Job ID = 11245071 sra ファイルのダウンロード中... Completed: 160580K bytes transferred in 5 seconds (248968K 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 4760438 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554783/SRR7696455.sra Written 4760438 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554783/SRR7696455.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:02:33 4760438 reads; of these: 4760438 (100.00%) were paired; of these: 2722382 (57.19%) aligned concordantly 0 times 1289391 (27.09%) aligned concordantly exactly 1 time 748665 (15.73%) aligned concordantly >1 times ---- 2722382 pairs aligned concordantly 0 times; of these: 2128 (0.08%) aligned discordantly 1 time ---- 2720254 pairs aligned 0 times concordantly or discordantly; of these: 5440508 mates make up the pairs; of these: 3956060 (72.71%) aligned 0 times 1019629 (18.74%) aligned exactly 1 time 464819 (8.54%) aligned >1 times 58.45% overall alignment rate Time searching: 00:02:34 Overall time: 00:02:34 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] 460626 / 2039857 = 0.2258 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 23:22:54: # Command line: callpeak -t SRX4554783.bam -f BAM -g 12100000 -n SRX4554783.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554783.20 # format = BAM # ChIP-seq file = ['SRX4554783.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 23:22:54: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:22:54: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:22:54: # Command line: callpeak -t SRX4554783.bam -f BAM -g 12100000 -n SRX4554783.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554783.10 # format = BAM # ChIP-seq file = ['SRX4554783.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 23:22:54: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:22:54: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:22:54: # Command line: callpeak -t SRX4554783.bam -f BAM -g 12100000 -n SRX4554783.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554783.05 # format = BAM # ChIP-seq file = ['SRX4554783.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 23:22:54: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:22:54: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:23:00: 1000000 INFO @ Tue, 09 Oct 2018 23:23:00: 1000000 INFO @ Tue, 09 Oct 2018 23:23:00: 1000000 INFO @ Tue, 09 Oct 2018 23:23:06: 2000000 INFO @ Tue, 09 Oct 2018 23:23:06: 2000000 INFO @ Tue, 09 Oct 2018 23:23:06: 2000000 INFO @ Tue, 09 Oct 2018 23:23:11: 3000000 INFO @ Tue, 09 Oct 2018 23:23:12: 3000000 INFO @ Tue, 09 Oct 2018 23:23:12: 3000000 INFO @ Tue, 09 Oct 2018 23:23:16: 4000000 INFO @ Tue, 09 Oct 2018 23:23:17: 4000000 INFO @ Tue, 09 Oct 2018 23:23:18: 4000000 INFO @ Tue, 09 Oct 2018 23:23:20: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:23:20: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:23:20: #1 total tags in treatment: 1577459 INFO @ Tue, 09 Oct 2018 23:23:20: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:23:20: #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 23:23:20: #1 tags after filtering in treatment: 816690 INFO @ Tue, 09 Oct 2018 23:23:20: #1 Redundant rate of treatment: 0.48 INFO @ Tue, 09 Oct 2018 23:23:20: #1 finished! INFO @ Tue, 09 Oct 2018 23:23:20: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:23:20: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:23:20: #2 number of paired peaks: 583 WARNING @ Tue, 09 Oct 2018 23:23:20: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Tue, 09 Oct 2018 23:23:20: start model_add_line... INFO @ Tue, 09 Oct 2018 23:23:20: start X-correlation... INFO @ Tue, 09 Oct 2018 23:23:20: end of X-cor INFO @ Tue, 09 Oct 2018 23:23:20: #2 finished! INFO @ Tue, 09 Oct 2018 23:23:20: #2 predicted fragment length is 286 bps INFO @ Tue, 09 Oct 2018 23:23:20: #2 alternative fragment length(s) may be 251,269,286,561 bps INFO @ Tue, 09 Oct 2018 23:23:20: #2.2 Generate R script for model : SRX4554783.10_model.r INFO @ Tue, 09 Oct 2018 23:23:20: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:23:20: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:23:21: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:23:21: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:23:21: #1 total tags in treatment: 1577459 INFO @ Tue, 09 Oct 2018 23:23:21: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:23:21: #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 23:23:21: #1 tags after filtering in treatment: 816690 INFO @ Tue, 09 Oct 2018 23:23:21: #1 Redundant rate of treatment: 0.48 INFO @ Tue, 09 Oct 2018 23:23:21: #1 finished! INFO @ Tue, 09 Oct 2018 23:23:21: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:23:21: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:23:21: #2 number of paired peaks: 583 WARNING @ Tue, 09 Oct 2018 23:23:21: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Tue, 09 Oct 2018 23:23:21: start model_add_line... INFO @ Tue, 09 Oct 2018 23:23:21: start X-correlation... INFO @ Tue, 09 Oct 2018 23:23:21: end of X-cor INFO @ Tue, 09 Oct 2018 23:23:21: #2 finished! INFO @ Tue, 09 Oct 2018 23:23:21: #2 predicted fragment length is 286 bps INFO @ Tue, 09 Oct 2018 23:23:21: #2 alternative fragment length(s) may be 251,269,286,561 bps INFO @ Tue, 09 Oct 2018 23:23:21: #2.2 Generate R script for model : SRX4554783.20_model.r INFO @ Tue, 09 Oct 2018 23:23:21: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:23:22: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:23:22: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:23:22: #1 total tags in treatment: 1577459 INFO @ Tue, 09 Oct 2018 23:23:22: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:23:22: #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 23:23:22: #1 tags after filtering in treatment: 816690 INFO @ Tue, 09 Oct 2018 23:23:22: #1 Redundant rate of treatment: 0.48 INFO @ Tue, 09 Oct 2018 23:23:22: #1 finished! INFO @ Tue, 09 Oct 2018 23:23:22: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:23:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:23:22: #2 number of paired peaks: 583 WARNING @ Tue, 09 Oct 2018 23:23:22: Fewer paired peaks (583) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 583 pairs to build model! INFO @ Tue, 09 Oct 2018 23:23:22: start model_add_line... INFO @ Tue, 09 Oct 2018 23:23:22: start X-correlation... INFO @ Tue, 09 Oct 2018 23:23:22: end of X-cor INFO @ Tue, 09 Oct 2018 23:23:22: #2 finished! INFO @ Tue, 09 Oct 2018 23:23:22: #2 predicted fragment length is 286 bps INFO @ Tue, 09 Oct 2018 23:23:22: #2 alternative fragment length(s) may be 251,269,286,561 bps INFO @ Tue, 09 Oct 2018 23:23:22: #2.2 Generate R script for model : SRX4554783.05_model.r INFO @ Tue, 09 Oct 2018 23:23:22: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:23:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:23:27: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:23:28: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:23:28: #4 Write output xls file... SRX4554783.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:23:28: #4 Write peak in narrowPeak format file... SRX4554783.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:23:28: #4 Write summits bed file... SRX4554783.10_summits.bed INFO @ Tue, 09 Oct 2018 23:23:28: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (204 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:23:28: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:23:29: #4 Write output xls file... SRX4554783.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:23:29: #4 Write peak in narrowPeak format file... SRX4554783.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:23:29: #4 Write summits bed file... SRX4554783.20_summits.bed INFO @ Tue, 09 Oct 2018 23:23:29: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (25 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:23:29: #4 Write output xls file... SRX4554783.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:23:29: #4 Write peak in narrowPeak format file... SRX4554783.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:23:29: #4 Write summits bed file... SRX4554783.05_summits.bed INFO @ Tue, 09 Oct 2018 23:23:29: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (386 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。