Job ID = 11162632 sra ファイルのダウンロード中... Completed: 84510K bytes transferred in 4 seconds (142865K 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 2467996 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709366/SRR6736418.sra Written 2467996 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3709366/SRR6736418.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: 00:01:31 2467996 reads; of these: 2467996 (100.00%) were paired; of these: 936996 (37.97%) aligned concordantly 0 times 1332865 (54.01%) aligned concordantly exactly 1 time 198135 (8.03%) aligned concordantly >1 times ---- 936996 pairs aligned concordantly 0 times; of these: 2131 (0.23%) aligned discordantly 1 time ---- 934865 pairs aligned 0 times concordantly or discordantly; of these: 1869730 mates make up the pairs; of these: 1115481 (59.66%) aligned 0 times 632679 (33.84%) aligned exactly 1 time 121570 (6.50%) aligned >1 times 77.40% overall alignment rate Time searching: 00:01:31 Overall time: 00:01:31 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] 283819 / 1531722 = 0.1853 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 @ Wed, 05 Sep 2018 10:39:30: # Command line: callpeak -t SRX3709366.bam -f BAM -g 12100000 -n SRX3709366.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3709366.20 # format = BAM # ChIP-seq file = ['SRX3709366.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 @ Wed, 05 Sep 2018 10:39:30: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:39:30: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:39:30: # Command line: callpeak -t SRX3709366.bam -f BAM -g 12100000 -n SRX3709366.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3709366.05 # format = BAM # ChIP-seq file = ['SRX3709366.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 @ Wed, 05 Sep 2018 10:39:30: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:39:30: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:39:30: # Command line: callpeak -t SRX3709366.bam -f BAM -g 12100000 -n SRX3709366.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3709366.10 # format = BAM # ChIP-seq file = ['SRX3709366.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 @ Wed, 05 Sep 2018 10:39:30: #1 read tag files... INFO @ Wed, 05 Sep 2018 10:39:30: #1 read treatment tags... INFO @ Wed, 05 Sep 2018 10:39:35: 1000000 INFO @ Wed, 05 Sep 2018 10:39:35: 1000000 INFO @ Wed, 05 Sep 2018 10:39:36: 1000000 INFO @ Wed, 05 Sep 2018 10:39:41: 2000000 INFO @ Wed, 05 Sep 2018 10:39:41: 2000000 INFO @ Wed, 05 Sep 2018 10:39:41: 2000000 INFO @ Wed, 05 Sep 2018 10:39:46: 3000000 INFO @ Wed, 05 Sep 2018 10:39:46: 3000000 INFO @ Wed, 05 Sep 2018 10:39:46: 3000000 INFO @ Wed, 05 Sep 2018 10:39:47: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:39:47: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:39:47: #1 total tags in treatment: 1247221 INFO @ Wed, 05 Sep 2018 10:39:47: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:39:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:39:47: #1 tags after filtering in treatment: 857055 INFO @ Wed, 05 Sep 2018 10:39:47: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 05 Sep 2018 10:39:47: #1 finished! INFO @ Wed, 05 Sep 2018 10:39:47: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:39:47: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:39:48: #2 number of paired peaks: 191 WARNING @ Wed, 05 Sep 2018 10:39:48: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Wed, 05 Sep 2018 10:39:48: start model_add_line... INFO @ Wed, 05 Sep 2018 10:39:48: start X-correlation... INFO @ Wed, 05 Sep 2018 10:39:48: end of X-cor INFO @ Wed, 05 Sep 2018 10:39:48: #2 finished! INFO @ Wed, 05 Sep 2018 10:39:48: #2 predicted fragment length is 162 bps INFO @ Wed, 05 Sep 2018 10:39:48: #2 alternative fragment length(s) may be 12,98,128,138,162,181 bps INFO @ Wed, 05 Sep 2018 10:39:48: #2.2 Generate R script for model : SRX3709366.05_model.r INFO @ Wed, 05 Sep 2018 10:39:48: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:39:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:39:48: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:39:48: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:39:48: #1 total tags in treatment: 1247221 INFO @ Wed, 05 Sep 2018 10:39:48: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:39:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:39:48: #1 tag size is determined as 40 bps INFO @ Wed, 05 Sep 2018 10:39:48: #1 tag size = 40 INFO @ Wed, 05 Sep 2018 10:39:48: #1 total tags in treatment: 1247221 INFO @ Wed, 05 Sep 2018 10:39:48: #1 user defined the maximum tags... INFO @ Wed, 05 Sep 2018 10:39:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 05 Sep 2018 10:39:48: #1 tags after filtering in treatment: 857055 INFO @ Wed, 05 Sep 2018 10:39:48: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 05 Sep 2018 10:39:48: #1 finished! INFO @ Wed, 05 Sep 2018 10:39:48: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:39:48: #1 tags after filtering in treatment: 857055 INFO @ Wed, 05 Sep 2018 10:39:48: #1 Redundant rate of treatment: 0.31 INFO @ Wed, 05 Sep 2018 10:39:48: #1 finished! INFO @ Wed, 05 Sep 2018 10:39:48: #2 Build Peak Model... INFO @ Wed, 05 Sep 2018 10:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 05 Sep 2018 10:39:48: #2 number of paired peaks: 191 WARNING @ Wed, 05 Sep 2018 10:39:48: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Wed, 05 Sep 2018 10:39:48: start model_add_line... INFO @ Wed, 05 Sep 2018 10:39:48: #2 number of paired peaks: 191 WARNING @ Wed, 05 Sep 2018 10:39:48: Fewer paired peaks (191) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 191 pairs to build model! INFO @ Wed, 05 Sep 2018 10:39:48: start model_add_line... INFO @ Wed, 05 Sep 2018 10:39:48: start X-correlation... INFO @ Wed, 05 Sep 2018 10:39:48: start X-correlation... INFO @ Wed, 05 Sep 2018 10:39:48: end of X-cor INFO @ Wed, 05 Sep 2018 10:39:48: #2 finished! INFO @ Wed, 05 Sep 2018 10:39:48: #2 predicted fragment length is 162 bps INFO @ Wed, 05 Sep 2018 10:39:48: #2 alternative fragment length(s) may be 12,98,128,138,162,181 bps INFO @ Wed, 05 Sep 2018 10:39:48: #2.2 Generate R script for model : SRX3709366.10_model.r INFO @ Wed, 05 Sep 2018 10:39:48: end of X-cor INFO @ Wed, 05 Sep 2018 10:39:48: #2 finished! INFO @ Wed, 05 Sep 2018 10:39:48: #2 predicted fragment length is 162 bps INFO @ Wed, 05 Sep 2018 10:39:48: #2 alternative fragment length(s) may be 12,98,128,138,162,181 bps INFO @ Wed, 05 Sep 2018 10:39:48: #2.2 Generate R script for model : SRX3709366.20_model.r INFO @ Wed, 05 Sep 2018 10:39:48: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:39:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:39:48: #3 Call peaks... INFO @ Wed, 05 Sep 2018 10:39:48: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 05 Sep 2018 10:39:50: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:39:50: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:39:50: #3 Call peaks for each chromosome... INFO @ Wed, 05 Sep 2018 10:39:51: #4 Write output xls file... SRX3709366.05_peaks.xls INFO @ Wed, 05 Sep 2018 10:39:51: #4 Write peak in narrowPeak format file... SRX3709366.05_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:39:51: #4 Write summits bed file... SRX3709366.05_summits.bed INFO @ Wed, 05 Sep 2018 10:39:51: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (495 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 05 Sep 2018 10:39:51: #4 Write output xls file... SRX3709366.20_peaks.xls INFO @ Wed, 05 Sep 2018 10:39:51: #4 Write peak in narrowPeak format file... SRX3709366.20_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:39:51: #4 Write summits bed file... SRX3709366.20_summits.bed INFO @ Wed, 05 Sep 2018 10:39:51: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (134 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Wed, 05 Sep 2018 10:39:51: #4 Write output xls file... SRX3709366.10_peaks.xls INFO @ Wed, 05 Sep 2018 10:39:51: #4 Write peak in narrowPeak format file... SRX3709366.10_peaks.narrowPeak INFO @ Wed, 05 Sep 2018 10:39:51: #4 Write summits bed file... SRX3709366.10_summits.bed INFO @ Wed, 05 Sep 2018 10:39:51: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (306 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。