Job ID = 9158722 sra ファイルのダウンロード中... Completed: 175801K bytes transferred in 7 seconds (194783K 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 2797610 spots for /home/okishinya/chipatlas/results/dm3/SRX2677154/SRR5382074.sra Written 2797610 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: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:10:24 2797610 reads; of these: 2797610 (100.00%) were paired; of these: 412120 (14.73%) aligned concordantly 0 times 1290277 (46.12%) aligned concordantly exactly 1 time 1095213 (39.15%) aligned concordantly >1 times ---- 412120 pairs aligned concordantly 0 times; of these: 12019 (2.92%) aligned discordantly 1 time ---- 400101 pairs aligned 0 times concordantly or discordantly; of these: 800202 mates make up the pairs; of these: 739288 (92.39%) aligned 0 times 28591 (3.57%) aligned exactly 1 time 32323 (4.04%) aligned >1 times 86.79% overall alignment rate Time searching: 00:10:24 Overall time: 00:10:24 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] 402749 / 1648629 = 0.2443 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 19:25:44: # Command line: callpeak -t SRX2677154.bam -f BAM -g dm -n SRX2677154.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2677154.20 # format = BAM # ChIP-seq file = ['SRX2677154.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 19:25:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:25:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:25:44: # Command line: callpeak -t SRX2677154.bam -f BAM -g dm -n SRX2677154.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2677154.10 # format = BAM # ChIP-seq file = ['SRX2677154.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 19:25:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:25:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:25:44: # Command line: callpeak -t SRX2677154.bam -f BAM -g dm -n SRX2677154.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2677154.05 # format = BAM # ChIP-seq file = ['SRX2677154.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 19:25:44: #1 read tag files... INFO @ Tue, 27 Jun 2017 19:25:44: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 19:25:51: 1000000 INFO @ Tue, 27 Jun 2017 19:25:52: 1000000 INFO @ Tue, 27 Jun 2017 19:25:52: 1000000 INFO @ Tue, 27 Jun 2017 19:25:58: 2000000 INFO @ Tue, 27 Jun 2017 19:26:00: 2000000 INFO @ Tue, 27 Jun 2017 19:26:00: 2000000 INFO @ Tue, 27 Jun 2017 19:26:05: 3000000 INFO @ Tue, 27 Jun 2017 19:26:07: 3000000 INFO @ Tue, 27 Jun 2017 19:26:07: 3000000 INFO @ Tue, 27 Jun 2017 19:26:12: 4000000 INFO @ Tue, 27 Jun 2017 19:26:12: #1 tag size is determined as 68 bps INFO @ Tue, 27 Jun 2017 19:26:12: #1 tag size = 68 INFO @ Tue, 27 Jun 2017 19:26:12: #1 total tags in treatment: 1983014 INFO @ Tue, 27 Jun 2017 19:26:12: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:26:12: #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 19:26:12: #1 tags after filtering in treatment: 1670964 INFO @ Tue, 27 Jun 2017 19:26:12: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 27 Jun 2017 19:26:12: #1 finished! INFO @ Tue, 27 Jun 2017 19:26:12: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:26:12: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:26:13: #2 number of paired peaks: 752 WARNING @ Tue, 27 Jun 2017 19:26:13: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Tue, 27 Jun 2017 19:26:13: start model_add_line... INFO @ Tue, 27 Jun 2017 19:26:13: start X-correlation... INFO @ Tue, 27 Jun 2017 19:26:13: end of X-cor INFO @ Tue, 27 Jun 2017 19:26:13: #2 finished! INFO @ Tue, 27 Jun 2017 19:26:13: #2 predicted fragment length is 93 bps INFO @ Tue, 27 Jun 2017 19:26:13: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 27 Jun 2017 19:26:13: #2.2 Generate R script for model : SRX2677154.20_model.r WARNING @ Tue, 27 Jun 2017 19:26:13: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:26:13: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 27 Jun 2017 19:26:13: #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 19:26:13: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:26:13: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:26:15: 4000000 INFO @ Tue, 27 Jun 2017 19:26:15: 4000000 INFO @ Tue, 27 Jun 2017 19:26:15: #1 tag size is determined as 68 bps INFO @ Tue, 27 Jun 2017 19:26:15: #1 tag size = 68 INFO @ Tue, 27 Jun 2017 19:26:15: #1 total tags in treatment: 1983014 INFO @ Tue, 27 Jun 2017 