Job ID = 11293687 sra ファイルのダウンロード中... Completed: 355297K bytes transferred in 17 seconds (165189K 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 10409128 spots for /home/okishinya/chipatlas/results/dm3/SRX4375849/SRR7506503.sra Written 10409128 spots for /home/okishinya/chipatlas/results/dm3/SRX4375849/SRR7506503.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: 00:03:07 10409128 reads; of these: 10409128 (100.00%) were unpaired; of these: 2337463 (22.46%) aligned 0 times 6347512 (60.98%) aligned exactly 1 time 1724153 (16.56%) aligned >1 times 77.54% overall alignment rate Time searching: 00:03:07 Overall time: 00:03:07 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] 711518 / 8071665 = 0.0882 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 17:53:24: # Command line: callpeak -t SRX4375849.bam -f BAM -g dm -n SRX4375849.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4375849.20 # format = BAM # ChIP-seq file = ['SRX4375849.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 17:53:24: # Command line: callpeak -t SRX4375849.bam -f BAM -g dm -n SRX4375849.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4375849.05 # format = BAM # ChIP-seq file = ['SRX4375849.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 17:53:24: # Command line: callpeak -t SRX4375849.bam -f BAM -g dm -n SRX4375849.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4375849.10 # format = BAM # ChIP-seq file = ['SRX4375849.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 17:53:24: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:24: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:24: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:24: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:24: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:24: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:30: 1000000 INFO @ Sun, 04 Nov 2018 17:53:30: 1000000 INFO @ Sun, 04 Nov 2018 17:53:30: 1000000 INFO @ Sun, 04 Nov 2018 17:53:36: 2000000 INFO @ Sun, 04 Nov 2018 17:53:36: 2000000 INFO @ Sun, 04 Nov 2018 17:53:37: 2000000 INFO @ Sun, 04 Nov 2018 17:53:43: 3000000 INFO @ Sun, 04 Nov 2018 17:53:43: 3000000 INFO @ Sun, 04 Nov 2018 17:53:44: 3000000 INFO @ Sun, 04 Nov 2018 17:53:49: 4000000 INFO @ Sun, 04 Nov 2018 17:53:49: 4000000 INFO @ Sun, 04 Nov 2018 17:53:50: 4000000 INFO @ Sun, 04 Nov 2018 17:53:56: 5000000 INFO @ Sun, 04 Nov 2018 17:53:56: 5000000 INFO @ Sun, 04 Nov 2018 17:53:57: 5000000 INFO @ Sun, 04 Nov 2018 17:54:02: 6000000 INFO @ Sun, 04 Nov 2018 17:54:03: 6000000 INFO @ Sun, 04 Nov 2018 17:54:04: 6000000 INFO @ Sun, 04 Nov 2018 17:54:08: 7000000 INFO @ Sun, 04 Nov 2018 17:54:09: 7000000 INFO @ Sun, 04 Nov 2018 17:54:11: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:54:11: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:54:11: #1 total tags in treatment: 7360147 INFO @ Sun, 04 Nov 2018 17:54:11: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:11: #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 17:54:11: #1 tags after filtering in treatment: 7360147 INFO @ Sun, 04 Nov 2018 17:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:11: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:11: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:54:11: 7000000 INFO @ Sun, 04 Nov 2018 17:54:11: #2 number of paired peaks: 315 WARNING @ Sun, 04 Nov 2018 17:54:11: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Sun, 04 Nov 2018 17:54:11: start model_add_line... INFO @ Sun, 04 Nov 2018 17:54:11: start X-correlation... INFO @ Sun, 04 Nov 2018 17:54:12: end of X-cor INFO @ Sun, 04 Nov 2018 17:54:12: #2 finished! INFO @ Sun, 04 Nov 2018 17:54:12: #2 predicted fragment length is 53 bps INFO @ Sun, 04 Nov 2018 17:54:12: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 04 Nov 2018 17:54:12: #2.2 Generate R script for model : SRX4375849.20_model.r WARNING @ Sun, 04 Nov 2018 17:54:12: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:54:12: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 04 Nov 2018 17:54:12: #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 17:54:12: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:54:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:54:12: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:54:12: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:54:12: #1 total