Job ID = 11192976 sra ファイルのダウンロード中... Completed: 99757K bytes transferred in 12 seconds (63452K 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 4507789 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233641/SRR7360908.sra Written 4507789 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4233641/SRR7360908.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: 00:00:46 4507789 reads; of these: 4507789 (100.00%) were unpaired; of these: 637753 (14.15%) aligned 0 times 3354359 (74.41%) aligned exactly 1 time 515677 (11.44%) aligned >1 times 85.85% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 1019005 / 3870036 = 0.2633 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 10:43:19: # Command line: callpeak -t SRX4233641.bam -f BAM -g 12100000 -n SRX4233641.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4233641.20 # format = BAM # ChIP-seq file = ['SRX4233641.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 10:43:19: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:43:19: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:43:19: # Command line: callpeak -t SRX4233641.bam -f BAM -g 12100000 -n SRX4233641.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4233641.10 # format = BAM # ChIP-seq file = ['SRX4233641.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 10:43:19: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:43:19: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:43:19: # Command line: callpeak -t SRX4233641.bam -f BAM -g 12100000 -n SRX4233641.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4233641.05 # format = BAM # ChIP-seq file = ['SRX4233641.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 10:43:19: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:43:19: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:43:25: 1000000 INFO @ Sat, 15 Sep 2018 10:43:25: 1000000 INFO @ Sat, 15 Sep 2018 10:43:25: 1000000 INFO @ Sat, 15 Sep 2018 10:43:31: 2000000 INFO @ Sat, 15 Sep 2018 10:43:31: 2000000 INFO @ Sat, 15 Sep 2018 10:43:31: 2000000 INFO @ Sat, 15 Sep 2018 10:43:35: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:43:35: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:43:35: #1 total tags in treatment: 2851031 INFO @ Sat, 15 Sep 2018 10:43:35: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:43:35: #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 10:43:35: #1 tags after filtering in treatment: 2851031 INFO @ Sat, 15 Sep 2018 10:43:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:43:35: #1 finished! INFO @ Sat, 15 Sep 2018 10:43:35: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:43:36: #2 number of paired peaks: 250 WARNING @ Sat, 15 Sep 2018 10:43:36: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sat, 15 Sep 2018 10:43:36: start model_add_line... INFO @ Sat, 15 Sep 2018 10:43:36: start X-correlation... INFO @ Sat, 15 Sep 2018 10:43:36: end of X-cor INFO @ Sat, 15 Sep 2018 10:43:36: #2 finished! INFO @ Sat, 15 Sep 2018 10:43:36: #2 predicted fragment length is 219 bps INFO @ Sat, 15 Sep 2018 10:43:36: #2 alternative fragment length(s) may be 4,219 bps INFO @ Sat, 15 Sep 2018 10:43:36: #2.2 Generate R script for model : SRX4233641.05_model.r INFO @ Sat, 15 Sep 2018 10:43:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:43:36: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:43:36: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:43:36: #1 total tags in treatment: 2851031 INFO @ Sat, 15 Sep 2018 10:43:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:43:36: #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 10:43:36: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:43:36: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:43:36: #1 total tags in treatment: 2851031 INFO @ Sat, 15 Sep 2018 10:43:36: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:43:36: #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 10:43:36: #1 tags after filtering in treatment: 2851031 INFO @ Sat, 15 Sep 2018 10:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:43:36: #1 finished! INFO @ Sat, 15 Sep 2018 10:43:36: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:43:36: #1 tags after filtering in treatment: 2851031 INFO @ Sat, 15 Sep 2018 10:43:36: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:43:36: #1 finished! INFO @ Sat, 15 Sep 2018 10:43:36: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:43:36: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:43:36: #2 number of paired peaks: 250 WARNING @ Sat, 15 Sep 2018 10:43:36: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sat, 15 Sep 2018 10:43:36: start model_add_line... INFO @ Sat, 15 Sep 2018 10:43:36: start X-correlation... INFO @ Sat, 15 Sep 2018 10:43:36: end of X-cor INFO @ Sat, 15 Sep 2018 10:43:36: #2 finished! INFO @ Sat, 15 Sep 2018 10:43:36: #2 predicted fragment length is 219 bps INFO @ Sat, 15 Sep 2018 10:43:36: #2 alternative fragment length(s) may be 4,219 bps INFO @ Sat, 15 Sep 2018 10:43:36: #2.2 Generate R script for model : SRX4233641.20_model.r INFO @ Sat, 15 Sep 2018 10:43:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:43:36: #2 number of paired peaks: 250 WARNING @ Sat, 15 Sep 2018 10:43:36: Fewer paired peaks (250) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 250 pairs to build model! INFO @ Sat, 15 Sep 2018 10:43:36: start model_add_line... INFO @ Sat, 15 Sep 2018 10:43:36: start X-correlation... INFO @ Sat, 15 Sep 2018 10:43:36: end of X-cor INFO @ Sat, 15 Sep 2018 10:43:36: #2 finished! INFO @ Sat, 15 Sep 2018 10:43:36: #2 predicted fragment length is 219 bps INFO @ Sat, 15 Sep 2018 10:43:36: #2 alternative fragment length(s) may be 4,219 bps INFO @ Sat, 15 Sep 2018 10:43:36: #2.2 Generate R script for model : SRX4233641.10_model.r INFO @ Sat, 15 Sep 2018 10:43:36: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:43:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:43:48: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:43:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:43:50: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:43:51: #4 Write output xls file... SRX4233641.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:43:51: #4 Write peak in narrowPeak format file... SRX4233641.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:43:51: #4 Write summits bed file... SRX4233641.05_summits.bed INFO @ Sat, 15 Sep 2018 10:43:51: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (1283 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:43:52: #4 Write output xls file... SRX4233641.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:43:52: #4 Write peak in narrowPeak format file... SRX4233641.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:43:52: #4 Write summits bed file... SRX4233641.20_summits.bed INFO @ Sat, 15 Sep 2018 10:43:52: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (557 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:43:53: #4 Write output xls file... SRX4233641.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:43:53: #4 Write peak in narrowPeak format file... SRX4233641.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:43:53: #4 Write summits bed file... SRX4233641.10_summits.bed INFO @ Sat, 15 Sep 2018 10:43:53: Done! pass1 - making usageList (16 chroms): 0 millis pass2 - checking and writing primary data (901 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。