Job ID = 11171343 sra ファイルのダウンロード中... Completed: 249893K bytes transferred in 12 seconds (165105K 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 6329909 spots for /home/okishinya/chipatlas/results/dm3/SRX3511953/SRR6418938.sra Written 6329909 spots for /home/okishinya/chipatlas/results/dm3/SRX3511953/SRR6418938.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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:53 6329909 reads; of these: 6329909 (100.00%) were unpaired; of these: 633334 (10.01%) aligned 0 times 4049359 (63.97%) aligned exactly 1 time 1647216 (26.02%) aligned >1 times 89.99% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 558365 / 5696575 = 0.0980 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 13:53:32: # Command line: callpeak -t SRX3511953.bam -f BAM -g dm -n SRX3511953.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3511953.05 # format = BAM # ChIP-seq file = ['SRX3511953.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 13:53:32: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:53:32: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:53:32: # Command line: callpeak -t SRX3511953.bam -f BAM -g dm -n SRX3511953.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3511953.20 # format = BAM # ChIP-seq file = ['SRX3511953.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 13:53:32: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:53:32: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:53:32: # Command line: callpeak -t SRX3511953.bam -f BAM -g dm -n SRX3511953.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3511953.10 # format = BAM # ChIP-seq file = ['SRX3511953.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 13:53:32: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:53:32: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:53:40: 1000000 INFO @ Sat, 08 Sep 2018 13:53:40: 1000000 INFO @ Sat, 08 Sep 2018 13:53:40: 1000000 INFO @ Sat, 08 Sep 2018 13:53:48: 2000000 INFO @ Sat, 08 Sep 2018 13:53:48: 2000000 INFO @ Sat, 08 Sep 2018 13:53:48: 2000000 INFO @ Sat, 08 Sep 2018 13:53:56: 3000000 INFO @ Sat, 08 Sep 2018 13:53:56: 3000000 INFO @ Sat, 08 Sep 2018 13:53:56: 3000000 INFO @ Sat, 08 Sep 2018 13:54:03: 4000000 INFO @ Sat, 08 Sep 2018 13:54:05: 4000000 INFO @ Sat, 08 Sep 2018 13:54:05: 4000000 INFO @ Sat, 08 Sep 2018 13:54:11: 5000000 INFO @ Sat, 08 Sep 2018 13:54:12: #1 tag size is determined as 99 bps INFO @ Sat, 08 Sep 2018 13:54:12: #1 tag size = 99 INFO @ Sat, 08 Sep 2018 13:54:12: #1 total tags in treatment: 5138210 INFO @ Sat, 08 Sep 2018 13:54:12: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:12: #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 13:54:12: #1 tags after filtering in treatment: 5138210 INFO @ Sat, 08 Sep 2018 13:54:12: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:12: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:12: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:13: #2 number of paired peaks: 176 WARNING @ Sat, 08 Sep 2018 13:54:13: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:13: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:13: 5000000 INFO @ Sat, 08 Sep 2018 13:54:13: 5000000 INFO @ Sat, 08 Sep 2018 13:54:13: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:13: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:13: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:13: #2 predicted fragment length is 141 bps INFO @ Sat, 08 Sep 2018 13:54:13: #2 alternative fragment length(s) may be 19,119,141,234,236,283,446,479,497,533,591 bps INFO @ Sat, 08 Sep 2018 13:54:13: #2.2 Generate R script for model : SRX3511953.05_model.r WARNING @ Sat, 08 Sep 2018 13:54:13: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:13: #2 You may need to consider one of the other alternative d(s): 19,119,141,234,236,283,446,479,497,533,591 WARNING @ Sat, 08 Sep 2018 13:54:13: #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 13:54:13: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:54:14: #1 tag size is determined as 99 bps INFO @ Sat, 08 Sep 2018 13:54:14: #1 tag size = 99 INFO @ Sat, 08 Sep 2018 13:54:14: #1 total tags in treatment: 5138210 INFO @ Sat, 08 Sep 2018 13:54:14: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:14: #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 13:54:14: #1 tag size is determined as 99 bps INFO @ Sat, 08 Sep 2018 13:54:14: #1 tag size = 99 INFO @ Sat, 08 Sep 2018 13:54:14: #1 total tags in treatment: 5138210 INFO @ Sat, 08 Sep 2018 13:54:14: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:54:14: #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 13:54:14: #1 tags after filtering in treatment: 5138210 INFO @ Sat, 08 Sep 2018 13:54:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:14: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:14: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:14: #1 tags after filtering in treatment: 5138210 INFO @ Sat, 08 Sep 2018 13:54:14: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:54:14: #1 finished! INFO @ Sat, 08 Sep 2018 13:54:14: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:54:14: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:54:14: #2 number of paired peaks: 176 WARNING @ Sat, 08 Sep 2018 13:54:14: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:14: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:14: #2 number of paired peaks: 176 WARNING @ Sat, 08 Sep 2018 13:54:14: Fewer paired peaks (176) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 176 pairs to build model! INFO @ Sat, 08 Sep 2018 13:54:14: start model_add_line... INFO @ Sat, 08 Sep 2018 13:54:14: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:14: start X-correlation... INFO @ Sat, 08 Sep 2018 13:54:14: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:14: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:14: #2 predicted fragment length is 141 bps INFO @ Sat, 08 Sep 2018 13:54:14: #2 alternative fragment length(s) may be 19,119,141,234,236,283,446,479,497,533,591 bps INFO @ Sat, 08 Sep 2018 13:54:14: #2.2 Generate R script for model : SRX3511953.20_model.r INFO @ Sat, 08 Sep 2018 13:54:14: end of X-cor INFO @ Sat, 08 Sep 2018 13:54:14: #2 finished! INFO @ Sat, 08 Sep 2018 13:54:14: #2 predicted fragment length is 141 bps INFO @ Sat, 08 Sep 2018 13:54:14: #2 alternative fragment length(s) may be 19,119,141,234,236,283,446,479,497,533,591 bps INFO @ Sat, 08 Sep 2018 13:54:14: #2.2 Generate R script for model : SRX3511953.10_model.r WARNING @ Sat, 08 Sep 2018 13:54:14: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:14: #2 You may need to consider one of the other alternative d(s): 19,119,141,234,236,283,446,479,497,533,591 WARNING @ Sat, 08 Sep 2018 13:54:14: #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 13:54:14: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:14: #3 Pre-compute pvalue-qvalue table... WARNING @ Sat, 08 Sep 2018 13:54:14: #2 Since the d (141) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 08 Sep 2018 13:54:14: #2 You may need to consider one of the other alternative d(s): 19,119,141,234,236,283,446,479,497,533,591 WARNING @ Sat, 08 Sep 2018 13:54:14: #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 13:54:14: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:54:24: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:54:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:54:26: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:54:30: #4 Write output xls file... SRX3511953.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:54:30: #4 Write peak in narrowPeak format file... SRX3511953.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:54:30: #4 Write summits bed file... SRX3511953.05_summits.bed INFO @ Sat, 08 Sep 2018 13:54:30: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (448 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:54:32: #4 Write output xls file... SRX3511953.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:54:32: #4 Write peak in narrowPeak format file... SRX3511953.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:54:32: #4 Write summits bed file... SRX3511953.20_summits.bed INFO @ Sat, 08 Sep 2018 13:54:32: Done! pass1 - making usageList (3 chroms): 0 millis pass2 - checking and writing primary data (24 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:54:33: #4 Write output xls file... SRX3511953.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:54:33: #4 Write peak in narrowPeak format file... SRX3511953.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:54:33: #4 Write summits bed file... SRX3511953.10_summits.bed INFO @ Sat, 08 Sep 2018 13:54:33: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (110 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。