Job ID = 11634714 sra ファイルのダウンロード中... Completed: 785935K bytes transferred in 13 seconds (495190K 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 44468692 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957450/SRR8136464.sra Written 44468692 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4957450/SRR8136464.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: 00:07:55 44468692 reads; of these: 44468692 (100.00%) were unpaired; of these: 2423535 (5.45%) aligned 0 times 34256593 (77.04%) aligned exactly 1 time 7788564 (17.51%) aligned >1 times 94.55% overall alignment rate Time searching: 00:07:55 Overall time: 00:07:55 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 20 files... [bam_rmdupse_core] 40146214 / 42045157 = 0.9548 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 10:45:19: # Command line: callpeak -t SRX4957450.bam -f BAM -g 12100000 -n SRX4957450.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4957450.05 # format = BAM # ChIP-seq file = ['SRX4957450.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 10:45:19: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:45:19: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:45:19: # Command line: callpeak -t SRX4957450.bam -f BAM -g 12100000 -n SRX4957450.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4957450.10 # format = BAM # ChIP-seq file = ['SRX4957450.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 10:45:19: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:45:19: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:45:19: # Command line: callpeak -t SRX4957450.bam -f BAM -g 12100000 -n SRX4957450.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4957450.20 # format = BAM # ChIP-seq file = ['SRX4957450.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 10:45:19: #1 read tag files... INFO @ Fri, 15 Feb 2019 10:45:19: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 10:45:25: 1000000 INFO @ Fri, 15 Feb 2019 10:45:26: 1000000 INFO @ Fri, 15 Feb 2019 10:45:26: 1000000 INFO @ Fri, 15 Feb 2019 10:45:31: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:45:31: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:45:31: #1 total tags in treatment: 1898943 INFO @ Fri, 15 Feb 2019 10:45:31: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:45:31: #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 10:45:31: #1 tags after filtering in treatment: 1898943 INFO @ Fri, 15 Feb 2019 10:45:31: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:45:31: #1 finished! INFO @ Fri, 15 Feb 2019 10:45:31: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:45:31: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:45:31: #2 number of paired peaks: 507 WARNING @ Fri, 15 Feb 2019 10:45:31: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Fri, 15 Feb 2019 10:45:31: start model_add_line... INFO @ Fri, 15 Feb 2019 10:45:31: start X-correlation... INFO @ Fri, 15 Feb 2019 10:45:31: end of X-cor INFO @ Fri, 15 Feb 2019 10:45:31: #2 finished! INFO @ Fri, 15 Feb 2019 10:45:31: #2 predicted fragment length is 244 bps INFO @ Fri, 15 Feb 2019 10:45:31: #2 alternative fragment length(s) may be 244 bps INFO @ Fri, 15 Feb 2019 10:45:31: #2.2 Generate R script for model : SRX4957450.10_model.r INFO @ Fri, 15 Feb 2019 10:45:31: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:45:31: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:45:32: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:45:32: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:45:32: #1 total tags in treatment: 1898943 INFO @ Fri, 15 Feb 2019 10:45:32: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:45:32: #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 10:45:32: #1 tags after filtering in treatment: 1898943 INFO @ Fri, 15 Feb 2019 10:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:45:32: #1 finished! INFO @ Fri, 15 Feb 2019 10:45:32: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:45:32: #1 tag size is determined as 50 bps INFO @ Fri, 15 Feb 2019 10:45:32: #1 tag size = 50 INFO @ Fri, 15 Feb 2019 10:45:32: #1 total tags in treatment: 1898943 INFO @ Fri, 15 Feb 2019 10:45:32: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 10:45:32: #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 10:45:32: #1 tags after filtering in treatment: 1898943 INFO @ Fri, 15 Feb 2019 10:45:32: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 10:45:32: #1 finished! INFO @ Fri, 15 Feb 2019 10:45:32: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 10:45:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 10:45:32: #2 number of paired peaks: 507 WARNING @ Fri, 15 Feb 2019 10:45:32: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Fri, 15 Feb 2019 10:45:32: start model_add_line... INFO @ Fri, 15 Feb 2019 10:45:32: start X-correlation... INFO @ Fri, 15 Feb 2019 10:45:32: end of X-cor INFO @ Fri, 15 Feb 2019 10:45:32: #2 finished! INFO @ Fri, 15 Feb 2019 10:45:32: #2 predicted fragment length is 244 bps INFO @ Fri, 15 Feb 2019 10:45:32: #2 alternative fragment length(s) may be 244 bps INFO @ Fri, 15 Feb 2019 10:45:32: #2.2 Generate R script for model : SRX4957450.05_model.r INFO @ Fri, 15 Feb 2019 10:45:32: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:45:32: #2 number of paired peaks: 507 WARNING @ Fri, 15 Feb 2019 10:45:32: Fewer paired peaks (507) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 507 pairs to build model! INFO @ Fri, 15 Feb 2019 10:45:32: start model_add_line... INFO @ Fri, 15 Feb 2019 10:45:32: start X-correlation... INFO @ Fri, 15 Feb 2019 10:45:32: end of X-cor INFO @ Fri, 15 Feb 2019 10:45:32: #2 finished! INFO @ Fri, 15 Feb 2019 10:45:32: #2 predicted fragment length is 244 bps INFO @ Fri, 15 Feb 2019 10:45:32: #2 alternative fragment length(s) may be 244 bps INFO @ Fri, 15 Feb 2019 10:45:32: #2.2 Generate R script for model : SRX4957450.20_model.r INFO @ Fri, 15 Feb 2019 10:45:32: #3 Call peaks... INFO @ Fri, 15 Feb 2019 10:45:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 10:45:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:45:42: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:45:43: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 10:45:44: #4 Write output xls file... SRX4957450.10_peaks.xls INFO @ Fri, 15 Feb 2019 10:45:44: #4 Write peak in narrowPeak format file... SRX4957450.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:45:44: #4 Write summits bed file... SRX4957450.10_summits.bed INFO @ Fri, 15 Feb 2019 10:45:44: Done! pass1 - making usageList (17 chroms): 2 millis pass2 - checking and writing primary data (555 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 10:45:45: #4 Write output xls file... SRX4957450.05_peaks.xls INFO @ Fri, 15 Feb 2019 10:45:45: #4 Write peak in narrowPeak format file... SRX4957450.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:45:45: #4 Write summits bed file... SRX4957450.05_summits.bed INFO @ Fri, 15 Feb 2019 10:45:45: Done! pass1 - making usageList (17 chroms): 3 millis pass2 - checking and writing primary data (694 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 10:45:45: #4 Write output xls file... SRX4957450.20_peaks.xls INFO @ Fri, 15 Feb 2019 10:45:45: #4 Write peak in narrowPeak format file... SRX4957450.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 10:45:45: #4 Write summits bed file... SRX4957450.20_summits.bed INFO @ Fri, 15 Feb 2019 10:45:45: Done! pass1 - making usageList (17 chroms): 3 millis pass2 - checking and writing primary data (425 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。