Job ID = 11192840 sra ファイルのダウンロード中... Completed: 696037K bytes transferred in 9 seconds (614017K 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 10184760 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252364/SRR4432855.sra Written 10184760 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252364/SRR4432855.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: 00:10:59 10184760 reads; of these: 10184760 (100.00%) were paired; of these: 1015594 (9.97%) aligned concordantly 0 times 7680230 (75.41%) aligned concordantly exactly 1 time 1488936 (14.62%) aligned concordantly >1 times ---- 1015594 pairs aligned concordantly 0 times; of these: 105195 (10.36%) aligned discordantly 1 time ---- 910399 pairs aligned 0 times concordantly or discordantly; of these: 1820798 mates make up the pairs; of these: 1372007 (75.35%) aligned 0 times 333011 (18.29%) aligned exactly 1 time 115780 (6.36%) aligned >1 times 93.26% overall alignment rate Time searching: 00:10:59 Overall time: 00:10:59 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] 8997943 / 9271897 = 0.9705 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 @ Sat, 15 Sep 2018 10:14:19: # Command line: callpeak -t SRX2252364.bam -f BAM -g 12100000 -n SRX2252364.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2252364.05 # format = BAM # ChIP-seq file = ['SRX2252364.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 @ Sat, 15 Sep 2018 10:14:19: # Command line: callpeak -t SRX2252364.bam -f BAM -g 12100000 -n SRX2252364.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2252364.10 # format = BAM # ChIP-seq file = ['SRX2252364.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 @ Sat, 15 Sep 2018 10:14:19: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:14:19: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:14:19: # Command line: callpeak -t SRX2252364.bam -f BAM -g 12100000 -n SRX2252364.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2252364.20 # format = BAM # ChIP-seq file = ['SRX2252364.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 @ Sat, 15 Sep 2018 10:14:19: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:14:19: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:14:19: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:14:19: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:14:27: 1000000 INFO @ Sat, 15 Sep 2018 10:14:27: 1000000 INFO @ Sat, 15 Sep 2018 10:14:27: 1000000 INFO @ Sat, 15 Sep 2018 10:14:27: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:14:27: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:14:27: #1 total tags in treatment: 262873 INFO @ Sat, 15 Sep 2018 10:14:27: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:14:27: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:14:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:14:27: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:14:27: #1 total tags in treatment: 262873 INFO @ Sat, 15 Sep 2018 10:14:27: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:14:27: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:14:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:14:27: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:14:27: #1 total tags in treatment: 262873 INFO @ Sat, 15 Sep 2018 10:14:27: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:14:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:14:27: #1 tags after filtering in treatment: 233600 INFO @ Sat, 15 Sep 2018 10:14:27: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Sep 2018 10:14:27: #1 tags after filtering in treatment: 233600 INFO @ Sat, 15 Sep 2018 10:14:27: #1 finished! INFO @ Sat, 15 Sep 2018 10:14:27: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Sep 2018 10:14:27: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:14:27: #1 finished! INFO @ Sat, 15 Sep 2018 10:14:27: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:14:27: #1 tags after filtering in treatment: 233600 INFO @ Sat, 15 Sep 2018 10:14:27: #1 Redundant rate of treatment: 0.11 INFO @ Sat, 15 Sep 2018 10:14:27: #1 finished! INFO @ Sat, 15 Sep 2018 10:14:27: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:14:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:14:27: #2 number of paired peaks: 360 WARNING @ Sat, 15 Sep 2018 10:14:27: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Sat, 15 Sep 2018 10:14:27: #2 number of paired peaks: 360 INFO @ Sat, 15 Sep 2018 10:14:27: start model_add_line... WARNING @ Sat, 15 Sep 2018 10:14:27: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Sat, 15 Sep 2018 10:14:27: #2 number of paired peaks: 360 INFO @ Sat, 15 Sep 2018 10:14:27: start model_add_line... WARNING @ Sat, 15 Sep 2018 10:14:27: Fewer paired peaks (360) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 360 pairs to build model! INFO @ Sat, 15 Sep 2018 10:14:27: start model_add_line... INFO @ Sat, 15 Sep 2018 10:14:27: start X-correlation... INFO @ Sat, 15 Sep 2018 10:14:27: start X-correlation... INFO @ Sat, 15 Sep 2018 10:14:27: start X-correlation... INFO @ Sat, 15 Sep 2018 10:14:27: end of X-cor INFO @ Sat, 15 Sep 2018 10:14:27: end of X-cor INFO @ Sat, 15 Sep 2018 10:14:27: end of X-cor INFO @ Sat, 15 Sep 2018 10:14:27: #2 finished! INFO @ Sat, 15 Sep 2018 10:14:27: #2 finished! INFO @ Sat, 15 Sep 2018 10:14:27: #2 finished! INFO @ Sat, 15 Sep 2018 10:14:27: #2 predicted fragment length is 206 bps INFO @ Sat, 15 Sep 2018 10:14:27: #2 predicted fragment length is 206 bps INFO @ Sat, 15 Sep 2018 10:14:27: #2 predicted fragment length is 206 bps INFO @ Sat, 15 Sep 2018 10:14:27: #2 alternative fragment length(s) may be 50,102,140,166,189,206,229,251,285,504,532,545,577 bps INFO @ Sat, 15 Sep 2018 10:14:27: #2 alternative fragment length(s) may be 50,102,140,166,189,206,229,251,285,504,532,545,577 bps INFO @ Sat, 15 Sep 2018 10:14:27: #2 alternative fragment length(s) may be 50,102,140,166,189,206,229,251,285,504,532,545,577 bps INFO @ Sat, 15 Sep 2018 10:14:27: #2.2 Generate R script for model : SRX2252364.10_model.r INFO @ Sat, 15 Sep 2018 10:14:27: #2.2 Generate R script for model : SRX2252364.20_model.r INFO @ Sat, 15 Sep 2018 10:14:27: #2.2 Generate R script for model : SRX2252364.05_model.r INFO @ Sat, 15 Sep 2018 10:14:27: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:14:27: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:14:27: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:14:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:14:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:14:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:14:28: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:14:29: #4 Write output xls file... SRX2252364.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:14:29: #4 Write peak in narrowPeak format file... SRX2252364.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:14:29: #4 Write summits bed file... SRX2252364.05_summits.bed INFO @ Sat, 15 Sep 2018 10:14:29: Done! INFO @ Sat, 15 Sep 2018 10:14:29: #4 Write output xls file... SRX2252364.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:14:29: #4 Write peak in narrowPeak format file... SRX2252364.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:14:29: #4 Write summits bed file... SRX2252364.20_summits.bed INFO @ Sat, 15 Sep 2018 10:14:29: Done! INFO @ Sat, 15 Sep 2018 10:14:29: #4 Write output xls file... SRX2252364.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:14:29: #4 Write peak in narrowPeak format file... SRX2252364.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:14:29: #4 Write summits bed file... SRX2252364.10_summits.bed INFO @ Sat, 15 Sep 2018 10:14:29: Done! pass1 - making usageList (14 chroms): 18 millis pass1 - making usageList (15 chroms): 18 millis pass1 - making usageList (10 chroms): 18 millis pass2 - checking and writing primary data (17 records, 4 fields): 28 millis pass2 - checking and writing primary data (56 records, 4 fields): 29 millis pass2 - checking and writing primary data (123 records, 4 fields): 29 millis CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。