Job ID = 9157991 sra ファイルのダウンロード中... Completed: 8113228K bytes transferred in 299 seconds (222074K 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 150601542 spots for /home/okishinya/chipatlas/results/dm3/SRX2788647/SRR5515267.sra Written 150601542 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: 00:55:06 150601542 reads; of these: 150601542 (100.00%) were unpaired; of these: 51484983 (34.19%) aligned 0 times 85575484 (56.82%) aligned exactly 1 time 13541075 (8.99%) aligned >1 times 65.81% overall alignment rate Time searching: 00:55:07 Overall time: 00:55:07 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_sort_core] merging from 44 files... [bam_rmdupse_core] 95465858 / 99116559 = 0.9632 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 15:55:18: # Command line: callpeak -t SRX2788647.bam -f BAM -g dm -n SRX2788647.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2788647.10 # format = BAM # ChIP-seq file = ['SRX2788647.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 15:55:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:55:18: # Command line: callpeak -t SRX2788647.bam -f BAM -g dm -n SRX2788647.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2788647.05 # format = BAM # ChIP-seq file = ['SRX2788647.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 15:55:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:55:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:55:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:55:18: # Command line: callpeak -t SRX2788647.bam -f BAM -g dm -n SRX2788647.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2788647.20 # format = BAM # ChIP-seq file = ['SRX2788647.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 15:55:18: #1 read tag files... INFO @ Tue, 27 Jun 2017 15:55:18: #1 read treatment tags... INFO @ Tue, 27 Jun 2017 15:55:28: 1000000 INFO @ Tue, 27 Jun 2017 15:55:28: 1000000 INFO @ Tue, 27 Jun 2017 15:55:28: 1000000 INFO @ Tue, 27 Jun 2017 15:55:38: 2000000 INFO @ Tue, 27 Jun 2017 15:55:38: 2000000 INFO @ Tue, 27 Jun 2017 15:55:38: 2000000 INFO @ Tue, 27 Jun 2017 15:55:48: 3000000 INFO @ Tue, 27 Jun 2017 15:55:48: 3000000 INFO @ Tue, 27 Jun 2017 15:55:48: 3000000 INFO @ Tue, 27 Jun 2017 15:55:54: #1 tag size is determined as 94 bps INFO @ Tue, 27 Jun 2017 15:55:54: #1 tag size = 94 INFO @ Tue, 27 Jun 2017 15:55:54: #1 total tags in treatment: 3650701 INFO @ Tue, 27 Jun 2017 15:55:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:55:54: #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 15:55:54: #1 tag size is determined as 94 bps INFO @ Tue, 27 Jun 2017 15:55:54: #1 tag size = 94 INFO @ Tue, 27 Jun 2017 15:55:54: #1 total tags in treatment: 3650701 INFO @ Tue, 27 Jun 2017 15:55:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:55:54: #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 15:55:54: #1 tags after filtering in treatment: 3650701 INFO @ Tue, 27 Jun 2017 15:55:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:55:54: #1 finished! INFO @ Tue, 27 Jun 2017 15:55:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:55:54: #1 tag size is determined as 94 bps INFO @ Tue, 27 Jun 2017 15:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:55:54: #1 tag size = 94 INFO @ Tue, 27 Jun 2017 15:55:54: #1 total tags in treatment: 3650701 INFO @ Tue, 27 Jun 2017 15:55:54: #1 user defined the maximum tags... INFO @ Tue, 27 Jun 2017 15:55:54: #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 15:55:54: #1 tags after filtering in treatment: 3650701 INFO @ Tue, 27 Jun 2017 15:55:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:55:54: #1 finished! INFO @ Tue, 27 Jun 2017 15:55:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:55:54: #1 tags after filtering in treatment: 3650701 INFO @ Tue, 27 Jun 2017 15:55:54: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 27 Jun 2017 15:55:54: #1 finished! INFO @ Tue, 27 Jun 2017 15:55:54: #2 Build Peak Model... INFO @ Tue, 27 Jun 2017 15:55:54: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 