Job ID = 11192860 sra ファイルのダウンロード中... Completed: 678753K bytes transferred in 7 seconds (760551K 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 12121151 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252384/SRR4432875.sra Written 12121151 spots for /home/okishinya/chipatlas/results/sacCer3/SRX2252384/SRR4432875.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: 00:11:35 12121151 reads; of these: 12121151 (100.00%) were paired; of these: 832130 (6.87%) aligned concordantly 0 times 9614822 (79.32%) aligned concordantly exactly 1 time 1674199 (13.81%) aligned concordantly >1 times ---- 832130 pairs aligned concordantly 0 times; of these: 128192 (15.41%) aligned discordantly 1 time ---- 703938 pairs aligned 0 times concordantly or discordantly; of these: 1407876 mates make up the pairs; of these: 938288 (66.65%) aligned 0 times 325303 (23.11%) aligned exactly 1 time 144285 (10.25%) aligned >1 times 96.13% overall alignment rate Time searching: 00:11:35 Overall time: 00:11:35 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 12 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] 11068136 / 11412585 = 0.9698 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 10:16:40: # Command line: callpeak -t SRX2252384.bam -f BAM -g 12100000 -n SRX2252384.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2252384.05 # format = BAM # ChIP-seq file = ['SRX2252384.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 10:16:40: # Command line: callpeak -t SRX2252384.bam -f BAM -g 12100000 -n SRX2252384.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2252384.20 # format = BAM # ChIP-seq file = ['SRX2252384.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 10:16:40: # Command line: callpeak -t SRX2252384.bam -f BAM -g 12100000 -n SRX2252384.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2252384.10 # format = BAM # ChIP-seq file = ['SRX2252384.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 10:16:40: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:16:40: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:16:40: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:16:40: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:16:40: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:16:40: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:16:46: 1000000 INFO @ Sat, 15 Sep 2018 10:16:46: 1000000 INFO @ Sat, 15 Sep 2018 10:16:46: 1000000 INFO @ Sat, 15 Sep 2018 10:16:47: #1 tag size is determined as 68 bps INFO @ Sat, 15 Sep 2018 10:16:47: #1 tag size = 68 INFO @ Sat, 15 Sep 2018 10:16:47: #1 total tags in treatment: 334671 INFO @ Sat, 15 Sep 2018 10:16:47: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:16:47: #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 10:16:47: #1 tags after filtering in treatment: 289002 INFO @ Sat, 15 Sep 2018 10:16:47: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Sep 2018 10:16:47: #1 finished! INFO @ Sat, 15 Sep 2018 10:16:47: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:16:47: #1 tag size is determined as 68 bps INFO @ Sat, 15 Sep 2018 10:16:47: #1 tag size = 68 INFO @ Sat, 15 Sep 2018 10:16:47: #1 total tags in treatment: 334671 INFO @ Sat, 15 Sep 2018 10:16:47: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:16:47: #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 10:16:47: #1 tags after filtering in treatment: 289002 INFO @ Sat, 15 Sep 2018 10:16:47: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Sep 2018 10:16:47: #1 finished! INFO @ Sat, 15 Sep 2018 10:16:47: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:16:47: #2 number of paired peaks: 367 WARNING @ Sat, 15 Sep 2018 10:16:47: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Sat, 15 Sep 2018 10:16:47: start model_add_line... INFO @ Sat, 15 Sep 2018 10:16:47: start X-correlation... INFO @ Sat, 15 Sep 2018 10:16:47: end of X-cor INFO @ Sat, 15 Sep 2018 10:16:47: #2 finished! INFO @ Sat, 15 Sep 2018 10:16:47: #2 predicted fragment length is 150 bps INFO @ Sat, 15 Sep 2018 10:16:47: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 15 Sep 2018 10:16:47: #2.2 Generate R script for model : SRX2252384.05_model.r INFO @ Sat, 15 Sep 2018 10:16:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:16:47: #2 number of paired peaks: 367 WARNING @ Sat, 15 Sep 2018 10:16:47: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Sat, 15 Sep 2018 10:16:47: start model_add_line... INFO @ Sat, 15 Sep 2018 10:16:47: start X-correlation... INFO @ Sat, 15 Sep 2018 10:16:47: end of X-cor INFO @ Sat, 15 Sep 2018 10:16:47: #2 finished! INFO @ Sat, 15 Sep 2018 10:16:47: #2 predicted fragment length is 150 bps INFO @ Sat, 15 Sep 2018 10:16:47: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 15 Sep 2018 10:16:47: #2.2 Generate R script for model : SRX2252384.20_model.r INFO @ Sat, 15 Sep 2018 10:16:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:16:47: #1 tag size is determined as 68 bps INFO @ Sat, 15 Sep 2018 10:16:47: #1 tag size = 68 INFO @ Sat, 15 Sep 2018 10:16:47: #1 total tags in treatment: 334671 INFO @ Sat, 15 Sep 2018 10:16:47: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:16:47: #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 10:16:47: #1 tags after filtering in treatment: 289002 INFO @ Sat, 15 Sep 2018 10:16:47: #1 Redundant rate of treatment: 0.14 INFO @ Sat, 15 Sep 2018 10:16:47: #1 finished! INFO @ Sat, 15 Sep 2018 10:16:47: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:16:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:16:47: #2 number of paired peaks: 367 WARNING @ Sat, 15 Sep 2018 10:16:47: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Sat, 15 Sep 2018 10:16:47: start model_add_line... INFO @ Sat, 15 Sep 2018 10:16:47: start X-correlation... INFO @ Sat, 15 Sep 2018 10:16:47: end of X-cor INFO @ Sat, 15 Sep 2018 10:16:47: #2 finished! INFO @ Sat, 15 Sep 2018 10:16:47: #2 predicted fragment length is 150 bps INFO @ Sat, 15 Sep 2018 10:16:47: #2 alternative fragment length(s) may be 150 bps INFO @ Sat, 15 Sep 2018 10:16:47: #2.2 Generate R script for model : SRX2252384.10_model.r INFO @ Sat, 15 Sep 2018 10:16:47: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:16:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:16:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:16:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:16:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:16:48: #4 Write output xls file... SRX2252384.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:16:48: #4 Write peak in narrowPeak format file... SRX2252384.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:16:48: #4 Write summits bed file... SRX2252384.05_summits.bed INFO @ Sat, 15 Sep 2018 10:16:48: Done! INFO @ Sat, 15 Sep 2018 10:16:49: #4 Write output xls file... SRX2252384.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:16:49: #4 Write peak in narrowPeak format file... SRX2252384.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:16:49: #4 Write summits bed file... SRX2252384.20_summits.bed INFO @ Sat, 15 Sep 2018 10:16:49: Done! INFO @ Sat, 15 Sep 2018 10:16:49: #4 Write output xls file... SRX2252384.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:16:49: #4 Write peak in narrowPeak format file... SRX2252384.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:16:49: #4 Write summits bed file... SRX2252384.10_summits.bed INFO @ Sat, 15 Sep 2018 10:16:49: Done! pass1 - making usageList (16 chroms): 11 millis pass1 - making usageList (15 chroms): 11 millis pass2 - checking and writing primary data (47 records, 4 fields): 11 millis pass2 - checking and writing primary data (256 records, 4 fields): 11 millis CompletedMACS2peakCalling CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。