19:26:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:26:15: #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 19:26:15: #1 tag size is determined as 68 bps INFO @ Tue, 27 Jun 2017 19:26:15: #1 tag size = 68 INFO @ Tue, 27 Jun 2017 19:26:15: #1 total tags in treatment: 1983014 INFO @ Tue, 27 Jun 2017 19:26:15: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 19:26:15: #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 19:26:15: #1 tags after filtering in treatment: 1670964 INFO @ Tue, 27 Jun 2017 19:26:15: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 27 Jun 2017 19:26:15: #1 finished! INFO @ Tue, 27 Jun 2017 19:26:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:26:15: #1 tags after filtering in treatment: 1670964 INFO @ Tue, 27 Jun 2017 19:26:15: #1 Redundant rate of treatment: 0.16 INFO @ Tue, 27 Jun 2017 19:26:15: #1 finished! INFO @ Tue, 27 Jun 2017 19:26:15: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 19:26:15: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 19:26:15: #2 number of paired peaks: 752 WARNING @ Tue, 27 Jun 2017 19:26:15: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Tue, 27 Jun 2017 19:26:15: start model_add_line... INFO @ Tue, 27 Jun 2017 19:26:15: start X-correlation... INFO @ Tue, 27 Jun 2017 19:26:15: end of X-cor INFO @ Tue, 27 Jun 2017 19:26:15: #2 finished! INFO @ Tue, 27 Jun 2017 19:26:15: #2 predicted fragment length is 93 bps INFO @ Tue, 27 Jun 2017 19:26:15: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 27 Jun 2017 19:26:15: #2.2 Generate R script for model : SRX2677154.10_model.r WARNING @ Tue, 27 Jun 2017 19:26:15: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:26:15: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 27 Jun 2017 19:26:15: #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 19:26:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:26:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:26:15: #2 number of paired peaks: 752 WARNING @ Tue, 27 Jun 2017 19:26:15: Fewer paired peaks (752) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 752 pairs to build model! INFO @ Tue, 27 Jun 2017 19:26:15: start model_add_line... INFO @ Tue, 27 Jun 2017 19:26:15: start X-correlation... INFO @ Tue, 27 Jun 2017 19:26:15: end of X-cor INFO @ Tue, 27 Jun 2017 19:26:15: #2 finished! INFO @ Tue, 27 Jun 2017 19:26:15: #2 predicted fragment length is 93 bps INFO @ Tue, 27 Jun 2017 19:26:15: #2 alternative fragment length(s) may be 93 bps INFO @ Tue, 27 Jun 2017 19:26:15: #2.2 Generate R script for model : SRX2677154.05_model.r WARNING @ Tue, 27 Jun 2017 19:26:15: #2 Since the d (93) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 19:26:15: #2 You may need to consider one of the other alternative d(s): 93 WARNING @ Tue, 27 Jun 2017 19:26:15: #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 19:26:15: #3 Call peaks... INFO @ Tue, 27 Jun 2017 19:26:15: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 19:26:17: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:26:19: #4 Write output xls file... SRX2677154.20_peaks.xls INFO @ Tue, 27 Jun 2017 19:26:19: #4 Write peak in narrowPeak format file... SRX2677154.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:26:19: #4 Write summits bed file... SRX2677154.20_summits.bed INFO @ Tue, 27 Jun 2017 19:26:19: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (358 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 19:26:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:26:19: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 19:26:21: #4 Write output xls file... SRX2677154.05_peaks.xls INFO @ Tue, 27 Jun 2017 19:26:21: #4 Write peak in narrowPeak format file... SRX2677154.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 19:26:21: #4 Write summits bed file... SRX2677154.05_summits.bed INFO @ Tue, 27 Jun 2017 19:26:21: Done! INFO @ Tue, 27 Jun 2017 19:26:22: #4 Write output xls file... SRX2677154.10_peaks.xls INFO @ Tue, 27 Jun 2017 19:26:22: #4 Write peak in narrowPeak format file... SRX2677154.10_peaks.narrowPeak pass1 - making usageList (10 chroms): 0 millis INFO @ Tue, 27 Jun 2017 19:26:22: #4 Write summits bed file... SRX2677154.10_summits.bed pass2 - checking and writing primary data (810 records, 4 fields): 3 millis INFO @ Tue, 27 Jun 2017 19:26:22: Done! CompletedMACS2peakCalling pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (575 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。