Job ID = 11193069 sra ファイルのダウンロード中... Completed: 59359K bytes transferred in 3 seconds (129233K 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 2642640 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233960/SRR7361141.sra Written 2642640 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233960/SRR7361141.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: 00:00:27 2642640 reads; of these: 2642640 (100.00%) were unpaired; of these: 206964 (7.83%) aligned 0 times 2117501 (80.13%) aligned exactly 1 time 318175 (12.04%) aligned >1 times 92.17% overall alignment rate Time searching: 00:00:27 Overall time: 00:00:27 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] 324612 / 2435676 = 0.1333 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 @ Sat, 15 Sep 2018 10:53:37: # Command line: callpeak -t SRX4233960.bam -f BAM -g 12100000 -n SRX4233960.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4233960.10 # format = BAM # ChIP-seq file = ['SRX4233960.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 @ Sat, 15 Sep 2018 10:53:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:53:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:53:37: # Command line: callpeak -t SRX4233960.bam -f BAM -g 12100000 -n SRX4233960.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4233960.20 # format = BAM # ChIP-seq file = ['SRX4233960.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 @ Sat, 15 Sep 2018 10:53:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:53:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:53:37: # Command line: callpeak -t SRX4233960.bam -f BAM -g 12100000 -n SRX4233960.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4233960.05 # format = BAM # ChIP-seq file = ['SRX4233960.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 @ Sat, 15 Sep 2018 10:53:37: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:53:37: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:53:44: 1000000 INFO @ Sat, 15 Sep 2018 10:53:44: 1000000 INFO @ Sat, 15 Sep 2018 10:53:44: 1000000 INFO @ Sat, 15 Sep 2018 10:53:50: 2000000 INFO @ Sat, 15 Sep 2018 10:53:51: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:53:51: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:53:51: #1 total tags in treatment: 2111064 INFO @ Sat, 15 Sep 2018 10:53:51: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:53:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:53:51: #1 tags after filtering in treatment: 2111064 INFO @ Sat, 15 Sep 2018 10:53:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:53:51: #1 finished! INFO @ Sat, 15 Sep 2018 10:53:51: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:53:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:53:51: #2 number of paired peaks: 219 WARNING @ Sat, 15 Sep 2018 10:53:51: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sat, 15 Sep 2018 10:53:51: start model_add_line... INFO @ Sat, 15 Sep 2018 10:53:51: start X-correlation... INFO @ Sat, 15 Sep 2018 10:53:51: end of X-cor INFO @ Sat, 15 Sep 2018 10:53:51: #2 finished! INFO @ Sat, 15 Sep 2018 10:53:51: #2 predicted fragment length is 191 bps INFO @ Sat, 15 Sep 2018 10:53:51: #2 alternative fragment length(s) may be 4,191,215,240,275 bps INFO @ Sat, 15 Sep 2018 10:53:51: #2.2 Generate R script for model : SRX4233960.10_model.r INFO @ Sat, 15 Sep 2018 10:53:51: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:53:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:53:51: 2000000 INFO @ Sat, 15 Sep 2018 10:53:51: 2000000 INFO @ Sat, 15 Sep 2018 10:53:52: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:53:52: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:53:52: #1 total tags in treatment: 2111064 INFO @ Sat, 15 Sep 2018 10:53:52: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:53:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:53:52: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:53:52: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:53:52: #1 total tags in treatment: 2111064 INFO @ Sat, 15 Sep 2018 10:53:52: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:53:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 10:53:52: #1 tags after filtering in treatment: 2111064 INFO @ Sat, 15 Sep 2018 10:53:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:53:52: #1 finished! INFO @ Sat, 15 Sep 2018 10:53:52: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:53:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:53:52: #1 tags after filtering in treatment: 2111064 INFO @ Sat, 15 Sep 2018 10:53:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:53:52: #1 finished! INFO @ Sat, 15 Sep 2018 10:53:52: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:53:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:53:52: #2 number of paired peaks: 219 WARNING @ Sat, 15 Sep 2018 10:53:52: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sat, 15 Sep 2018 10:53:52: start model_add_line... INFO @ Sat, 15 Sep 2018 10:53:52: #2 number of paired peaks: 219 WARNING @ Sat, 15 Sep 2018 10:53:52: Fewer paired peaks (219) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 219 pairs to build model! INFO @ Sat, 15 Sep 2018 10:53:52: start model_add_line... INFO @ Sat, 15 Sep 2018 10:53:52: start X-correlation... INFO @ Sat, 15 Sep 2018 10:53:52: end of X-cor INFO @ Sat, 15 Sep 2018 10:53:52: #2 finished! INFO @ Sat, 15 Sep 2018 10:53:52: #2 predicted fragment length is 191 bps INFO @ Sat, 15 Sep 2018 10:53:52: #2 alternative fragment length(s) may be 4,191,215,240,275 bps INFO @ Sat, 15 Sep 2018 10:53:52: #2.2 Generate R script for model : SRX4233960.20_model.r INFO @ Sat, 15 Sep 2018 10:53:52: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:53:52: start X-correlation... INFO @ Sat, 15 Sep 2018 10:53:52: end of X-cor INFO @ Sat, 15 Sep 2018 10:53:52: #2 finished! INFO @ Sat, 15 Sep 2018 10:53:52: #2 predicted fragment length is 191 bps INFO @ Sat, 15 Sep 2018 10:53:52: #2 alternative fragment length(s) may be 4,191,215,240,275 bps INFO @ Sat, 15 Sep 2018 10:53:52: #2.2 Generate R script for model : SRX4233960.05_model.r INFO @ Sat, 15 Sep 2018 10:53:52: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:53:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:53:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:54:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:54:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:54:01: #4 Write output xls file... SRX4233960.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:54:01: #4 Write peak in narrowPeak format file... SRX4233960.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:54:01: #4 Write summits bed file... SRX4233960.10_summits.bed INFO @ Sat, 15 Sep 2018 10:54:01: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (604 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:54:03: #4 Write output xls file... SRX4233960.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:54:03: #4 Write peak in narrowPeak format file... SRX4233960.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:54:03: #4 Write summits bed file... SRX4233960.05_summits.bed INFO @ Sat, 15 Sep 2018 10:54:03: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (951 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:54:03: #4 Write output xls file... SRX4233960.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:54:03: #4 Write peak in narrowPeak format file... SRX4233960.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:54:03: #4 Write summits bed file... SRX4233960.20_summits.bed INFO @ Sat, 15 Sep 2018 10:54:03: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (349 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。