Job ID = 11244952 sra ファイルのダウンロード中... Completed: 371866K bytes transferred in 7 seconds (385678K 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 11466164 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554682/SRR7696355.sra Written 11466164 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4554682/SRR7696355.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: 00:04:50 11466164 reads; of these: 11466164 (100.00%) were paired; of these: 6047671 (52.74%) aligned concordantly 0 times 3280864 (28.61%) aligned concordantly exactly 1 time 2137629 (18.64%) aligned concordantly >1 times ---- 6047671 pairs aligned concordantly 0 times; of these: 107491 (1.78%) aligned discordantly 1 time ---- 5940180 pairs aligned 0 times concordantly or discordantly; of these: 11880360 mates make up the pairs; of these: 11556978 (97.28%) aligned 0 times 112695 (0.95%) aligned exactly 1 time 210687 (1.77%) aligned >1 times 49.60% overall alignment rate Time searching: 00:04:50 Overall time: 00:04:50 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] 984350 / 5500554 = 0.1790 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 23:04:16: # Command line: callpeak -t SRX4554682.bam -f BAM -g 12100000 -n SRX4554682.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4554682.10 # format = BAM # ChIP-seq file = ['SRX4554682.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 23:04:16: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:04:16: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:04:16: # Command line: callpeak -t SRX4554682.bam -f BAM -g 12100000 -n SRX4554682.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4554682.05 # format = BAM # ChIP-seq file = ['SRX4554682.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 23:04:16: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:04:16: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:04:16: # Command line: callpeak -t SRX4554682.bam -f BAM -g 12100000 -n SRX4554682.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4554682.20 # format = BAM # ChIP-seq file = ['SRX4554682.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 23:04:16: #1 read tag files... INFO @ Tue, 09 Oct 2018 23:04:16: #1 read treatment tags... INFO @ Tue, 09 Oct 2018 23:04:23: 1000000 INFO @ Tue, 09 Oct 2018 23:04:23: 1000000 INFO @ Tue, 09 Oct 2018 23:04:23: 1000000 INFO @ Tue, 09 Oct 2018 23:04:31: 2000000 INFO @ Tue, 09 Oct 2018 23:04:31: 2000000 INFO @ Tue, 09 Oct 2018 23:04:31: 2000000 INFO @ Tue, 09 Oct 2018 23:04:38: 3000000 INFO @ Tue, 09 Oct 2018 23:04:38: 3000000 INFO @ Tue, 09 Oct 2018 23:04:38: 3000000 INFO @ Tue, 09 Oct 2018 23:04:45: 4000000 INFO @ Tue, 09 Oct 2018 23:04:45: 4000000 INFO @ Tue, 09 Oct 2018 23:04:45: 4000000 INFO @ Tue, 09 Oct 2018 23:04:52: 5000000 INFO @ Tue, 09 Oct 2018 23:04:52: 5000000 INFO @ Tue, 09 Oct 2018 23:04:52: 5000000 INFO @ Tue, 09 Oct 2018 23:04:58: 6000000 INFO @ Tue, 09 Oct 2018 23:04:58: 6000000 INFO @ Tue, 09 Oct 2018 23:04:58: 6000000 INFO @ Tue, 09 Oct 2018 23:05:05: 7000000 INFO @ Tue, 09 Oct 2018 23:05:05: 7000000 INFO @ Tue, 09 Oct 2018 23:05:05: 7000000 INFO @ Tue, 09 Oct 2018 23:05:12: 8000000 INFO @ Tue, 09 Oct 2018 23:05:12: 8000000 INFO @ Tue, 09 Oct 2018 23:05:12: 8000000 INFO @ Tue, 09 Oct 2018 23:05:19: 9000000 INFO @ Tue, 09 Oct 2018 23:05:19: 9000000 INFO @ Tue, 09 Oct 2018 23:05:19: 9000000 INFO @ Tue, 09 Oct 2018 23:05:22: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:05:22: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:05:22: #1 total tags in treatment: 4443316 INFO @ Tue, 09 Oct 2018 23:05:22: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:05:22: #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 23:05:22: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:05:22: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:05:22: #1 total tags in treatment: 4443316 INFO @ Tue, 09 Oct 2018 23:05:22: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:05:22: #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 23:05:22: #1 tag size is determined as 37 bps INFO @ Tue, 09 Oct 2018 23:05:22: #1 tag size = 37 INFO @ Tue, 09 Oct 2018 23:05:22: #1 total tags in treatment: 4443316 INFO @ Tue, 09 Oct 2018 23:05:22: #1 user defined the maximum tags... INFO @ Tue, 09 Oct 2018 23:05:22: #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 23:05:22: #1 tags after filtering in treatment: 2169631 INFO @ Tue, 09 Oct 2018 23:05:22: #1 Redundant rate of treatment: 0.51 INFO @ Tue, 09 Oct 2018 23:05:22: #1 finished! INFO @ Tue, 09 Oct 2018 