Job ID = 11192843 sra ファイルのダウンロード中... Completed: 592496K bytes transferred in 8 seconds (565997K 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 8624921 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252367/SRR4432858.sra Written 8624921 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252367/SRR4432858.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: 00:08:25 8624921 reads; of these: 8624921 (100.00%) were paired; of these: 909913 (10.55%) aligned concordantly 0 times 6341623 (73.53%) aligned concordantly exactly 1 time 1373385 (15.92%) aligned concordantly >1 times ---- 909913 pairs aligned concordantly 0 times; of these: 124373 (13.67%) aligned discordantly 1 time ---- 785540 pairs aligned 0 times concordantly or discordantly; of these: 1571080 mates make up the pairs; of these: 1185096 (75.43%) aligned 0 times 267271 (17.01%) aligned exactly 1 time 118713 (7.56%) aligned >1 times 93.13% overall alignment rate Time searching: 00:08:25 Overall time: 00:08:25 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] 7639201 / 7838099 = 0.9746 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 10:11:00: # Command line: callpeak -t SRX2252367.bam -f BAM -g 12100000 -n SRX2252367.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2252367.20 # format = BAM # ChIP-seq file = ['SRX2252367.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 10:11:00: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:11:00: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:11:00: # Command line: callpeak -t SRX2252367.bam -f BAM -g 12100000 -n SRX2252367.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2252367.05 # format = BAM # ChIP-seq file = ['SRX2252367.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 10:11:00: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:11:00: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:11:00: # Command line: callpeak -t SRX2252367.bam -f BAM -g 12100000 -n SRX2252367.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2252367.10 # format = BAM # ChIP-seq file = ['SRX2252367.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 10:11:00: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:11:00: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:11:05: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:11:05: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:11:05: #1 total tags in treatment: 188763 INFO @ Sat, 15 Sep 2018 10:11:05: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:11:05: #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 10:11:05: #1 tags after filtering in treatment: 166434 INFO @ Sat, 15 Sep 2018 10:11:05: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Sep 2018 10:11:05: #1 finished! INFO @ Sat, 15 Sep 2018 10:11:05: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:11:05: #2 number of paired peaks: 359 WARNING @ Sat, 15 Sep 2018 10:11:05: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sat, 15 Sep 2018 10:11:05: start model_add_line... INFO @ Sat, 15 Sep 2018 10:11:05: start X-correlation... INFO @ Sat, 15 Sep 2018 10:11:05: end of X-cor INFO @ Sat, 15 Sep 2018 10:11:05: #2 finished! INFO @ Sat, 15 Sep 2018 10:11:05: #2 predicted fragment length is 170 bps INFO @ Sat, 15 Sep 2018 10:11:05: #2 alternative fragment length(s) may be 99,170,191,546,582 bps INFO @ Sat, 15 Sep 2018 10:11:05: #2.2 Generate R script for model : SRX2252367.10_model.r INFO @ Sat, 15 Sep 2018 10:11:05: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:11:05: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:11:05: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:11:05: #1 total tags in treatment: 188763 INFO @ Sat, 15 Sep 2018 10:11:05: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:11:05: #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 10:11:05: #1 tag size is determined as 76 bps INFO @ Sat, 15 Sep 2018 10:11:05: #1 tag size = 76 INFO @ Sat, 15 Sep 2018 10:11:05: #1 total tags in treatment: 188763 INFO @ Sat, 15 Sep 2018 10:11:05: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:11:05: #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 10:11:05: #1 tags after filtering in treatment: 166434 INFO @ Sat, 15 Sep 2018 10:11:05: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Sep 2018 10:11:05: #1 finished! INFO @ Sat, 15 Sep 2018 10:11:05: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:11:05: #1 tags after filtering in treatment: 166434 INFO @ Sat, 15 Sep 2018 10:11:05: #1 Redundant rate of treatment: 0.12 INFO @ Sat, 15 Sep 2018 10:11:05: #1 finished! INFO @ Sat, 15 Sep 2018 10:11:05: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:11:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:11:05: #2 number of paired peaks: 359 WARNING @ Sat, 15 Sep 2018 10:11:05: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sat, 15 Sep 2018 10:11:05: start model_add_line... INFO @ Sat, 15 Sep 2018 10:11:05: #2 number of paired peaks: 359 WARNING @ Sat, 15 Sep 2018 10:11:05: Fewer paired peaks (359) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 359 pairs to build model! INFO @ Sat, 15 Sep 2018 10:11:05: start model_add_line... INFO @ Sat, 15 Sep 2018 10:11:05: start X-correlation... INFO @ Sat, 15 Sep 2018 10:11:05: start X-correlation... INFO @ Sat, 15 Sep 2018 10:11:05: end of X-cor INFO @ Sat, 15 Sep 2018 10:11:05: #2 finished! INFO @ Sat, 15 Sep 2018 10:11:05: #2 predicted fragment length is 170 bps INFO @ Sat, 15 Sep 2018 10:11:05: #2 alternative fragment length(s) may be 99,170,191,546,582 bps INFO @ Sat, 15 Sep 2018 10:11:05: #2.2 Generate R script for model : SRX2252367.05_model.r INFO @ Sat, 15 Sep 2018 10:11:05: end of X-cor INFO @ Sat, 15 Sep 2018 10:11:05: #2 finished! INFO @ Sat, 15 Sep 2018 10:11:05: #2 predicted fragment length is 170 bps INFO @ Sat, 15 Sep 2018 10:11:05: #2 alternative fragment length(s) may be 99,170,191,546,582 bps INFO @ Sat, 15 Sep 2018 10:11:05: #2.2 Generate R script for model : SRX2252367.20_model.r INFO @ Sat, 15 Sep 2018 10:11:05: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:11:05: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:11:05: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:11:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:11:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:11:06: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:11:06: #4 Write output xls file... SRX2252367.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:11:06: #4 Write peak in narrowPeak format file... SRX2252367.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:11:06: #4 Write summits bed file... SRX2252367.10_summits.bed INFO @ Sat, 15 Sep 2018 10:11:06: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (81 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:11:06: #4 Write output xls file... SRX2252367.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:11:06: #4 Write peak in narrowPeak format file... SRX2252367.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:11:06: #4 Write summits bed file... SRX2252367.05_summits.bed INFO @ Sat, 15 Sep 2018 10:11:06: Done! INFO @ Sat, 15 Sep 2018 10:11:06: #4 Write output xls file... SRX2252367.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:11:06: #4 Write peak in narrowPeak format file... SRX2252367.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:11:06: #4 Write summits bed file... SRX2252367.20_summits.bed INFO @ Sat, 15 Sep 2018 10:11:06: Done! pass1 - making usageList (15 chroms): 0 millis pass2 - checking and writing primary data (140 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (40 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。