Job ID = 11171331 sra ファイルのダウンロード中... Completed: 258515K bytes transferred in 5 seconds (377688K 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 6525150 spots for /home/okishinya/chipatlas/results/dm3/SRX3511958/SRR6418943.sra Written 6525150 spots for /home/okishinya/chipatlas/results/dm3/SRX3511958/SRR6418943.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: 00:03:49 6525150 reads; of these: 6525150 (100.00%) were unpaired; of these: 629414 (9.65%) aligned 0 times 4343621 (66.57%) aligned exactly 1 time 1552115 (23.79%) aligned >1 times 90.35% overall alignment rate Time searching: 00:03:49 Overall time: 00:03:49 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] 658491 / 5895736 = 0.1117 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, 08 Sep 2018 13:50:52: # Command line: callpeak -t SRX3511958.bam -f BAM -g dm -n SRX3511958.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511958.20 # format = BAM # ChIP-seq file = ['SRX3511958.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 @ Sat, 08 Sep 2018 13:50:52: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:50:52: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:50:52: # Command line: callpeak -t SRX3511958.bam -f BAM -g dm -n SRX3511958.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511958.10 # format = BAM # ChIP-seq file = ['SRX3511958.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 @ Sat, 08 Sep 2018 13:50:52: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:50:52: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:50:52: # Command line: callpeak -t SRX3511958.bam -f BAM -g dm -n SRX3511958.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511958.05 # format = BAM # ChIP-seq file = ['SRX3511958.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 @ Sat, 08 Sep 2018 13:50:52: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:50:52: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:51:00: 1000000 INFO @ Sat, 08 Sep 2018 13:51:00: 1000000 INFO @ Sat, 08 Sep 2018 13:51:00: 1000000 INFO @ Sat, 08 Sep 2018 13:51:08: 2000000 INFO @ Sat, 08 Sep 2018 13:51:08: 2000000 INFO @ Sat, 08 Sep 2018 13:51:08: 2000000 INFO @ Sat, 08 Sep 2018 13:51:16: 3000000 INFO @ Sat, 08 Sep 2018 13:51:16: 3000000 INFO @ Sat, 08 Sep 2018 13:51:16: 3000000 INFO @ Sat, 08 Sep 2018 13:51:23: 4000000 INFO @ Sat, 08 Sep 2018 13:51:24: 4000000 INFO @ Sat, 08 Sep 2018 13:51:24: 4000000 INFO @ Sat, 08 Sep 2018 13:51:31: 5000000 INFO @ Sat, 08 Sep 2018 13:51:32: 5000000 INFO @ Sat, 08 Sep 2018 13:51:32: 5000000 INFO @ Sat, 08 Sep 2018 13:51:33: #1 tag size is determined as 96 bps INFO @ Sat, 08 Sep 2018 13:51:33: #1 tag size = 96 INFO @ Sat, 08 Sep 2018 13:51:33: #1 total tags in treatment: 5237245 INFO @ Sat, 08 Sep 2018 13:51:33: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:51:33: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:51:33: #1 tags after filtering in treatment: 5237245 INFO @ Sat, 08 Sep 2018 13:51:33: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:51:33: #1 finished! INFO @ Sat, 08 Sep 2018 13:51:33: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:51:33: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:51:34: #2 number of paired peaks: 673 WARNING @ Sat, 08 Sep 2018 13:51:34: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Sat, 08 Sep 2018 13:51:34: start model_add_line... INFO @ Sat, 08 Sep 2018 13:51:34: start X-correlation... INFO @ Sat, 08 Sep 2018 13:51:34: end of X-cor INFO @ Sat, 08 Sep 2018 13:51:34: #2 finished! INFO @ Sat, 08 Sep 2018 13:51:34: #2 predicted fragment length is 147 bps INFO @ Sat, 08 Sep 2018 13:51:34: #2 alternative fragment length(s) may be 1,147,493,501 bps INFO @ Sat, 08 Sep 2018 13:51:34: #2.2 Generate R script for model : SRX3511958.10_model.r WARNING @ Sat, 08 Sep 2018 13:51:34: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:51:34: #2 You may need to consider one of the other alternative d(s): 1,147,493,501 WARNING @ Sat, 08 Sep 2018 13:51:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:51:34: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:51:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:51:34: #1 tag size is determined as 96 bps INFO @ Sat, 08 Sep 2018 13:51:34: #1 tag size = 96 INFO @ Sat, 08 Sep 2018 13:51:34: #1 total tags in treatment: 5237245 INFO @ Sat, 08 Sep 2018 