Job ID = 10937561 sra ファイルのダウンロード中... Completed: 578372K bytes transferred in 75 seconds (62477K 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 5909536 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010340/SRR5833340.sra Written 5909536 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3010340/SRR5833340.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: 00:02:19 5909536 reads; of these: 5909536 (100.00%) were paired; of these: 4858544 (82.22%) aligned concordantly 0 times 836965 (14.16%) aligned concordantly exactly 1 time 214027 (3.62%) aligned concordantly >1 times ---- 4858544 pairs aligned concordantly 0 times; of these: 6963 (0.14%) aligned discordantly 1 time ---- 4851581 pairs aligned 0 times concordantly or discordantly; of these: 9703162 mates make up the pairs; of these: 9680818 (99.77%) aligned 0 times 14328 (0.15%) aligned exactly 1 time 8016 (0.08%) aligned >1 times 18.09% overall alignment rate Time searching: 00:02:19 Overall time: 00:02:19 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_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] 54911 / 1057213 = 0.0519 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 Aug 2018 02:38:21: # Command line: callpeak -t SRX3010340.bam -f BAM -g 12100000 -n SRX3010340.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3010340.20 # format = BAM # ChIP-seq file = ['SRX3010340.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 @ Fri, 10 Aug 2018 02:38:21: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:38:21: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:38:21: # Command line: callpeak -t SRX3010340.bam -f BAM -g 12100000 -n SRX3010340.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3010340.05 # format = BAM # ChIP-seq file = ['SRX3010340.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 @ Fri, 10 Aug 2018 02:38:21: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:38:21: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:38:21: # Command line: callpeak -t SRX3010340.bam -f BAM -g 12100000 -n SRX3010340.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3010340.10 # format = BAM # ChIP-seq file = ['SRX3010340.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 @ Fri, 10 Aug 2018 02:38:21: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:38:21: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:38:31: 1000000 INFO @ Fri, 10 Aug 2018 02:38:32: 1000000 INFO @ Fri, 10 Aug 2018 02:38:32: 1000000 INFO @ Fri, 10 Aug 2018 02:38:41: 2000000 INFO @ Fri, 10 Aug 2018 02:38:42: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:38:42: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:38:42: #1 total tags in treatment: 996248 INFO @ Fri, 10 Aug 2018 02:38:42: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:38:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:38:42: #1 tags after filtering in treatment: 783722 INFO @ Fri, 10 Aug 2018 02:38:42: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:38:42: #1 finished! INFO @ Fri, 10 Aug 2018 02:38:42: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:38:42: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:38:42: #2 number of paired peaks: 304 WARNING @ Fri, 10 Aug 2018 02:38:42: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Fri, 10 Aug 2018 02:38:42: start model_add_line... INFO @ Fri, 10 Aug 2018 02:38:42: start X-correlation... INFO @ Fri, 10 Aug 2018 02:38:42: end of X-cor INFO @ Fri, 10 Aug 2018 02:38:42: #2 finished! INFO @ Fri, 10 Aug 2018 02:38:42: #2 predicted fragment length is 206 bps INFO @ Fri, 10 Aug 2018 02:38:42: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 10 Aug 2018 02:38:42: #2.2 Generate R script for model : SRX3010340.20_model.r INFO @ Fri, 10 Aug 2018 02:38:42: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:38:42: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:38:44: 2000000 INFO @ Fri, 10 Aug 2018 02:38:44: 2000000 INFO @ Fri, 10 Aug 2018 02:38:44: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:38:44: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:38:44: #1 total tags in treatment: 996248 INFO @ Fri, 10 Aug 2018 02:38:44: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:38:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:38:44: #1 tag size is determined as 101 bps INFO @ Fri, 10 Aug 2018 02:38:44: #1 tag size = 101 INFO @ Fri, 10 Aug 2018 02:38:44: #1 total tags in treatment: 996248 INFO @ Fri, 10 Aug 2018 02:38:44: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:38:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:38:44: #1 tags after filtering in treatment: 783722 INFO @ Fri, 10 Aug 2018 02:38:44: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:38:44: #1 finished! INFO @ Fri, 10 Aug 2018 02:38:44: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:38:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:38:44: #1 tags after filtering in treatment: 783722 INFO @ Fri, 10 Aug 2018 02:38:44: #1 Redundant rate of treatment: 0.21 INFO @ Fri, 10 Aug 2018 02:38:44: #1 finished! INFO @ Fri, 10 Aug 2018 02:38:44: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:38:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:38:44: #2 number of paired peaks: 304 WARNING @ Fri, 10 Aug 2018 02:38:44: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Fri, 10 Aug 2018 02:38:44: start model_add_line... INFO @ Fri, 10 Aug 2018 02:38:44: #2 number of paired peaks: 304 WARNING @ Fri, 10 Aug 2018 02:38:44: Fewer paired peaks (304) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 304 pairs to build model! INFO @ Fri, 10 Aug 2018 02:38:44: start model_add_line... INFO @ Fri, 10 Aug 2018 02:38:44: start X-correlation... INFO @ Fri, 10 Aug 2018 02:38:44: start X-correlation... INFO @ Fri, 10 Aug 2018 02:38:44: end of X-cor INFO @ Fri, 10 Aug 2018 02:38:44: end of X-cor INFO @ Fri, 10 Aug 2018 02:38:44: #2 finished! INFO @ Fri, 10 Aug 2018 02:38:44: #2 finished! INFO @ Fri, 10 Aug 2018 02:38:44: #2 predicted fragment length is 206 bps INFO @ Fri, 10 Aug 2018 02:38:44: #2 predicted fragment length is 206 bps INFO @ Fri, 10 Aug 2018 02:38:44: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 10 Aug 2018 02:38:44: #2 alternative fragment length(s) may be 206 bps INFO @ Fri, 10 Aug 2018 02:38:44: #2.2 Generate R script for model : SRX3010340.05_model.r INFO @ Fri, 10 Aug 2018 02:38:44: #2.2 Generate R script for model : SRX3010340.10_model.r INFO @ Fri, 10 Aug 2018 02:38:44: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:38:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:38:44: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:38:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:38:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:38:46: #4 Write output xls file... SRX3010340.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:38:46: #4 Write peak in narrowPeak format file... SRX3010340.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:38:46: #4 Write summits bed file... SRX3010340.20_summits.bed INFO @ Fri, 10 Aug 2018 02:38:46: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (149 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:38:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:38:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:38:49: #4 Write output xls file... SRX3010340.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:38:49: #4 Write peak in narrowPeak format file... SRX3010340.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:38:49: #4 Write summits bed file... SRX3010340.05_summits.bed INFO @ Fri, 10 Aug 2018 02:38:49: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (264 records, 4 fields): 2 millis INFO @ Fri, 10 Aug 2018 02:38:49: #4 Write output xls file... SRX3010340.10_peaks.xls CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:38:49: #4 Write peak in narrowPeak format file... SRX3010340.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:38:49: #4 Write summits bed file... SRX3010340.10_summits.bed INFO @ Fri, 10 Aug 2018 02:38:49: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (192 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。