Job ID = 11634706 sra ファイルのダウンロード中... Completed: 460137K bytes transferred in 7 seconds (481214K 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: SINGLE fastq に変換中... Read 25398702 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957442/SRR8136456.sra Written 25398702 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957442/SRR8136456.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: 00:04:30 25398702 reads; of these: 25398702 (100.00%) were unpaired; of these: 3183841 (12.54%) aligned 0 times 15140636 (59.61%) aligned exactly 1 time 7074225 (27.85%) aligned >1 times 87.46% overall alignment rate Time searching: 00:04:30 Overall time: 00:04:30 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_rmdupse_core] 20085786 / 22214861 = 0.9042 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 @ Fri, 15 Feb 2019 10:37:04: # Command line: callpeak -t SRX4957442.bam -f BAM -g 12100000 -n SRX4957442.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4957442.20 # format = BAM # ChIP-seq file = ['SRX4957442.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 @ Fri, 15 Feb 2019 10:37:04: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:37:04: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:37:04: # Command line: callpeak -t SRX4957442.bam -f BAM -g 12100000 -n SRX4957442.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4957442.10 # format = BAM # ChIP-seq file = ['SRX4957442.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 @ Fri, 15 Feb 2019 10:37:04: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:37:04: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:37:04: # Command line: callpeak -t SRX4957442.bam -f BAM -g 12100000 -n SRX4957442.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4957442.05 # format = BAM # ChIP-seq file = ['SRX4957442.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 @ Fri, 15 Feb 2019 10:37:04: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:37:04: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:37:10: 1000000 INFO @ Fri, 15 Feb 2019 10:37:10: 1000000 INFO @ Fri, 15 Feb 2019 10:37:10: 1000000 INFO @ Fri, 15 Feb 2019 10:37:16: 2000000 INFO @ Fri, 15 Feb 2019 10:37:16: 2000000 INFO @ Fri, 15 Feb 2019 10:37:16: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:37:16: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:37:16: #1 total tags in treatment: 2129075 INFO @ Fri, 15 Feb 2019 10:37:16: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:37:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:37:16: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:37:16: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:37:16: #1 total tags in treatment: 2129075 INFO @ Fri, 15 Feb 2019 10:37:16: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:37:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:37:16: #1 tags after filtering in treatment: 2129075 INFO @ Fri, 15 Feb 2019 10:37:16: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:37:16: #1 finished! INFO @ Fri, 15 Feb 2019 10:37:16: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:37:16: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:37:17: 2000000 INFO @ Fri, 15 Feb 2019 10:37:17: #1 tags after filtering in treatment: 2129075 INFO @ Fri, 15 Feb 2019 10:37:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:37:17: #1 finished! INFO @ Fri, 15 Feb 2019 10:37:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:37:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:37:17: #2 number of paired peaks: 388 WARNING @ Fri, 15 Feb 2019 10:37:17: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Fri, 15 Feb 2019 10:37:17: start model_add_line... INFO @ Fri, 15 Feb 2019 10:37:17: start X-correlation... INFO @ Fri, 15 Feb 2019 10:37:17: #2 number of paired peaks: 388 WARNING @ Fri, 15 Feb 2019 10:37:17: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Fri, 15 Feb 2019 10:37:17: start model_add_line... INFO @ Fri, 15 Feb 2019 10:37:17: end of X-cor INFO @ Fri, 15 Feb 2019 10:37:17: #2 finished! INFO @ Fri, 15 Feb 2019 10:37:17: #2 predicted fragment length is 365 bps INFO @ Fri, 15 Feb 2019 10:37:17: #2 alternative fragment length(s) may be 365 bps INFO @ Fri, 15 Feb 2019 10:37:17: #2.2 Generate R script for model : SRX4957442.05_model.r INFO @ Fri, 15 Feb 2019 10:37:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:37:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:37:17: start X-correlation... INFO @ Fri, 15 Feb 2019 10:37:17: end of X-cor INFO @ Fri, 15 Feb 2019 10:37:17: #2 finished! INFO @ Fri, 15 Feb 2019 10:37:17: #2 predicted fragment length is 365 bps INFO @ Fri, 15 Feb 2019 10:37:17: #2 alternative fragment length(s) may be 365 bps INFO @ Fri, 15 Feb 2019 10:37:17: #2.2 Generate R script for model : SRX4957442.10_model.r INFO @ Fri, 15 Feb 2019 10:37:17: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:37:17: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:37:17: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:37:17: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:37:17: #1 total tags in treatment: 2129075 INFO @ Fri, 15 Feb 2019 10:37:17: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:37:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 10:37:17: #1 tags after filtering in treatment: 2129075 INFO @ Fri, 15 Feb 2019 10:37:17: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:37:17: #1 finished! INFO @ Fri, 15 Feb 2019 10:37:17: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:37:17: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:37:18: #2 number of paired peaks: 388 WARNING @ Fri, 15 Feb 2019 10:37:18: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Fri, 15 Feb 2019 10:37:18: start model_add_line... INFO @ Fri, 15 Feb 2019 10:37:18: start X-correlation... INFO @ Fri, 15 Feb 2019 10:37:18: end of X-cor INFO @ Fri, 15 Feb 2019 10:37:18: #2 finished! INFO @ Fri, 15 Feb 2019 10:37:18: #2 predicted fragment length is 365 bps INFO @ Fri, 15 Feb 2019 10:37:18: #2 alternative fragment length(s) may be 365 bps INFO @ Fri, 15 Feb 2019 10:37:18: #2.2 Generate R script for model : SRX4957442.20_model.r INFO @ Fri, 15 Feb 2019 10:37:18: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:37:18: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:37:31: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:37:32: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:37:33: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:37:34: #4 Write output xls file... SRX4957442.10_peaks.xls INFO @ Fri, 15 Feb 2019 10:37:34: #4 Write peak in narrowPeak format file... SRX4957442.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:37:34: #4 Write summits bed file... SRX4957442.10_summits.bed INFO @ Fri, 15 Feb 2019 10:37:34: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (747 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 10:37:34: #4 Write output xls file... SRX4957442.05_peaks.xls INFO @ Fri, 15 Feb 2019 10:37:34: #4 Write peak in narrowPeak format file... SRX4957442.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:37:34: #4 Write summits bed file... SRX4957442.05_summits.bed INFO @ Fri, 15 Feb 2019 10:37:34: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (887 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 10:37:35: #4 Write output xls file... SRX4957442.20_peaks.xls INFO @ Fri, 15 Feb 2019 10:37:35: #4 Write peak in narrowPeak format file... SRX4957442.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:37:35: #4 Write summits bed file... SRX4957442.20_summits.bed INFO @ Fri, 15 Feb 2019 10:37:35: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (618 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。