Job ID = 11245032 sra ファイルのダウンロード中... Completed: 405021K bytes transferred in 8 seconds (405099K 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: PAIRED fastq に変換中... Read 6586038 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554746/SRR7696419.sra Written 6586038 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554746/SRR7696419.sra 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: 00:05:06 6586038 reads; of these: 6586038 (100.00%) were paired; of these: 1331706 (20.22%) aligned concordantly 0 times 4515055 (68.55%) aligned concordantly exactly 1 time 739277 (11.22%) aligned concordantly >1 times ---- 1331706 pairs aligned concordantly 0 times; of these: 55128 (4.14%) aligned discordantly 1 time ---- 1276578 pairs aligned 0 times concordantly or discordantly; of these: 2553156 mates make up the pairs; of these: 2459538 (96.33%) aligned 0 times 58144 (2.28%) aligned exactly 1 time 35474 (1.39%) aligned >1 times 81.33% overall alignment rate Time searching: 00:05:06 Overall time: 00:05:06 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 3405264 / 5304359 = 0.6420 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 @ Tue, 09 Oct 2018 23:18:25: # Command line: callpeak -t SRX4554746.bam -f BAM -g 12100000 -n SRX4554746.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554746.10 # format = BAM # ChIP-seq file = ['SRX4554746.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Tue, 09 Oct 2018 23:18:25: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:25: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:25: # Command line: callpeak -t SRX4554746.bam -f BAM -g 12100000 -n SRX4554746.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554746.20 # format = BAM # ChIP-seq file = ['SRX4554746.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Tue, 09 Oct 2018 23:18:25: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:25: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:25: # Command line: callpeak -t SRX4554746.bam -f BAM -g 12100000 -n SRX4554746.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554746.05 # format = BAM # ChIP-seq file = ['SRX4554746.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Tue, 09 Oct 2018 23:18:25: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:18:25: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:18:31: 1000000 INFO @ Tue, 09 Oct 2018 23:18:31: 1000000 INFO @ Tue, 09 Oct 2018 23:18:31: 1000000 INFO @ Tue, 09 Oct 2018 23:18:36: 2000000 INFO @ Tue, 09 Oct 2018 23:18:36: 2000000 INFO @ Tue, 09 Oct 2018 23:18:36: 2000000 INFO @ Tue, 09 Oct 2018 23:18:41: 3000000 INFO @ Tue, 09 Oct 2018 23:18:41: 3000000 INFO @ Tue, 09 Oct 2018 23:18:41: 3000000 INFO @ Tue, 09 Oct 2018 23:18:46: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:18:46: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:18:46: #1 total tags in treatment: 1885961 INFO @ Tue, 09 Oct 2018 23:18:46: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:18:46: #1 tags after filtering in treatment: 1046505 INFO @ Tue, 09 Oct 2018 23:18:46: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 09 Oct 2018 23:18:46: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:46: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:46: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:18:46: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:18:46: #1 total tags in treatment: 1885961 INFO @ Tue, 09 Oct 2018 23:18:46: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:18:46: #1 tags after filtering in treatment: 1046505 INFO @ Tue, 09 Oct 2018 23:18:46: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 09 Oct 2018 23:18:46: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:46: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:46: #2 number of paired peaks: 1028 INFO @ Tue, 09 Oct 2018 23:18:46: start model_add_line... INFO @ Tue, 09 Oct 2018 23:18:46: start X-correlation... INFO @ Tue, 09 Oct 2018 23:18:46: end of X-cor INFO @ Tue, 09 Oct 2018 23:18:46: #2 finished! INFO @ Tue, 09 Oct 2018 23:18:46: #2 predicted fragment length is 132 bps INFO @ Tue, 09 Oct 2018 23:18:46: #2 alternative fragment length(s) may be 1,132,154,248,309,517,531,555 bps INFO @ Tue, 09 Oct 2018 23:18:46: #2.2 Generate R script for model : SRX4554746.20_model.r INFO @ Tue, 09 Oct 2018 23:18:46: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:18:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:18:46: #2 number of paired peaks: 1028 INFO @ Tue, 09 Oct 2018 23:18:46: start model_add_line... INFO @ Tue, 09 Oct 2018 23:18:46: #1 tag size is determined as 51 bps INFO @ Tue, 09 Oct 2018 23:18:46: #1 tag size = 51 INFO @ Tue, 09 Oct 2018 23:18:46: #1 total tags in treatment: 1885961 INFO @ Tue, 09 Oct 2018 23:18:46: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:18:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:18:46: start X-correlation... INFO @ Tue, 09 Oct 2018 23:18:46: end of X-cor INFO @ Tue, 09 Oct 2018 23:18:46: #2 finished! INFO @ Tue, 09 Oct 2018 23:18:46: #2 predicted fragment length is 132 bps INFO @ Tue, 09 Oct 2018 23:18:46: #2 alternative fragment length(s) may be 1,132,154,248,309,517,531,555 bps INFO @ Tue, 09 Oct 2018 23:18:46: #2.2 Generate R script for model : SRX4554746.10_model.r INFO @ Tue, 09 Oct 2018 23:18:46: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:18:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:18:46: #1 tags after filtering in treatment: 1046505 INFO @ Tue, 09 Oct 2018 23:18:46: #1 Redundant rate of treatment: 0.45 INFO @ Tue, 09 Oct 2018 23:18:46: #1 finished! INFO @ Tue, 09 Oct 2018 23:18:46: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:18:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:18:46: #2 number of paired peaks: 1028 INFO @ Tue, 09 Oct 2018 23:18:46: start model_add_line... INFO @ Tue, 09 Oct 2018 23:18:47: start X-correlation... INFO @ Tue, 09 Oct 2018 23:18:47: end of X-cor INFO @ Tue, 09 Oct 2018 23:18:47: #2 finished! INFO @ Tue, 09 Oct 2018 23:18:47: #2 predicted fragment length is 132 bps INFO @ Tue, 09 Oct 2018 23:18:47: #2 alternative fragment length(s) may be 1,132,154,248,309,517,531,555 bps INFO @ Tue, 09 Oct 2018 23:18:47: #2.2 Generate R script for model : SRX4554746.05_model.r INFO @ Tue, 09 Oct 2018 23:18:47: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:18:47: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:18:51: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:18:52: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:18:52: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:18:53: #4 Write output xls file... SRX4554746.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:18:53: #4 Write peak in narrowPeak format file... SRX4554746.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:18:53: #4 Write summits bed file... SRX4554746.20_summits.bed INFO @ Tue, 09 Oct 2018 23:18:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (214 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:18:53: #4 Write output xls file... SRX4554746.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:18:53: #4 Write peak in narrowPeak format file... SRX4554746.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:18:53: #4 Write summits bed file... SRX4554746.10_summits.bed INFO @ Tue, 09 Oct 2018 23:18:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (493 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:18:53: #4 Write output xls file... SRX4554746.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:18:53: #4 Write peak in narrowPeak format file... SRX4554746.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:18:53: #4 Write summits bed file... SRX4554746.05_summits.bed INFO @ Tue, 09 Oct 2018 23:18:53: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (660 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。