Job ID = 9158720 sra ファイルのダウンロード中... Completed: 91149K bytes transferred in 5 seconds (137326K 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: PAIRED fastq に変換中... Written 1575494 spots for /home/okishinya/chipatlas/results/dm3/SRX2677152/SRR5382072.sra Written 1575494 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: 00:00:01 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:34 1575494 reads; of these: 1575494 (100.00%) were paired; of these: 266292 (16.90%) aligned concordantly 0 times 917715 (58.25%) aligned concordantly exactly 1 time 391487 (24.85%) aligned concordantly >1 times ---- 266292 pairs aligned concordantly 0 times; of these: 5322 (2.00%) aligned discordantly 1 time ---- 260970 pairs aligned 0 times concordantly or discordantly; of these: 521940 mates make up the pairs; of these: 500767 (95.94%) aligned 0 times 12905 (2.47%) aligned exactly 1 time 8268 (1.58%) aligned >1 times 84.11% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 86310 / 587107 = 0.1470 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 19:17:51: # Command line: callpeak -t SRX2677152.bam -f BAM -g dm -n SRX2677152.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2677152.10 # format = BAM # ChIP-seq file = ['SRX2677152.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 19:17:51: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:17:51: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:17:51: # Command line: callpeak -t SRX2677152.bam -f BAM -g dm -n SRX2677152.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2677152.05 # format = BAM # ChIP-seq file = ['SRX2677152.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 19:17:51: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:17:51: # Command line: callpeak -t SRX2677152.bam -f BAM -g dm -n SRX2677152.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2677152.20 # format = BAM # ChIP-seq file = ['SRX2677152.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 19:17:51: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:17:51: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:17:51: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:17:57: 1000000 INFO @ Tue, 27 Jun 2017 19:17:59: 1000000 INFO @ Tue, 27 Jun 2017 19:17:59: 1000000 INFO @ Tue, 27 Jun 2017 19:18:03: 2000000 INFO @ Tue, 27 Jun 2017 19:18:06: #1 tag size is determined as 60 bps INFO @ Tue, 27 Jun 2017 19:18:06: #1 tag size = 60 INFO @ Tue, 27 Jun 2017 19:18:06: #1 total tags in treatment: 1222944 INFO @ Tue, 27 Jun 2017 19:18:06: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:18:06: #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 19:18:06: #1 tags after filtering in treatment: 1058240 INFO @ Tue, 27 Jun 2017 19:18:06: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 27 Jun 2017 19:18:06: #1 finished! INFO @ Tue, 27 Jun 2017 19:18:06: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:18:06: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:18:06: #2 number of paired peaks: 758 WARNING @ Tue, 27 Jun 2017 19:18:06: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 27 Jun 2017 19:18:06: start model_add_line... INFO @ Tue, 27 Jun 2017 19:18:06: start X-correlation... INFO @ Tue, 27 Jun 2017 19:18:06: end of X-cor INFO @ Tue, 27 Jun 2017 19:18:06: #2 finished! INFO @ Tue, 27 Jun 2017 19:18:06: #2 predicted fragment length is 88 bps INFO @ Tue, 27 Jun 2017 19:18:06: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 27 Jun 2017 19:18:06: #2.2 Generate R script for model : SRX2677152.10_model.r WARNING @ Tue, 27 Jun 2017 19:18:06: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:18:06: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 27 Jun 2017 19:18:06: #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 19:18:06: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:18:06: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:18:06: 2000000 INFO @ Tue, 27 Jun 2017 19:18:06: 2000000 INFO @ Tue, 27 Jun 2017 19:18:09: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:18:10: #1 tag size is determined as 60 bps INFO @ Tue, 27 Jun 2017 19:18:10: #1 tag size = 60 INFO @ Tue, 27 Jun 2017 19:18:10: #1 total tags in treatment: 1222944 INFO @ Tue, 27 Jun 2017 19:18:10: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:18:10: #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 19:18:10: #1 tag size is determined as 60 bps INFO @ Tue, 27 Jun 2017 19:18:10: #1 tag size = 60 INFO @ Tue, 27 Jun 2017 19:18:10: #1 total tags in treatment: 1222944 INFO @ Tue, 27 Jun 2017 19:18:10: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:18:10: #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 19:18:10: #1 tags after filtering in treatment: 1058240 INFO @ Tue, 27 Jun 2017 19:18:10: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 27 Jun 2017 19:18:10: #1 finished! INFO @ Tue, 27 Jun 2017 19:18:10: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:18:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:18:10: #1 tags after filtering in treatment: 1058240 INFO @ Tue, 27 Jun 2017 19:18:10: #1 Redundant rate of treatment: 0.13 INFO @ Tue, 27 Jun 2017 19:18:10: #1 finished! INFO @ Tue, 27 Jun 2017 19:18:10: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:18:10: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:18:10: #2 number of paired peaks: 758 WARNING @ Tue, 27 Jun 2017 19:18:10: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 27 Jun 2017 19:18:10: start model_add_line... INFO @ Tue, 27 Jun 2017 19:18:10: start X-correlation... INFO @ Tue, 27 Jun 2017 19:18:10: end of X-cor INFO @ Tue, 27 Jun 2017 19:18:10: #2 finished! INFO @ Tue, 27 Jun 2017 19:18:10: #2 predicted fragment length is 88 bps INFO @ Tue, 27 Jun 2017 19:18:10: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 27 Jun 2017 19:18:10: #2.2 Generate R script for model : SRX2677152.20_model.r INFO @ Tue, 27 Jun 2017 19:18:10: #2 number of paired peaks: 758 WARNING @ Tue, 27 Jun 2017 19:18:10: Fewer paired peaks (758) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 758 pairs to build model! INFO @ Tue, 27 Jun 2017 19:18:10: start model_add_line... WARNING @ Tue, 27 Jun 2017 19:18:10: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:18:10: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 27 Jun 2017 19:18:10: #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 19:18:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:18:10: start X-correlation... INFO @ Tue, 27 Jun 2017 19:18:10: end of X-cor INFO @ Tue, 27 Jun 2017 19:18:10: #2 finished! INFO @ Tue, 27 Jun 2017 19:18:10: #2 predicted fragment length is 88 bps INFO @ Tue, 27 Jun 2017 19:18:10: #2 alternative fragment length(s) may be 88 bps INFO @ Tue, 27 Jun 2017 19:18:10: #2.2 Generate R script for model : SRX2677152.05_model.r WARNING @ Tue, 27 Jun 2017 19:18:10: #2 Since the d (88) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:18:10: #2 You may need to consider one of the other alternative d(s): 88 WARNING @ Tue, 27 Jun 2017 19:18:10: #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 19:18:10: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:18:10: #4 Write output xls file... SRX2677152.10_peaks.xls INFO @ Tue, 27 Jun 2017 19:18:10: #4 Write peak in narrowPeak format file... SRX2677152.10_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:18:10: #4 Write summits bed file... SRX2677152.10_summits.bed INFO @ Tue, 27 Jun 2017 19:18:10: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (425 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:18:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:18:13: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:18:14: #4 Write output xls file... SRX2677152.20_peaks.xls INFO @ Tue, 27 Jun 2017 19:18:14: #4 Write peak in narrowPeak format file... SRX2677152.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:18:14: #4 Write summits bed file... SRX2677152.20_summits.bed INFO @ Tue, 27 Jun 2017 19:18:14: Done! pass1 - making usageList (5 chroms): 1 millis pass2 - checking and writing primary data (189 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:18:14: #4 Write output xls file... SRX2677152.05_peaks.xls INFO @ Tue, 27 Jun 2017 19:18:14: #4 Write peak in narrowPeak format file... SRX2677152.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:18:14: #4 Write summits bed file... SRX2677152.05_summits.bed INFO @ Tue, 27 Jun 2017 19:18:14: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (643 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。