13:51:34: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:51:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:51:34: #1 tag size is determined as 96 bps INFO @ Sat, 08 Sep 2018 13:51:34: #1 tag size = 96 INFO @ Sat, 08 Sep 2018 13:51:34: #1 total tags in treatment: 5237245 INFO @ Sat, 08 Sep 2018 13:51:34: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:51:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:51:34: #1 tags after filtering in treatment: 5237245 INFO @ Sat, 08 Sep 2018 13:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:51:34: #1 finished! INFO @ Sat, 08 Sep 2018 13:51:34: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:51:34: #1 tags after filtering in treatment: 5237245 INFO @ Sat, 08 Sep 2018 13:51:34: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:51:34: #1 finished! INFO @ Sat, 08 Sep 2018 13:51:34: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:51:34: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:51:35: #2 number of paired peaks: 673 WARNING @ Sat, 08 Sep 2018 13:51:35: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Sat, 08 Sep 2018 13:51:35: start model_add_line... INFO @ Sat, 08 Sep 2018 13:51:35: #2 number of paired peaks: 673 WARNING @ Sat, 08 Sep 2018 13:51:35: Fewer paired peaks (673) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 673 pairs to build model! INFO @ Sat, 08 Sep 2018 13:51:35: start model_add_line... INFO @ Sat, 08 Sep 2018 13:51:35: start X-correlation... INFO @ Sat, 08 Sep 2018 13:51:35: end of X-cor INFO @ Sat, 08 Sep 2018 13:51:35: #2 finished! INFO @ Sat, 08 Sep 2018 13:51:35: #2 predicted fragment length is 147 bps INFO @ Sat, 08 Sep 2018 13:51:35: #2 alternative fragment length(s) may be 1,147,493,501 bps INFO @ Sat, 08 Sep 2018 13:51:35: #2.2 Generate R script for model : SRX3511958.20_model.r INFO @ Sat, 08 Sep 2018 13:51:35: start X-correlation... WARNING @ Sat, 08 Sep 2018 13:51:35: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:51:35: #2 You may need to consider one of the other alternative d(s): 1,147,493,501 WARNING @ Sat, 08 Sep 2018 13:51:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:51:35: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:51:35: end of X-cor INFO @ Sat, 08 Sep 2018 13:51:35: #2 finished! INFO @ Sat, 08 Sep 2018 13:51:35: #2 predicted fragment length is 147 bps INFO @ Sat, 08 Sep 2018 13:51:35: #2 alternative fragment length(s) may be 1,147,493,501 bps INFO @ Sat, 08 Sep 2018 13:51:35: #2.2 Generate R script for model : SRX3511958.05_model.r WARNING @ Sat, 08 Sep 2018 13:51:35: #2 Since the d (147) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:51:35: #2 You may need to consider one of the other alternative d(s): 1,147,493,501 WARNING @ Sat, 08 Sep 2018 13:51:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 08 Sep 2018 13:51:35: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:51:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:51:46: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:51:46: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:51:47: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:51:53: #4 Write output xls file... SRX3511958.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:51:53: #4 Write peak in narrowPeak format file... SRX3511958.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:51:53: #4 Write summits bed file... SRX3511958.10_summits.bed INFO @ Sat, 08 Sep 2018 13:51:53: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (85 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:51:53: #4 Write output xls file... SRX3511958.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:51:53: #4 Write peak in narrowPeak format file... SRX3511958.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:51:53: #4 Write summits bed file... SRX3511958.20_summits.bed INFO @ Sat, 08 Sep 2018 13:51:53: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (31 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:51:54: #4 Write output xls file... SRX3511958.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:51:54: #4 Write peak in narrowPeak format file... SRX3511958.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:51:54: #4 Write summits bed file... SRX3511958.05_summits.bed INFO @ Sat, 08 Sep 2018 13:51:54: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (312 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。