Job ID = 9157974 sra ファイルのダウンロード中... Completed: 3855661K bytes transferred in 135 seconds (233948K bits/sec), in 1 file, 2 directories. 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... Written 68200884 spots for /home/okishinya/chipatlas/results/dm3/SRX2788637/SRR5515257.sra Written 68200884 spots total 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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:24:41 68200884 reads; of these: 68200884 (100.00%) were unpaired; of these: 24932271 (36.56%) aligned 0 times 37733476 (55.33%) aligned exactly 1 time 5535137 (8.12%) aligned >1 times 63.44% overall alignment rate Time searching: 00:24:42 Overall time: 00:24:42 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_sort_core] merging from 20 files... [bam_rmdupse_core] 38916970 / 43268613 = 0.8994 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 @ Tue, 27 Jun 2017 15:00:11: # Command line: callpeak -t SRX2788637.bam -f BAM -g dm -n SRX2788637.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788637.10 # format = BAM # ChIP-seq file = ['SRX2788637.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 @ Tue, 27 Jun 2017 15:00:11: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:00:11: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:00:11: # Command line: callpeak -t SRX2788637.bam -f BAM -g dm -n SRX2788637.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788637.05 # format = BAM # ChIP-seq file = ['SRX2788637.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 @ Tue, 27 Jun 2017 15:00:11: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:00:11: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:00:11: # Command line: callpeak -t SRX2788637.bam -f BAM -g dm -n SRX2788637.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788637.20 # format = BAM # ChIP-seq file = ['SRX2788637.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 @ Tue, 27 Jun 2017 15:00:11: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:00:11: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:00:19: 1000000 INFO @ Tue, 27 Jun 2017 15:00:19: 1000000 INFO @ Tue, 27 Jun 2017 15:00:19: 1000000 INFO @ Tue, 27 Jun 2017 15:00:27: 2000000 INFO @ Tue, 27 Jun 2017 15:00:27: 2000000 INFO @ Tue, 27 Jun 2017 15:00:27: 2000000 INFO @ Tue, 27 Jun 2017 15:00:35: 3000000 INFO @ Tue, 27 Jun 2017 15:00:35: 3000000 INFO @ Tue, 27 Jun 2017 15:00:35: 3000000 INFO @ Tue, 27 Jun 2017 15:00:43: 4000000 INFO @ Tue, 27 Jun 2017 15:00:43: 4000000 INFO @ Tue, 27 Jun 2017 15:00:43: 4000000 INFO @ Tue, 27 Jun 2017 15:00:45: #1 tag size is determined as 85 bps INFO @ Tue, 27 Jun 2017 15:00:45: #1 tag size = 85 INFO @ Tue, 27 Jun 2017 15:00:45: #1 total tags in treatment: 4351643 INFO @ Tue, 27 Jun 2017 15:00:45: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:00:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:00:45: #1 tags after filtering in treatment: 4351643 INFO @ Tue, 27 Jun 2017 15:00:45: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:00:45: #1 finished! INFO @ Tue, 27 Jun 2017 15:00:45: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:00:45: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:00:45: #1 tag size is determined as 85 bps INFO @ Tue, 27 Jun 2017 15:00:45: #1 tag size = 85 INFO @ Tue, 27 Jun 2017 15:00:45: #1 total tags in treatment: 4351643 INFO @ Tue, 27 Jun 2017 15:00:45: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:00:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:00:46: #1 tags after filtering in treatment: 4351643 INFO @ Tue, 27 Jun 2017 15:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:00:46: #1 finished! INFO @ Tue, 27 Jun 2017 15:00:46: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:00:46: #1 tag size is determined as 85 bps INFO @ Tue, 27 Jun 2017 15:00:46: #1 tag size = 85 INFO @ Tue, 27 Jun 2017 15:00:46: #1 total tags in treatment: 4351643 INFO @ Tue, 27 Jun 2017 15:00:46: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:00:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 27 Jun 2017 15:00:46: #1 tags after filtering in treatment: 4351643 INFO @ Tue, 27 Jun 2017 15:00:46: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:00:46: #1 finished! INFO @ Tue, 27 Jun 2017 15:00:46: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:00:46: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:00:46: #2 number of paired peaks: 835 WARNING @ Tue, 27 Jun 2017 15:00:46: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Tue, 27 Jun 2017 15:00:46: start model_add_line... INFO @ Tue, 27 Jun 2017 15:00:46: start X-correlation... INFO @ Tue, 27 Jun 2017 15:00:46: end of X-cor INFO @ Tue, 27 Jun 2017 15:00:46: #2 finished! INFO @ Tue, 27 Jun 2017 15:00:46: #2 predicted fragment length is 105 bps INFO @ Tue, 27 Jun 2017 15:00:46: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 27 Jun 2017 15:00:46: #2.2 Generate R script for model : SRX2788637.10_model.r WARNING @ Tue, 27 Jun 2017 15:00:46: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:00:46: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Tue, 27 Jun 2017 15:00:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 15:00:46: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:00:46: #2 number of paired peaks: 835 WARNING @ Tue, 27 Jun 2017 15:00:46: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Tue, 27 Jun 2017 15:00:46: start model_add_line... INFO @ Tue, 27 Jun 2017 15:00:46: start X-correlation... INFO @ Tue, 27 Jun 2017 15:00:46: end of X-cor INFO @ Tue, 27 Jun 2017 15:00:46: #2 finished! INFO @ Tue, 27 Jun 2017 15:00:46: #2 predicted fragment length is 105 bps INFO @ Tue, 27 Jun 2017 15:00:46: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 27 Jun 2017 15:00:46: #2.2 Generate R script for model : SRX2788637.20_model.r WARNING @ Tue, 27 Jun 2017 15:00:46: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:00:46: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Tue, 27 Jun 2017 15:00:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 15:00:46: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:00:46: #2 number of paired peaks: 835 WARNING @ Tue, 27 Jun 2017 15:00:46: Fewer paired peaks (835) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 835 pairs to build model! INFO @ Tue, 27 Jun 2017 15:00:46: start model_add_line... INFO @ Tue, 27 Jun 2017 15:00:46: start X-correlation... INFO @ Tue, 27 Jun 2017 15:00:46: end of X-cor INFO @ Tue, 27 Jun 2017 15:00:46: #2 finished! INFO @ Tue, 27 Jun 2017 15:00:46: #2 predicted fragment length is 105 bps INFO @ Tue, 27 Jun 2017 15:00:46: #2 alternative fragment length(s) may be 105 bps INFO @ Tue, 27 Jun 2017 15:00:46: #2.2 Generate R script for model : SRX2788637.05_model.r WARNING @ Tue, 27 Jun 2017 15:00:46: #2 Since the d (105) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:00:46: #2 You may need to consider one of the other alternative d(s): 105 WARNING @ Tue, 27 Jun 2017 15:00:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 27 Jun 2017 15:00:46: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:00:46: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:00:56: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:00:57: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:00:57: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:01:02: #4 Write output xls file... SRX2788637.10_peaks.xls INFO @ Tue, 27 Jun 2017 15:01:02: #4 Write peak in narrowPeak format file... SRX2788637.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:01:02: #4 Write summits bed file... SRX2788637.10_summits.bed INFO @ Tue, 27 Jun 2017 15:01:02: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1322 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:01:02: #4 Write output xls file... SRX2788637.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:01:02: #4 Write peak in narrowPeak format file... SRX2788637.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:01:02: #4 Write summits bed file... SRX2788637.20_summits.bed INFO @ Tue, 27 Jun 2017 15:01:02: Done! pass1 - making usageList (12 chroms): 0 millis pass2 - checking and writing primary data (590 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:01:04: #4 Write output xls file... SRX2788637.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:01:04: #4 Write peak in narrowPeak format file... SRX2788637.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:01:04: #4 Write summits bed file... SRX2788637.05_summits.bed INFO @ Tue, 27 Jun 2017 15:01:04: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4257 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。