27 Jun 2017 15:55:55: #2 number of paired peaks: 4557 INFO @ Tue, 27 Jun 2017 15:55:55: start model_add_line... INFO @ Tue, 27 Jun 2017 15:55:55: #2 number of paired peaks: 4557 INFO @ Tue, 27 Jun 2017 15:55:55: start model_add_line... INFO @ Tue, 27 Jun 2017 15:55:55: #2 number of paired peaks: 4557 INFO @ Tue, 27 Jun 2017 15:55:55: start model_add_line... INFO @ Tue, 27 Jun 2017 15:55:55: start X-correlation... INFO @ Tue, 27 Jun 2017 15:55:55: start X-correlation... INFO @ Tue, 27 Jun 2017 15:55:55: end of X-cor INFO @ Tue, 27 Jun 2017 15:55:55: end of X-cor INFO @ Tue, 27 Jun 2017 15:55:55: #2 finished! INFO @ Tue, 27 Jun 2017 15:55:55: #2 finished! INFO @ Tue, 27 Jun 2017 15:55:55: #2 predicted fragment length is 91 bps INFO @ Tue, 27 Jun 2017 15:55:55: #2 predicted fragment length is 91 bps INFO @ Tue, 27 Jun 2017 15:55:55: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 27 Jun 2017 15:55:55: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 27 Jun 2017 15:55:55: #2.2 Generate R script for model : SRX2788647.05_model.r INFO @ Tue, 27 Jun 2017 15:55:55: #2.2 Generate R script for model : SRX2788647.10_model.r WARNING @ Tue, 27 Jun 2017 15:55:55: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:55:55: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:55:55: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 27 Jun 2017 15:55:55: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 27 Jun 2017 15:55:55: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. WARNING @ Tue, 27 Jun 2017 15:55:55: #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 15:55:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:55:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:55:55: start X-correlation... INFO @ Tue, 27 Jun 2017 15:55:55: end of X-cor INFO @ Tue, 27 Jun 2017 15:55:55: #2 finished! INFO @ Tue, 27 Jun 2017 15:55:55: #2 predicted fragment length is 91 bps INFO @ Tue, 27 Jun 2017 15:55:55: #2 alternative fragment length(s) may be 91 bps INFO @ Tue, 27 Jun 2017 15:55:55: #2.2 Generate R script for model : SRX2788647.20_model.r WARNING @ Tue, 27 Jun 2017 15:55:55: #2 Since the d (91) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 27 Jun 2017 15:55:55: #2 You may need to consider one of the other alternative d(s): 91 WARNING @ Tue, 27 Jun 2017 15:55:55: #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 15:55:55: #3 Call peaks... INFO @ Tue, 27 Jun 2017 15:55:55: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 27 Jun 2017 15:56:05: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:56:05: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:56:05: #3 Call peaks for each chromosome... INFO @ Tue, 27 Jun 2017 15:56:10: #4 Write output xls file... SRX2788647.05_peaks.xls INFO @ Tue, 27 Jun 2017 15:56:10: #4 Write peak in narrowPeak format file... SRX2788647.05_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:56:10: #4 Write summits bed file... SRX2788647.05_summits.bed INFO @ Tue, 27 Jun 2017 15:56:10: Done! INFO @ Tue, 27 Jun 2017 15:56:10: #4 Write output xls file... SRX2788647.20_peaks.xls INFO @ Tue, 27 Jun 2017 15:56:10: #4 Write peak in narrowPeak format file... SRX2788647.20_peaks.narrowPeak INFO @ Tue, 27 Jun 2017 15:56:10: #4 Write summits bed file... SRX2788647.20_summits.bed INFO @ Tue, 27 Jun 2017 15:56:10: Done! INFO @ Tue, 27 Jun 2017 15:56:10: #4 Write output xls file... SRX2788647.10_peaks.xls pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3364 records, 4 fields): 6 millis pass1 - making usageList (15 chroms): 3 millis CompletedMACS2peakCalling pass2 - checking and writing primary data (10541 records, 4 fields): 13 millis INFO @ Tue, 27 Jun 2017 15:56:10: #4 Write peak in narrowPeak format file... SRX2788647.10_peaks.narrowPeak CompletedMACS2peakCalling INFO @ Tue, 27 Jun 2017 15:56:11: #4 Write summits bed file... SRX2788647.10_summits.bed INFO @ Tue, 27 Jun 2017 15:56:11: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (6385 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。