23:05:22: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:05:22: #1 tags after filtering in treatment: 2169631 INFO @ Tue, 09 Oct 2018 23:05:22: #1 Redundant rate of treatment: 0.51 INFO @ Tue, 09 Oct 2018 23:05:22: #1 finished! INFO @ Tue, 09 Oct 2018 23:05:22: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:05:22: #1 tags after filtering in treatment: 2169631 INFO @ Tue, 09 Oct 2018 23:05:22: #1 Redundant rate of treatment: 0.51 INFO @ Tue, 09 Oct 2018 23:05:22: #1 finished! INFO @ Tue, 09 Oct 2018 23:05:22: #2 Build Peak Model... INFO @ Tue, 09 Oct 2018 23:05:22: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 09 Oct 2018 23:05:22: #2 number of paired peaks: 792 WARNING @ Tue, 09 Oct 2018 23:05:22: Fewer paired peaks (792) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 792 pairs to build model! INFO @ Tue, 09 Oct 2018 23:05:22: start model_add_line... INFO @ Tue, 09 Oct 2018 23:05:22: #2 number of paired peaks: 792 WARNING @ Tue, 09 Oct 2018 23:05:22: Fewer paired peaks (792) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 792 pairs to build model! INFO @ Tue, 09 Oct 2018 23:05:22: start model_add_line... INFO @ Tue, 09 Oct 2018 23:05:22: #2 number of paired peaks: 792 WARNING @ Tue, 09 Oct 2018 23:05:22: Fewer paired peaks (792) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 792 pairs to build model! INFO @ Tue, 09 Oct 2018 23:05:22: start model_add_line... INFO @ Tue, 09 Oct 2018 23:05:22: start X-correlation... INFO @ Tue, 09 Oct 2018 23:05:22: start X-correlation... INFO @ Tue, 09 Oct 2018 23:05:22: end of X-cor INFO @ Tue, 09 Oct 2018 23:05:22: #2 finished! INFO @ Tue, 09 Oct 2018 23:05:22: #2 predicted fragment length is 257 bps INFO @ Tue, 09 Oct 2018 23:05:22: #2 alternative fragment length(s) may be 0,201,223,242,257,277 bps INFO @ Tue, 09 Oct 2018 23:05:22: #2.2 Generate R script for model : SRX4554682.10_model.r INFO @ Tue, 09 Oct 2018 23:05:22: end of X-cor INFO @ Tue, 09 Oct 2018 23:05:22: #2 finished! INFO @ Tue, 09 Oct 2018 23:05:22: #2 predicted fragment length is 257 bps INFO @ Tue, 09 Oct 2018 23:05:22: #2 alternative fragment length(s) may be 0,201,223,242,257,277 bps INFO @ Tue, 09 Oct 2018 23:05:22: #2.2 Generate R script for model : SRX4554682.05_model.r INFO @ Tue, 09 Oct 2018 23:05:22: start X-correlation... INFO @ Tue, 09 Oct 2018 23:05:22: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:05:22: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:05:22: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 09 Oct 2018 23:05:22: end of X-cor INFO @ Tue, 09 Oct 2018 23:05:22: #2 finished! INFO @ Tue, 09 Oct 2018 23:05:22: #2 predicted fragment length is 257 bps INFO @ Tue, 09 Oct 2018 23:05:22: #2 alternative fragment length(s) may be 0,201,223,242,257,277 bps INFO @ Tue, 09 Oct 2018 23:05:22: #2.2 Generate R script for model : SRX4554682.20_model.r INFO @ Tue, 09 Oct 2018 23:05:22: #3 Call peaks... INFO @ Tue, 09 Oct 2018 23:05:22: #3 Pre-compute pvalue-qvalue table... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Tue, 09 Oct 2018 23:05:41: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:05:41: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:05:41: #3 Call peaks for each chromosome... INFO @ Tue, 09 Oct 2018 23:05:43: #4 Write output xls file... SRX4554682.05_peaks.xls INFO @ Tue, 09 Oct 2018 23:05:43: #4 Write output xls file... SRX4554682.10_peaks.xls INFO @ Tue, 09 Oct 2018 23:05:43: #4 Write peak in narrowPeak format file... SRX4554682.05_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:05:43: #4 Write peak in narrowPeak format file... SRX4554682.10_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:05:43: #4 Write summits bed file... SRX4554682.05_summits.bed INFO @ Tue, 09 Oct 2018 23:05:43: #4 Write summits bed file... SRX4554682.10_summits.bed INFO @ Tue, 09 Oct 2018 23:05:43: Done! INFO @ Tue, 09 Oct 2018 23:05:43: Done! pass1 - making usageList (17 chroms): 0 millis pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (267 records, 4 fields): 3 millis pass2 - checking and writing primary data (447 records, 4 fields): 3 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Tue, 09 Oct 2018 23:05:44: #4 Write output xls file... SRX4554682.20_peaks.xls INFO @ Tue, 09 Oct 2018 23:05:44: #4 Write peak in narrowPeak format file... SRX4554682.20_peaks.narrowPeak INFO @ Tue, 09 Oct 2018 23:05:44: #4 Write summits bed file... SRX4554682.20_summits.bed INFO @ Tue, 09 Oct 2018 23:05:44: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (73 records, 4 fields): 2 millis CompletedMACS2peakCalling