Job ID = 11193119 sra ファイルのダウンロード中... Completed: 61167K bytes transferred in 4 seconds (121969K 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 2732871 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234141/SRR7360960.sra Written 2732871 spots for /home/okishinya/chipatlas/results/sacCer3/SRX4234141/SRR7360960.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: 00:00:29 2732871 reads; of these: 2732871 (100.00%) were unpaired; of these: 213480 (7.81%) aligned 0 times 2207825 (80.79%) aligned exactly 1 time 311566 (11.40%) aligned >1 times 92.19% overall alignment rate Time searching: 00:00:29 Overall time: 00:00:29 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] 381171 / 2519391 = 0.1513 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 10:58:42: # Command line: callpeak -t SRX4234141.bam -f BAM -g 12100000 -n SRX4234141.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4234141.05 # format = BAM # ChIP-seq file = ['SRX4234141.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 10:58:42: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:58:42: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:58:42: # Command line: callpeak -t SRX4234141.bam -f BAM -g 12100000 -n SRX4234141.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4234141.10 # format = BAM # ChIP-seq file = ['SRX4234141.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 10:58:42: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:58:42: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:58:42: # Command line: callpeak -t SRX4234141.bam -f BAM -g 12100000 -n SRX4234141.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4234141.20 # format = BAM # ChIP-seq file = ['SRX4234141.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 10:58:42: #1 read tag files... INFO @ Sat, 15 Sep 2018 10:58:42: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 10:58:48: 1000000 INFO @ Sat, 15 Sep 2018 10:58:50: 1000000 INFO @ Sat, 15 Sep 2018 10:58:50: 1000000 INFO @ Sat, 15 Sep 2018 10:58:55: 2000000 INFO @ Sat, 15 Sep 2018 10:58:56: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:58:56: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:58:56: #1 total tags in treatment: 2138220 INFO @ Sat, 15 Sep 2018 10:58:56: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:56: #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 10:58:56: #1 tags after filtering in treatment: 2138220 INFO @ Sat, 15 Sep 2018 10:58:56: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:58:56: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:56: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:56: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:56: #2 number of paired peaks: 220 WARNING @ Sat, 15 Sep 2018 10:58:56: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Sat, 15 Sep 2018 10:58:56: start model_add_line... INFO @ Sat, 15 Sep 2018 10:58:56: start X-correlation... INFO @ Sat, 15 Sep 2018 10:58:56: end of X-cor INFO @ Sat, 15 Sep 2018 10:58:56: #2 finished! INFO @ Sat, 15 Sep 2018 10:58:56: #2 predicted fragment length is 218 bps INFO @ Sat, 15 Sep 2018 10:58:56: #2 alternative fragment length(s) may be 4,196,218,246 bps INFO @ Sat, 15 Sep 2018 10:58:56: #2.2 Generate R script for model : SRX4234141.05_model.r INFO @ Sat, 15 Sep 2018 10:58:56: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:58:58: 2000000 INFO @ Sat, 15 Sep 2018 10:58:58: 2000000 INFO @ Sat, 15 Sep 2018 10:58:59: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:58:59: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:58:59: #1 total tags in treatment: 2138220 INFO @ Sat, 15 Sep 2018 10:58:59: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:59: #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 10:58:59: #1 tag size is determined as 49 bps INFO @ Sat, 15 Sep 2018 10:58:59: #1 tag size = 49 INFO @ Sat, 15 Sep 2018 10:58:59: #1 total tags in treatment: 2138220 INFO @ Sat, 15 Sep 2018 10:58:59: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 10:58:59: #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 10:58:59: #1 tags after filtering in treatment: 2138220 INFO @ Sat, 15 Sep 2018 10:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:58:59: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:59: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:59: #1 tags after filtering in treatment: 2138220 INFO @ Sat, 15 Sep 2018 10:58:59: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 10:58:59: #1 finished! INFO @ Sat, 15 Sep 2018 10:58:59: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 10:58:59: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 10:58:59: #2 number of paired peaks: 220 WARNING @ Sat, 15 Sep 2018 10:58:59: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Sat, 15 Sep 2018 10:58:59: start model_add_line... INFO @ Sat, 15 Sep 2018 10:58:59: start X-correlation... INFO @ Sat, 15 Sep 2018 10:58:59: end of X-cor INFO @ Sat, 15 Sep 2018 10:58:59: #2 finished! INFO @ Sat, 15 Sep 2018 10:58:59: #2 predicted fragment length is 218 bps INFO @ Sat, 15 Sep 2018 10:58:59: #2 alternative fragment length(s) may be 4,196,218,246 bps INFO @ Sat, 15 Sep 2018 10:58:59: #2.2 Generate R script for model : SRX4234141.10_model.r INFO @ Sat, 15 Sep 2018 10:58:59: #2 number of paired peaks: 220 WARNING @ Sat, 15 Sep 2018 10:58:59: Fewer paired peaks (220) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 220 pairs to build model! INFO @ Sat, 15 Sep 2018 10:58:59: start model_add_line... INFO @ Sat, 15 Sep 2018 10:58:59: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:58:59: start X-correlation... INFO @ Sat, 15 Sep 2018 10:58:59: end of X-cor INFO @ Sat, 15 Sep 2018 10:58:59: #2 finished! INFO @ Sat, 15 Sep 2018 10:58:59: #2 predicted fragment length is 218 bps INFO @ Sat, 15 Sep 2018 10:58:59: #2 alternative fragment length(s) may be 4,196,218,246 bps INFO @ Sat, 15 Sep 2018 10:58:59: #2.2 Generate R script for model : SRX4234141.20_model.r INFO @ Sat, 15 Sep 2018 10:58:59: #3 Call peaks... INFO @ Sat, 15 Sep 2018 10:58:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 10:59:05: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:59:07: #4 Write output xls file... SRX4234141.05_peaks.xls INFO @ Sat, 15 Sep 2018 10:59:07: #4 Write peak in narrowPeak format file... SRX4234141.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:59:07: #4 Write summits bed file... SRX4234141.05_summits.bed INFO @ Sat, 15 Sep 2018 10:59:07: Done! pass1 - making usageList (17 chroms): 0 millis pass2 - checking and writing primary data (920 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 10:59:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:59:08: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 10:59:10: #4 Write output xls file... SRX4234141.20_peaks.xls INFO @ Sat, 15 Sep 2018 10:59:10: #4 Write peak in narrowPeak format file... SRX4234141.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:59:10: #4 Write summits bed file... SRX4234141.20_summits.bed INFO @ Sat, 15 Sep 2018 10:59:10: Done! INFO @ Sat, 15 Sep 2018 10:59:10: #4 Write output xls file... SRX4234141.10_peaks.xls INFO @ Sat, 15 Sep 2018 10:59:10: #4 Write peak in narrowPeak format file... SRX4234141.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 10:59:10: #4 Write summits bed file... SRX4234141.10_summits.bed INFO @ Sat, 15 Sep 2018 10:59:10: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (400 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (621 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。