Job ID = 10714585 sra ファイルのダウンロード中... Completed: 29259K bytes transferred in 3 seconds (73960K 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 1667403 spots for /home/okishinya/chipatlas/results/dm3/SRX4053365/SRR7132348.sra Written 1667403 spots for /home/okishinya/chipatlas/results/dm3/SRX4053365/SRR7132348.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: 00:00:38 1667403 reads; of these: 1667403 (100.00%) were unpaired; of these: 320353 (19.21%) aligned 0 times 929008 (55.72%) aligned exactly 1 time 418042 (25.07%) aligned >1 times 80.79% overall alignment rate Time searching: 00:00:38 Overall time: 00:00:38 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 116255 / 1347050 = 0.0863 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, 03 Jun 2018 13:37:18: # Command line: callpeak -t SRX4053365.bam -f BAM -g dm -n SRX4053365.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053365.20 # format = BAM # ChIP-seq file = ['SRX4053365.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2018 13:37:18: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:37:18: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:37:18: # Command line: callpeak -t SRX4053365.bam -f BAM -g dm -n SRX4053365.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053365.10 # format = BAM # ChIP-seq file = ['SRX4053365.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2018 13:37:18: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:37:18: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:37:18: # Command line: callpeak -t SRX4053365.bam -f BAM -g dm -n SRX4053365.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053365.05 # format = BAM # ChIP-seq file = ['SRX4053365.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 03 Jun 2018 13:37:18: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:37:18: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:37:25: 1000000 INFO @ Sun, 03 Jun 2018 13:37:25: 1000000 INFO @ Sun, 03 Jun 2018 13:37:25: 1000000 INFO @ Sun, 03 Jun 2018 13:37:26: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:37:26: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:37:26: #1 total tags in treatment: 1230795 INFO @ Sun, 03 Jun 2018 13:37:26: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:37:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:37:26: #1 tags after filtering in treatment: 1230795 INFO @ Sun, 03 Jun 2018 13:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:37:26: #1 finished! INFO @ Sun, 03 Jun 2018 13:37:26: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:37:26: #2 number of paired peaks: 575 WARNING @ Sun, 03 Jun 2018 13:37:26: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sun, 03 Jun 2018 13:37:26: start model_add_line... INFO @ Sun, 03 Jun 2018 13:37:26: start X-correlation... INFO @ Sun, 03 Jun 2018 13:37:26: end of X-cor INFO @ Sun, 03 Jun 2018 13:37:26: #2 finished! INFO @ Sun, 03 Jun 2018 13:37:26: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:37:26: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:37:26: #2.2 Generate R script for model : SRX4053365.05_model.r WARNING @ Sun, 03 Jun 2018 13:37:26: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:37:26: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:37:26: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:37:26: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:37:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:37:26: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:37:26: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:37:26: #1 total tags in treatment: 1230795 INFO @ Sun, 03 Jun 2018 13:37:26: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:37:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:37:26: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:37:26: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:37:26: #1 total tags in treatment: 1230795 INFO @ Sun, 03 Jun 2018 13:37:26: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:37:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:37:26: #1 tags after filtering in treatment: 1230795 INFO @ Sun, 03 Jun 2018 13:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:37:26: #1 finished! INFO @ Sun, 03 Jun 2018 13:37:26: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:37:26: #1 tags after filtering in treatment: 1230795 INFO @ Sun, 03 Jun 2018 13:37:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:37:26: #1 finished! INFO @ Sun, 03 Jun 2018 13:37:26: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:37:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:37:27: #2 number of paired peaks: 575 WARNING @ Sun, 03 Jun 2018 13:37:27: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sun, 03 Jun 2018 13:37:27: start model_add_line... INFO @ Sun, 03 Jun 2018 13:37:27: start X-correlation... INFO @ Sun, 03 Jun 2018 13:37:27: #2 number of paired peaks: 575 WARNING @ Sun, 03 Jun 2018 13:37:27: Fewer paired peaks (575) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 575 pairs to build model! INFO @ Sun, 03 Jun 2018 13:37:27: start model_add_line... INFO @ Sun, 03 Jun 2018 13:37:27: end of X-cor INFO @ Sun, 03 Jun 2018 13:37:27: #2 finished! INFO @ Sun, 03 Jun 2018 13:37:27: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:37:27: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:37:27: #2.2 Generate R script for model : SRX4053365.20_model.r INFO @ Sun, 03 Jun 2018 13:37:27: start X-correlation... WARNING @ Sun, 03 Jun 2018 13:37:27: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:37:27: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:37:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:37:27: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:37:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:37:27: end of X-cor INFO @ Sun, 03 Jun 2018 13:37:27: #2 finished! INFO @ Sun, 03 Jun 2018 13:37:27: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:37:27: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:37:27: #2.2 Generate R script for model : SRX4053365.10_model.r WARNING @ Sun, 03 Jun 2018 13:37:27: #2 Since the d (48) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 03 Jun 2018 13:37:27: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:37:27: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 03 Jun 2018 13:37:27: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:37:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:37:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:29: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:37:31: #4 Write output xls file... SRX4053365.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:31: #4 Write peak in narrowPeak format file... SRX4053365.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:31: #4 Write summits bed file... SRX4053365.05_summits.bed INFO @ Sun, 03 Jun 2018 13:37:31: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (858 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:37:31: #4 Write output xls file... SRX4053365.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:31: #4 Write peak in narrowPeak format file... SRX4053365.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:31: #4 Write summits bed file... SRX4053365.20_summits.bed INFO @ Sun, 03 Jun 2018 13:37:31: Done! INFO @ Sun, 03 Jun 2018 13:37:31: #4 Write output xls file... SRX4053365.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:37:31: #4 Write peak in narrowPeak format file... SRX4053365.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:37:31: #4 Write summits bed file... SRX4053365.10_summits.bed INFO @ Sun, 03 Jun 2018 13:37:31: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (183 records, 4 fields): 1 millis CompletedMACS2peakCalling pass1 - making usageList (8 chroms): 0 millis pass2 - checking and writing primary data (407 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。