag size is determined as 36 bps INFO @ Fri, 10 Nov 2017 19:07:52: #1 tag size = 36 INFO @ Fri, 10 Nov 2017 19:07:52: #1 total tags in treatment: 5847842 INFO @ Fri, 10 Nov 2017 19:07:52: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:07:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 19:07:52: #1 tag size is determined as 36 bps INFO @ Fri, 10 Nov 2017 19:07:52: #1 tag size = 36 INFO @ Fri, 10 Nov 2017 19:07:52: #1 total tags in treatment: 5847842 INFO @ Fri, 10 Nov 2017 19:07:52: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:07:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 19:07:53: #1 tags after filtering in treatment: 5847604 INFO @ Fri, 10 Nov 2017 19:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:07:53: #1 finished! INFO @ Fri, 10 Nov 2017 19:07:53: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:07:53: #1 tags after filtering in treatment: 5847604 INFO @ Fri, 10 Nov 2017 19:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:07:53: #1 finished! INFO @ Fri, 10 Nov 2017 19:07:53: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:07:53: #1 tags after filtering in treatment: 5847604 INFO @ Fri, 10 Nov 2017 19:07:53: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:07:53: #1 finished! INFO @ Fri, 10 Nov 2017 19:07:53: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:07:53: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:07:56: #2 number of paired peaks: 73144 INFO @ Fri, 10 Nov 2017 19:07:56: start model_add_line... INFO @ Fri, 10 Nov 2017 19:07:56: #2 number of paired peaks: 73144 INFO @ Fri, 10 Nov 2017 19:07:56: start model_add_line... INFO @ Fri, 10 Nov 2017 19:07:56: start X-correlation... INFO @ Fri, 10 Nov 2017 19:07:56: end of X-cor INFO @ Fri, 10 Nov 2017 19:07:56: #2 finished! INFO @ Fri, 10 Nov 2017 19:07:56: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Nov 2017 19:07:56: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Nov 2017 19:07:56: #2.2 Generate R script for model : SRX831351.20_model.r INFO @ Fri, 10 Nov 2017 19:07:56: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:07:56: #2 number of paired peaks: 73144 INFO @ Fri, 10 Nov 2017 19:07:56: start model_add_line... INFO @ Fri, 10 Nov 2017 19:07:56: start X-correlation... INFO @ Fri, 10 Nov 2017 19:07:56: end of X-cor INFO @ Fri, 10 Nov 2017 19:07:56: #2 finished! INFO @ Fri, 10 Nov 2017 19:07:56: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Nov 2017 19:07:56: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Nov 2017 19:07:56: #2.2 Generate R script for model : SRX831351.10_model.r INFO @ Fri, 10 Nov 2017 19:07:56: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:07:56: start X-correlation... INFO @ Fri, 10 Nov 2017 19:07:56: end of X-cor INFO @ Fri, 10 Nov 2017 19:07:56: #2 finished! INFO @ Fri, 10 Nov 2017 19:07:56: #2 predicted fragment length is 212 bps INFO @ Fri, 10 Nov 2017 19:07:56: #2 alternative fragment length(s) may be 212 bps INFO @ Fri, 10 Nov 2017 19:07:56: #2.2 Generate R script for model : SRX831351.05_model.r INFO @ Fri, 10 Nov 2017 19:07:56: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:07:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:08:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:08:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:08:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:08:20: #4 Write output xls file... SRX831351.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:08:20: #4 Write peak in narrowPeak format file... SRX831351.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:08:20: #4 Write summits bed file... SRX831351.05_summits.bed INFO @ Fri, 10 Nov 2017 19:08:20: Done! INFO @ Fri, 10 Nov 2017 19:08:20: #4 Write output xls file... SRX831351.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:08:20: #4 Write peak in narrowPeak format file... SRX831351.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:08:20: #4 Write summits bed file... SRX831351.10_summits.bed INFO @ Fri, 10 Nov 2017 19:08:20: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (5112 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:08:20: #4 Write output xls file... SRX831351.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:08:20: #4 Write peak in narrowPeak format file... SRX831351.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:08:20: #4 Write summits bed file... SRX831351.20_summits.bed pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (1798 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:08:20: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (396 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。