Job ID = 10714583 sra ファイルのダウンロード中... Completed: 109311K bytes transferred in 4 seconds (216542K 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 6952537 spots for /home/okishinya/chipatlas/results/dm3/SRX4053337/SRR7132376.sra Written 6952537 spots for /home/okishinya/chipatlas/results/dm3/SRX4053337/SRR7132376.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: 00:04:18 6952537 reads; of these: 6952537 (100.00%) were unpaired; of these: 1148707 (16.52%) aligned 0 times 2519591 (36.24%) aligned exactly 1 time 3284239 (47.24%) aligned >1 times 83.48% overall alignment rate Time searching: 00:04:18 Overall time: 00:04:18 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] 2381005 / 5803830 = 0.4102 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 13:41:35: # Command line: callpeak -t SRX4053337.bam -f BAM -g dm -n SRX4053337.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053337.05 # format = BAM # ChIP-seq file = ['SRX4053337.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 13:41:35: # Command line: callpeak -t SRX4053337.bam -f BAM -g dm -n SRX4053337.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053337.20 # format = BAM # ChIP-seq file = ['SRX4053337.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 13:41:35: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:41:35: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:41:35: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:41:35: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:41:35: # Command line: callpeak -t SRX4053337.bam -f BAM -g dm -n SRX4053337.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053337.10 # format = BAM # ChIP-seq file = ['SRX4053337.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 13:41:35: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:41:35: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:41:41: 1000000 INFO @ Sun, 03 Jun 2018 13:41:42: 1000000 INFO @ Sun, 03 Jun 2018 13:41:42: 1000000 INFO @ Sun, 03 Jun 2018 13:41:48: 2000000 INFO @ Sun, 03 Jun 2018 13:41:48: 2000000 INFO @ Sun, 03 Jun 2018 13:41:49: 2000000 INFO @ Sun, 03 Jun 2018 13:41:55: 3000000 INFO @ Sun, 03 Jun 2018 13:41:55: 3000000 INFO @ Sun, 03 Jun 2018 13:41:56: 3000000 INFO @ Sun, 03 Jun 2018 13:41:57: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:41:57: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:41:57: #1 total tags in treatment: 3422825 INFO @ Sun, 03 Jun 2018 13:41:57: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:41:57: #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 13:41:58: #1 tags after filtering in treatment: 3422825 INFO @ Sun, 03 Jun 2018 13:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:41:58: #1 finished! INFO @ Sun, 03 Jun 2018 13:41:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:41:58: #2 number of paired peaks: 968 WARNING @ Sun, 03 Jun 2018 13:41:58: Fewer paired peaks (968) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 968 pairs to build model! INFO @ Sun, 03 Jun 2018 13:41:58: start model_add_line... INFO @ Sun, 03 Jun 2018 13:41:58: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:41:58: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:41:58: #1 total tags in treatment: 3422825 INFO @ Sun, 03 Jun 2018 13:41:58: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:41:58: #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 13:41:58: start X-correlation... INFO @ Sun, 03 Jun 2018 13:41:58: end of X-cor INFO @ Sun, 03 Jun 2018 13:41:58: #2 finished! INFO @ Sun, 03 Jun 2018 13:41:58: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:41:58: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:41:58: #2.2 Generate R script for model : SRX4053337.05_model.r WARNING @ Sun, 03 Jun 2018 13:41:58: #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 13:41:58: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:41:58: #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 13:41:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:41:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:41:58: #1 tags after filtering in treatment: 3422825 INFO @ Sun, 03 Jun 2018 13:41:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:41:58: #1 finished! INFO @ Sun, 03 Jun 2018 13:41:58: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:41:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:41:58: #2 number of paired peaks: 968 WARNING @ Sun, 03 Jun 2018 13:41:58: Fewer paired peaks (968) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 968 pairs to build model! INFO @ Sun, 03 Jun 2018 13:41:58: start model_add_line... INFO @ Sun, 03 Jun 2018 13:41:58: start X-correlation... INFO @ Sun, 03 Jun 2018 13:41:58: end of X-cor INFO @ Sun, 03 Jun 2018 13:41:58: #2 finished! INFO @ Sun, 03 Jun 2018 13:41:58: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:41:58: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:41:58: #2.2 Generate R script for model : SRX4053337.20_model.r WARNING @ Sun, 03 Jun 2018 13:41:58: #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 13:41:58: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:41:58: #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 13:41:58: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:41:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:41:59: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:41:59: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:41:59: #1 total tags in treatment: 3422825 INFO @ Sun, 03 Jun 2018 13:41:59: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:41:59: #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 13:41:59: #1 tags after filtering in treatment: 3422825 INFO @ Sun, 03 Jun 2018 13:41:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:41:59: #1 finished! INFO @ Sun, 03 Jun 2018 13:41:59: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:41:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:42:00: #2 number of paired peaks: 968 WARNING @ Sun, 03 Jun 2018 13:42:00: Fewer paired peaks (968) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 968 pairs to build model! INFO @ Sun, 03 Jun 2018 13:42:00: start model_add_line... INFO @ Sun, 03 Jun 2018 13:42:00: start X-correlation... INFO @ Sun, 03 Jun 2018 13:42:00: end of X-cor INFO @ Sun, 03 Jun 2018 13:42:00: #2 finished! INFO @ Sun, 03 Jun 2018 13:42:00: #2 predicted fragment length is 48 bps INFO @ Sun, 03 Jun 2018 13:42:00: #2 alternative fragment length(s) may be 48 bps INFO @ Sun, 03 Jun 2018 13:42:00: #2.2 Generate R script for model : SRX4053337.10_model.r WARNING @ Sun, 03 Jun 2018 13:42:00: #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 13:42:00: #2 You may need to consider one of the other alternative d(s): 48 WARNING @ Sun, 03 Jun 2018 13:42:00: #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 13:42:00: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:42:00: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:42:06: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:42:07: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:42:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:42:10: #4 Write output xls file... SRX4053337.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:42:10: #4 Write peak in narrowPeak format file... SRX4053337.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:42:10: #4 Write summits bed file... SRX4053337.05_summits.bed INFO @ Sun, 03 Jun 2018 13:42:10: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1912 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:42:11: #4 Write output xls file... SRX4053337.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:42:11: #4 Write peak in narrowPeak format file... SRX4053337.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:42:11: #4 Write summits bed file... SRX4053337.20_summits.bed INFO @ Sun, 03 Jun 2018 13:42:11: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (987 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:42:12: #4 Write output xls file... SRX4053337.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:42:12: #4 Write peak in narrowPeak format file... SRX4053337.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:42:12: #4 Write summits bed file... SRX4053337.10_summits.bed INFO @ Sun, 03 Jun 2018 13:42:12: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1474 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。