Job ID = 11245059 sra ファイルのダウンロード中... Completed: 149128K bytes transferred in 6 seconds (202317K 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 4387467 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554772/SRR7696444.sra Written 4387467 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554772/SRR7696444.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: 00:00:01 Multiseed full-index search: 00:02:19 4387467 reads; of these: 4387467 (100.00%) were paired; of these: 2807070 (63.98%) aligned concordantly 0 times 1397594 (31.85%) aligned concordantly exactly 1 time 182803 (4.17%) aligned concordantly >1 times ---- 2807070 pairs aligned concordantly 0 times; of these: 2187 (0.08%) aligned discordantly 1 time ---- 2804883 pairs aligned 0 times concordantly or discordantly; of these: 5609766 mates make up the pairs; of these: 4033227 (71.90%) aligned 0 times 1396287 (24.89%) aligned exactly 1 time 180252 (3.21%) aligned >1 times 54.04% overall alignment rate Time searching: 00:02:20 Overall time: 00:02:20 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] 206856 / 1582193 = 0.1307 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 @ Tue, 09 Oct 2018 23:19:05: # Command line: callpeak -t SRX4554772.bam -f BAM -g 12100000 -n SRX4554772.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554772.05 # format = BAM # ChIP-seq file = ['SRX4554772.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 @ Tue, 09 Oct 2018 23:19:05: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:19:05: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:19:05: # Command line: callpeak -t SRX4554772.bam -f BAM -g 12100000 -n SRX4554772.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554772.20 # format = BAM # ChIP-seq file = ['SRX4554772.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 @ Tue, 09 Oct 2018 23:19:05: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:19:05: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:19:05: # Command line: callpeak -t SRX4554772.bam -f BAM -g 12100000 -n SRX4554772.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554772.10 # format = BAM # ChIP-seq file = ['SRX4554772.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 @ Tue, 09 Oct 2018 23:19:05: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:19:05: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:19:11: 1000000 INFO @ Tue, 09 Oct 2018 23:19:11: 1000000 INFO @ Tue, 09 Oct 2018 23:19:11: 1000000 INFO @ Tue, 09 Oct 2018 23:19:17: 2000000 INFO @ Tue, 09 Oct 2018 23:19:17: 2000000 INFO @ Tue, 09 Oct 2018 23:19:17: 2000000 INFO @ Tue, 09 Oct 2018 23:19:23: 3000000 INFO @ Tue, 09 Oct 2018 23:19:23: 3000000 INFO @ Tue, 09 Oct 2018 23:19:23: 3000000 INFO @ Tue, 09 Oct 2018 23:19:28: 4000000 INFO @ Tue, 09 Oct 2018 23:19:28: 4000000 INFO @ Tue, 09 Oct 2018 23:19:29: 4000000 INFO @ Tue, 09 Oct 2018 23:19:30: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:30: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:30: #1 total tags in treatment: 1373607 INFO @ Tue, 09 Oct 2018 23:19:30: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:19:30: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:30: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:30: #1 total tags in treatment: 1373607 INFO @ Tue, 09 Oct 2018 23:19:30: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:19:30: #1 tags after filtering in treatment: 732014 INFO @ Tue, 09 Oct 2018 23:19:30: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:19:30: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:30: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:30: #1 tags after filtering in treatment: 732014 INFO @ Tue, 09 Oct 2018 23:19:30: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:19:30: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:30: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:30: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:19:30: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:19:30: #1 total tags in treatment: 1373607 INFO @ Tue, 09 Oct 2018 23:19:30: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:19:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 09 Oct 2018 23:19:30: #2 number of paired peaks: 859 WARNING @ Tue, 09 Oct 2018 23:19:30: Fewer paired peaks (859) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 859 pairs to build model! INFO @ Tue, 09 Oct 2018 23:19:30: start model_add_line... INFO @ Tue, 09 Oct 2018 23:19:30: #2 number of paired peaks: 859 WARNING @ Tue, 09 Oct 2018 23:19:30: Fewer paired peaks (859) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 859 pairs to build model! INFO @ Tue, 09 Oct 2018 23:19:30: start model_add_line... INFO @ Tue, 09 Oct 2018 23:19:30: #1 tags after filtering in treatment: 732014 INFO @ Tue, 09 Oct 2018 23:19:30: #1 Redundant rate of treatment: 0.47 INFO @ Tue, 09 Oct 2018 23:19:30: #1 finished! INFO @ Tue, 09 Oct 2018 23:19:30: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:19:30: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:19:30: start X-correlation... INFO @ Tue, 09 Oct 2018 23:19:30: start X-correlation... INFO @ Tue, 09 Oct 2018 23:19:30: end of X-cor INFO @ Tue, 09 Oct 2018 23:19:30: #2 finished! INFO @ Tue, 09 Oct 2018 23:19:30: #2 predicted fragment length is 276 bps INFO @ Tue, 09 Oct 2018 23:19:30: #2 alternative fragment length(s) may be 0,209,276,291,308,588 bps INFO @ Tue, 09 Oct 2018 23:19:30: #2.2 Generate R script for model : SRX4554772.20_model.r INFO @ Tue, 09 Oct 2018 23:19:30: end of X-cor INFO @ Tue, 09 Oct 2018 23:19:30: #2 finished! INFO @ Tue, 09 Oct 2018 23:19:30: #2 predicted fragment length is 276 bps INFO @ Tue, 09 Oct 2018 23:19:30: #2 alternative fragment length(s) may be 0,209,276,291,308,588 bps INFO @ Tue, 09 Oct 2018 23:19:30: #2.2 Generate R script for model : SRX4554772.05_model.r INFO @ Tue, 09 Oct 2018 23:19:30: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:19:30: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:19:30: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:19:31: #2 number of paired peaks: 859 WARNING @ Tue, 09 Oct 2018 23:19:31: Fewer paired peaks (859) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 859 pairs to build model! INFO @ Tue, 09 Oct 2018 23:19:31: start model_add_line... INFO @ Tue, 09 Oct 2018 23:19:31: start X-correlation... INFO @ Tue, 09 Oct 2018 23:19:31: end of X-cor INFO @ Tue, 09 Oct 2018 23:19:31: #2 finished! INFO @ Tue, 09 Oct 2018 23:19:31: #2 predicted fragment length is 276 bps INFO @ Tue, 09 Oct 2018 23:19:31: #2 alternative fragment length(s) may be 0,209,276,291,308,588 bps INFO @ Tue, 09 Oct 2018 23:19:31: #2.2 Generate R script for model : SRX4554772.10_model.r INFO @ Tue, 09 Oct 2018 23:19:31: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:19:31: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:19:36: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:19:36: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:19:37: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:19:37: #4 Write output xls file... SRX4554772.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:19:37: #4 Write peak in narrowPeak format file... SRX4554772.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:19:37: #4 Write summits bed file... SRX4554772.20_summits.bed INFO @ Tue, 09 Oct 2018 23:19:37: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (299 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:19:37: #4 Write output xls file... SRX4554772.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:19:37: #4 Write peak in narrowPeak format file... SRX4554772.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:19:37: #4 Write summits bed file... SRX4554772.05_summits.bed INFO @ Tue, 09 Oct 2018 23:19:37: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (401 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:19:38: #4 Write output xls file... SRX4554772.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:19:38: #4 Write peak in narrowPeak format file... SRX4554772.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:19:38: #4 Write summits bed file... SRX4554772.10_summits.bed INFO @ Tue, 09 Oct 2018 23:19:38: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (368 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。