Job ID = 9159956 sra ファイルのダウンロード中... Completed: 1255355K bytes transferred in 13 seconds (773509K 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 8156820 spots for /home/okishinya/chipatlas/results/dm3/SRX970861/SRR1943297.sra Written 8156820 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: 00:12:16 8156820 reads; of these: 8156820 (100.00%) were paired; of these: 4079066 (50.01%) aligned concordantly 0 times 3547250 (43.49%) aligned concordantly exactly 1 time 530504 (6.50%) aligned concordantly >1 times ---- 4079066 pairs aligned concordantly 0 times; of these: 238750 (5.85%) aligned discordantly 1 time ---- 3840316 pairs aligned 0 times concordantly or discordantly; of these: 7680632 mates make up the pairs; of these: 7428325 (96.72%) aligned 0 times 170109 (2.21%) aligned exactly 1 time 82198 (1.07%) aligned >1 times 54.47% overall alignment rate Time searching: 00:12:16 Overall time: 00:12:16 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] 3831687 / 4289860 = 0.8932 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 @ Wed, 28 Jun 2017 01:36:25: # Command line: callpeak -t SRX970861.bam -f BAM -g dm -n SRX970861.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX970861.10 # format = BAM # ChIP-seq file = ['SRX970861.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 @ Wed, 28 Jun 2017 01:36:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:36:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:36:25: # Command line: callpeak -t SRX970861.bam -f BAM -g dm -n SRX970861.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX970861.20 # format = BAM # ChIP-seq file = ['SRX970861.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 @ Wed, 28 Jun 2017 01:36:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:36:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:36:25: # Command line: callpeak -t SRX970861.bam -f BAM -g dm -n SRX970861.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX970861.05 # format = BAM # ChIP-seq file = ['SRX970861.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 @ Wed, 28 Jun 2017 01:36:25: #1 read tag files... INFO @ Wed, 28 Jun 2017 01:36:25: #1 read treatment tags... INFO @ Wed, 28 Jun 2017 01:36:32: 1000000 INFO @ Wed, 28 Jun 2017 01:36:33: 1000000 INFO @ Wed, 28 Jun 2017 01:36:33: 1000000 INFO @ Wed, 28 Jun 2017 01:36:34: #1 tag size is determined as 111 bps INFO @ Wed, 28 Jun 2017 01:36:34: #1 tag size = 111 INFO @ Wed, 28 Jun 2017 01:36:34: #1 total tags in treatment: 437894 INFO @ Wed, 28 Jun 2017 01:36:34: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:36:34: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:36:34: #1 tags after filtering in treatment: 402177 INFO @ Wed, 28 Jun 2017 01:36:34: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 01:36:34: #1 finished! INFO @ Wed, 28 Jun 2017 01:36:34: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:36:34: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:36:34: #2 number of paired peaks: 4498 INFO @ Wed, 28 Jun 2017 01:36:34: start model_add_line... INFO @ Wed, 28 Jun 2017 01:36:34: start X-correlation... INFO @ Wed, 28 Jun 2017 01:36:34: end of X-cor INFO @ Wed, 28 Jun 2017 01:36:34: #2 finished! INFO @ Wed, 28 Jun 2017 01:36:34: #2 predicted fragment length is 172 bps INFO @ Wed, 28 Jun 2017 01:36:34: #2 alternative fragment length(s) may be 172 bps INFO @ Wed, 28 Jun 2017 01:36:34: #2.2 Generate R script for model : SRX970861.10_model.r WARNING @ Wed, 28 Jun 2017 01:36:34: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 01:36:34: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Wed, 28 Jun 2017 01:36:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 01:36:34: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:36:34: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:36:35: #1 tag size is determined as 111 bps INFO @ Wed, 28 Jun 2017 01:36:35: #1 tag size is determined as 111 bps INFO @ Wed, 28 Jun 2017 01:36:35: #1 tag size = 111 INFO @ Wed, 28 Jun 2017 01:36:35: #1 tag size = 111 INFO @ Wed, 28 Jun 2017 01:36:35: #1 total tags in treatment: 437894 INFO @ Wed, 28 Jun 2017 01:36:35: #1 total tags in treatment: 437894 INFO @ Wed, 28 Jun 2017 01:36:35: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:36:35: #1 user defined the maximum tags... INFO @ Wed, 28 Jun 2017 01:36:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:36:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 28 Jun 2017 01:36:35: #1 tags after filtering in treatment: 402177 INFO @ Wed, 28 Jun 2017 01:36:35: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 01:36:35: #1 tags after filtering in treatment: 402177 INFO @ Wed, 28 Jun 2017 01:36:35: #1 finished! INFO @ Wed, 28 Jun 2017 01:36:35: #1 Redundant rate of treatment: 0.08 INFO @ Wed, 28 Jun 2017 01:36:35: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:36:35: #1 finished! INFO @ Wed, 28 Jun 2017 01:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:36:35: #2 Build Peak Model... INFO @ Wed, 28 Jun 2017 01:36:35: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 28 Jun 2017 01:36:35: #2 number of paired peaks: 4498 INFO @ Wed, 28 Jun 2017 01:36:35: start model_add_line... INFO @ Wed, 28 Jun 2017 01:36:35: start X-correlation... INFO @ Wed, 28 Jun 2017 01:36:35: #2 number of paired peaks: 4498 INFO @ Wed, 28 Jun 2017 01:36:35: start model_add_line... INFO @ Wed, 28 Jun 2017 01:36:35: end of X-cor INFO @ Wed, 28 Jun 2017 01:36:35: #2 finished! INFO @ Wed, 28 Jun 2017 01:36:35: #2 predicted fragment length is 172 bps INFO @ Wed, 28 Jun 2017 01:36:35: #2 alternative fragment length(s) may be 172 bps INFO @ Wed, 28 Jun 2017 01:36:35: #2.2 Generate R script for model : SRX970861.05_model.r INFO @ Wed, 28 Jun 2017 01:36:35: start X-correlation... INFO @ Wed, 28 Jun 2017 01:36:35: end of X-cor INFO @ Wed, 28 Jun 2017 01:36:35: #2 finished! INFO @ Wed, 28 Jun 2017 01:36:35: #2 predicted fragment length is 172 bps INFO @ Wed, 28 Jun 2017 01:36:35: #2 alternative fragment length(s) may be 172 bps INFO @ Wed, 28 Jun 2017 01:36:35: #2.2 Generate R script for model : SRX970861.20_model.r WARNING @ Wed, 28 Jun 2017 01:36:35: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 01:36:35: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Wed, 28 Jun 2017 01:36:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 01:36:35: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:36:35: #3 Pre-compute pvalue-qvalue table... WARNING @ Wed, 28 Jun 2017 01:36:35: #2 Since the d (172) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 28 Jun 2017 01:36:35: #2 You may need to consider one of the other alternative d(s): 172 WARNING @ Wed, 28 Jun 2017 01:36:35: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 28 Jun 2017 01:36:35: #3 Call peaks... INFO @ Wed, 28 Jun 2017 01:36:35: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 28 Jun 2017 01:36:35: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:36:36: #4 Write output xls file... SRX970861.10_peaks.xls INFO @ Wed, 28 Jun 2017 01:36:36: #4 Write peak in narrowPeak format file... SRX970861.10_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:36:36: #4 Write summits bed file... SRX970861.10_summits.bed INFO @ Wed, 28 Jun 2017 01:36:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (136 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:36:36: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:36:36: #3 Call peaks for each chromosome... INFO @ Wed, 28 Jun 2017 01:36:37: #4 Write output xls file... SRX970861.05_peaks.xls INFO @ Wed, 28 Jun 2017 01:36:37: #4 Write peak in narrowPeak format file... SRX970861.05_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:36:37: #4 Write summits bed file... SRX970861.05_summits.bed INFO @ Wed, 28 Jun 2017 01:36:37: Done! pass1 - making usageList (9 chroms): 0 millis pass2 - checking and writing primary data (622 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Wed, 28 Jun 2017 01:36:37: #4 Write output xls file... SRX970861.20_peaks.xls INFO @ Wed, 28 Jun 2017 01:36:37: #4 Write peak in narrowPeak format file... SRX970861.20_peaks.narrowPeak INFO @ Wed, 28 Jun 2017 01:36:37: #4 Write summits bed file... SRX970861.20_summits.bed INFO @ Wed, 28 Jun 2017 01:36:37: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (32 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。