Job ID = 10488217 sra ファイルのダウンロード中... Completed: 88910K bytes transferred in 10 seconds (68816K 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... Written 5321909 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3451534/SRR6354924.sra Written 5321909 spots total 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: 00:00:49 5321909 reads; of these: 5321909 (100.00%) were unpaired; of these: 202937 (3.81%) aligned 0 times 3220521 (60.51%) aligned exactly 1 time 1898451 (35.67%) aligned >1 times 96.19% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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_rmdupse_core] 3235313 / 5118972 = 0.6320 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 @ Sun, 18 Mar 2018 12:20:48: # Command line: callpeak -t SRX3451534.bam -f BAM -g 12100000 -n SRX3451534.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3451534.10 # format = BAM # ChIP-seq file = ['SRX3451534.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 @ Sun, 18 Mar 2018 12:20:48: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:20:48: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:20:48: # Command line: callpeak -t SRX3451534.bam -f BAM -g 12100000 -n SRX3451534.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3451534.05 # format = BAM # ChIP-seq file = ['SRX3451534.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 @ Sun, 18 Mar 2018 12:20:48: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:20:48: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:20:48: # Command line: callpeak -t SRX3451534.bam -f BAM -g 12100000 -n SRX3451534.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3451534.20 # format = BAM # ChIP-seq file = ['SRX3451534.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 @ Sun, 18 Mar 2018 12:20:48: #1 read tag files... INFO @ Sun, 18 Mar 2018 12:20:48: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 12:20:55: 1000000 INFO @ Sun, 18 Mar 2018 12:20:55: 1000000 INFO @ Sun, 18 Mar 2018 12:20:55: 1000000 INFO @ Sun, 18 Mar 2018 12:21:00: #1 tag size is determined as 40 bps INFO @ Sun, 18 Mar 2018 12:21:00: #1 tag size = 40 INFO @ Sun, 18 Mar 2018 12:21:00: #1 total tags in treatment: 1883659 INFO @ Sun, 18 Mar 2018 12:21:00: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:21:00: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:21:00: #1 tags after filtering in treatment: 1883659 INFO @ Sun, 18 Mar 2018 12:21:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 12:21:00: #1 finished! INFO @ Sun, 18 Mar 2018 12:21:00: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:21:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:21:01: #2 number of paired peaks: 228 WARNING @ Sun, 18 Mar 2018 12:21:01: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 18 Mar 2018 12:21:01: start model_add_line... INFO @ Sun, 18 Mar 2018 12:21:01: start X-correlation... INFO @ Sun, 18 Mar 2018 12:21:01: end of X-cor INFO @ Sun, 18 Mar 2018 12:21:01: #2 finished! INFO @ Sun, 18 Mar 2018 12:21:01: #2 predicted fragment length is 185 bps INFO @ Sun, 18 Mar 2018 12:21:01: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 18 Mar 2018 12:21:01: #2.2 Generate R script for model : SRX3451534.20_model.r INFO @ Sun, 18 Mar 2018 12:21:01: #3 Call peaks... INFO @ Sun, 18 Mar 2018 12:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 12:21:01: #1 tag size is determined as 40 bps INFO @ Sun, 18 Mar 2018 12:21:01: #1 tag size = 40 INFO @ Sun, 18 Mar 2018 12:21:01: #1 total tags in treatment: 1883659 INFO @ Sun, 18 Mar 2018 12:21:01: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:21:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:21:01: #1 tag size is determined as 40 bps INFO @ Sun, 18 Mar 2018 12:21:01: #1 tag size = 40 INFO @ Sun, 18 Mar 2018 12:21:01: #1 total tags in treatment: 1883659 INFO @ Sun, 18 Mar 2018 12:21:01: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 12:21:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 12:21:01: #1 tags after filtering in treatment: 1883659 INFO @ Sun, 18 Mar 2018 12:21:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 12:21:01: #1 finished! INFO @ Sun, 18 Mar 2018 12:21:01: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:21:01: #1 tags after filtering in treatment: 1883659 INFO @ Sun, 18 Mar 2018 12:21:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 12:21:01: #1 finished! INFO @ Sun, 18 Mar 2018 12:21:01: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 12:21:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 12:21:01: #2 number of paired peaks: 228 WARNING @ Sun, 18 Mar 2018 12:21:01: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 18 Mar 2018 12:21:01: start model_add_line... INFO @ Sun, 18 Mar 2018 12:21:01: start X-correlation... INFO @ Sun, 18 Mar 2018 12:21:01: end of X-cor INFO @ Sun, 18 Mar 2018 12:21:01: #2 finished! INFO @ Sun, 18 Mar 2018 12:21:01: #2 predicted fragment length is 185 bps INFO @ Sun, 18 Mar 2018 12:21:01: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 18 Mar 2018 12:21:01: #2.2 Generate R script for model : SRX3451534.10_model.r INFO @ Sun, 18 Mar 2018 12:21:01: #2 number of paired peaks: 228 WARNING @ Sun, 18 Mar 2018 12:21:01: Fewer paired peaks (228) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 228 pairs to build model! INFO @ Sun, 18 Mar 2018 12:21:01: start model_add_line... INFO @ Sun, 18 Mar 2018 12:21:01: #3 Call peaks... INFO @ Sun, 18 Mar 2018 12:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 12:21:01: start X-correlation... INFO @ Sun, 18 Mar 2018 12:21:01: end of X-cor INFO @ Sun, 18 Mar 2018 12:21:01: #2 finished! INFO @ Sun, 18 Mar 2018 12:21:01: #2 predicted fragment length is 185 bps INFO @ Sun, 18 Mar 2018 12:21:01: #2 alternative fragment length(s) may be 185 bps INFO @ Sun, 18 Mar 2018 12:21:01: #2.2 Generate R script for model : SRX3451534.05_model.r INFO @ Sun, 18 Mar 2018 12:21:01: #3 Call peaks... INFO @ Sun, 18 Mar 2018 12:21:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 12:21:06: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 12:21:07: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 12:21:07: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 12:21:08: #4 Write output xls file... SRX3451534.20_peaks.xls INFO @ Sun, 18 Mar 2018 12:21:08: #4 Write peak in narrowPeak format file... SRX3451534.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 12:21:08: #4 Write summits bed file... SRX3451534.20_summits.bed INFO @ Sun, 18 Mar 2018 12:21:08: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (409 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 12:21:09: #4 Write output xls file... SRX3451534.05_peaks.xls INFO @ Sun, 18 Mar 2018 12:21:09: #4 Write peak in narrowPeak format file... SRX3451534.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 12:21:09: #4 Write summits bed file... SRX3451534.05_summits.bed INFO @ Sun, 18 Mar 2018 12:21:09: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (743 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 12:21:09: #4 Write output xls file... SRX3451534.10_peaks.xls INFO @ Sun, 18 Mar 2018 12:21:09: #4 Write peak in narrowPeak format file... SRX3451534.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 12:21:09: #4 Write summits bed file... SRX3451534.10_summits.bed INFO @ Sun, 18 Mar 2018 12:21:09: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (527 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。