tags in treatment: 7360147 INFO @ Sun, 04 Nov 2018 17:54:12: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:12: #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 17:54:12: #1 tags after filtering in treatment: 7360147 INFO @ Sun, 04 Nov 2018 17:54:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:12: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:12: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:54:12: #2 number of paired peaks: 315 WARNING @ Sun, 04 Nov 2018 17:54:12: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Sun, 04 Nov 2018 17:54:12: start model_add_line... INFO @ Sun, 04 Nov 2018 17:54:13: start X-correlation... INFO @ Sun, 04 Nov 2018 17:54:13: end of X-cor INFO @ Sun, 04 Nov 2018 17:54:13: #2 finished! INFO @ Sun, 04 Nov 2018 17:54:13: #2 predicted fragment length is 53 bps INFO @ Sun, 04 Nov 2018 17:54:13: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 04 Nov 2018 17:54:13: #2.2 Generate R script for model : SRX4375849.05_model.r WARNING @ Sun, 04 Nov 2018 17:54:13: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:54:13: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 04 Nov 2018 17:54:13: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:54:13: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:54:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:54:13: #1 tag size is determined as 51 bps INFO @ Sun, 04 Nov 2018 17:54:13: #1 tag size = 51 INFO @ Sun, 04 Nov 2018 17:54:13: #1 total tags in treatment: 7360147 INFO @ Sun, 04 Nov 2018 17:54:13: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:13: #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 17:54:13: #1 tags after filtering in treatment: 7360147 INFO @ Sun, 04 Nov 2018 17:54:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:13: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:13: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:54:14: #2 number of paired peaks: 315 WARNING @ Sun, 04 Nov 2018 17:54:14: Fewer paired peaks (315) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 315 pairs to build model! INFO @ Sun, 04 Nov 2018 17:54:14: start model_add_line... INFO @ Sun, 04 Nov 2018 17:54:14: start X-correlation... INFO @ Sun, 04 Nov 2018 17:54:14: end of X-cor INFO @ Sun, 04 Nov 2018 17:54:14: #2 finished! INFO @ Sun, 04 Nov 2018 17:54:14: #2 predicted fragment length is 53 bps INFO @ Sun, 04 Nov 2018 17:54:14: #2 alternative fragment length(s) may be 53 bps INFO @ Sun, 04 Nov 2018 17:54:14: #2.2 Generate R script for model : SRX4375849.10_model.r WARNING @ Sun, 04 Nov 2018 17:54:14: #2 Since the d (53) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 04 Nov 2018 17:54:14: #2 You may need to consider one of the other alternative d(s): 53 WARNING @ Sun, 04 Nov 2018 17:54:14: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 04 Nov 2018 17:54:14: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:54:27: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:54:31: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:54:31: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:54:36: #4 Write output xls file... SRX4375849.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:54:36: #4 Write peak in narrowPeak format file... SRX4375849.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:54:36: #4 Write summits bed file... SRX4375849.20_summits.bed INFO @ Sun, 04 Nov 2018 17:54:36: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (550 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:54:40: #4 Write output xls file... SRX4375849.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:54:40: #4 Write peak in narrowPeak format file... SRX4375849.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:54:40: #4 Write summits bed file... SRX4375849.05_summits.bed INFO @ Sun, 04 Nov 2018 17:54:40: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1538 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:54:40: #4 Write output xls file... SRX4375849.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:54:41: #4 Write peak in narrowPeak format file... SRX4375849.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:54:41: #4 Write summits bed file... SRX4375849.10_summits.bed INFO @ Sun, 04 Nov 2018 17:54:41: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (876 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。