Job ID = 11293690 sra ファイルのダウンロード中... Completed: 274750K bytes transferred in 14 seconds (160515K 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 7821684 spots for /home/okishinya/chipatlas/results/dm3/SRX4375852/SRR7506506.sra Written 7821684 spots for /home/okishinya/chipatlas/results/dm3/SRX4375852/SRR7506506.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: 00:02:43 7821684 reads; of these: 7821684 (100.00%) were unpaired; of these: 1585508 (20.27%) aligned 0 times 4720333 (60.35%) aligned exactly 1 time 1515843 (19.38%) aligned >1 times 79.73% overall alignment rate Time searching: 00:02:43 Overall time: 00:02:43 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] 1063335 / 6236176 = 0.1705 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, 04 Nov 2018 17:52:18: # Command line: callpeak -t SRX4375852.bam -f BAM -g dm -n SRX4375852.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375852.10 # format = BAM # ChIP-seq file = ['SRX4375852.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, 04 Nov 2018 17:52:18: # Command line: callpeak -t SRX4375852.bam -f BAM -g dm -n SRX4375852.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375852.20 # format = BAM # ChIP-seq file = ['SRX4375852.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, 04 Nov 2018 17:52:18: # Command line: callpeak -t SRX4375852.bam -f BAM -g dm -n SRX4375852.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375852.05 # format = BAM # ChIP-seq file = ['SRX4375852.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, 04 Nov 2018 17:52:18: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:52:18: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:52:18: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:52:18: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:18: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:18: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:52:25: 1000000 INFO @ Sun, 04 Nov 2018 17:52:25: 1000000 INFO @ Sun, 04 Nov 2018 17:52:25: 1000000 INFO @ Sun, 04 Nov 2018 17:52:31: 2000000 INFO @ Sun, 04 Nov 2018 17:52:31: 2000000 INFO @ Sun, 04 Nov 2018 17:52:31: 2000000 INFO @ Sun, 04 Nov 2018 17:52:38: 3000000 INFO @ Sun, 04 Nov 2018 17:52:38: 3000000 INFO @ Sun, 04 Nov 2018 17:52:38: 3000000 INFO @ Sun, 04 Nov 2018 17:52:44: 4000000 INFO @ Sun, 04 Nov 2018 17:52:44: 4000000 INFO @ Sun, 04 Nov 2018 17:52:45: 4000000 INFO @ Sun, 04 Nov 2018 17:52:50: 5000000 INFO @ Sun, 04 Nov 2018 17:52:50: 5000000 INFO @ Sun, 04 Nov 2018 17:52:51: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:52:51: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:52:51: #1 total tags in treatment: 5172841 INFO @ Sun, 04 Nov 2018 17:52:51: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:52:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:52:51: 5000000 INFO @ Sun, 04 Nov 2018 17:52:51: #1 tags after filtering in treatment: 5172841 INFO @ Sun, 04 Nov 2018 17:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:52:51: #1 finished! INFO @ Sun, 04 Nov 2018 17:52:51: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:52:52: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:52:52: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:52:52: #1 total tags in treatment: 5172841 INFO @ Sun, 04 Nov 2018 17:52:52: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:52:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:52:52: #1 tags after filtering in treatment: 5172841 INFO @ Sun, 04 Nov 2018 17:52:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:52:52: #1 finished! INFO @ Sun, 04 Nov 2018 17:52:52: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:52:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:52:52: #2 number of paired peaks: 571 WARNING @ Sun, 04 Nov 2018 17:52:52: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Sun, 04 Nov 2018 17:52:52: start model_add_line... INFO @ Sun, 04 Nov 2018 17:52:52: start X-correlation... INFO @ Sun, 04 Nov 2018 17:52:52: #2 number of paired peaks: 571 WARNING @ Sun, 04 Nov 2018 17:52:52: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Sun, 04 Nov 2018 17:52:52: start model_add_line... INFO @ Sun, 04 Nov 2018 17:52:52: start X-correlation... INFO @ Sun, 04 Nov 2018 17:52:52: end of X-cor INFO @ Sun, 04 Nov 2018 17:52:52: #2 finished! INFO @ Sun, 04 Nov 2018 17:52:52: end of X-cor INFO @ Sun, 04 Nov 2018 17:52:52: #2 predicted fragment length is 51 bps INFO @ Sun, 04 Nov 2018 17:52:52: #2 finished! INFO @ Sun, 04 Nov 2018 17:52:52: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 04 Nov 2018 17:52:52: #2 predicted fragment length is 51 bps INFO @ Sun, 04 Nov 2018 17:52:52: #2.2 Generate R script for model : SRX4375852.10_model.r INFO @ Sun, 04 Nov 2018 17:52:52: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 04 Nov 2018 17:52:52: #2.2 Generate R script for model : SRX4375852.20_model.r WARNING @ Sun, 04 Nov 2018 17:52:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:52:52: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 04 Nov 2018 17:52:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:52:52: #3 Call peaks... WARNING @ Sun, 04 Nov 2018 17:52:52: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:52:52: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 04 Nov 2018 17:52:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:52:52: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:52:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:52:53: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:52:53: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:52:53: #1 total tags in treatment: 5172841 INFO @ Sun, 04 Nov 2018 17:52:53: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:52:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:52:53: #1 tags after filtering in treatment: 5172841 INFO @ Sun, 04 Nov 2018 17:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:52:53: #1 finished! INFO @ Sun, 04 Nov 2018 17:52:53: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:52:53: #2 number of paired peaks: 571 WARNING @ Sun, 04 Nov 2018 17:52:53: Fewer paired peaks (571) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 571 pairs to build model! INFO @ Sun, 04 Nov 2018 17:52:53: start model_add_line... INFO @ Sun, 04 Nov 2018 17:52:53: start X-correlation... INFO @ Sun, 04 Nov 2018 17:52:53: end of X-cor INFO @ Sun, 04 Nov 2018 17:52:53: #2 finished! INFO @ Sun, 04 Nov 2018 17:52:53: #2 predicted fragment length is 51 bps INFO @ Sun, 04 Nov 2018 17:52:53: #2 alternative fragment length(s) may be 51 bps INFO @ Sun, 04 Nov 2018 17:52:53: #2.2 Generate R script for model : SRX4375852.05_model.r WARNING @ Sun, 04 Nov 2018 17:52:53: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:52:53: #2 You may need to consider one of the other alternative d(s): 51 WARNING @ Sun, 04 Nov 2018 17:52:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:52:53: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:53:03: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:04: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:53:10: #4 Write output xls file... SRX4375852.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:53:10: #4 Write peak in narrowPeak format file... SRX4375852.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:53:10: #4 Write output xls file... SRX4375852.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:53:10: #4 Write summits bed file... SRX4375852.10_summits.bed INFO @ Sun, 04 Nov 2018 17:53:10: Done! INFO @ Sun, 04 Nov 2018 17:53:10: #4 Write peak in narrowPeak format file... SRX4375852.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:53:10: #4 Write summits bed file... SRX4375852.20_summits.bed INFO @ Sun, 04 Nov 2018 17:53:10: Done! pass1 - making usageList (8 chroms): 1 millis pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (722 records, 4 fields): 4 millis pass2 - checking and writing primary data (945 records, 4 fields): 4 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:53:11: #4 Write output xls file... SRX4375852.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:53:11: #4 Write peak in narrowPeak format file... SRX4375852.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:53:11: #4 Write summits bed file... SRX4375852.05_summits.bed INFO @ Sun, 04 Nov 2018 17:53:11: Done! pass1 - making usageList (14 chroms): 0 millis pass2 - checking and writing primary data (1299 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。