Job ID = 9371919 sra ファイルのダウンロード中... Completed: 381492K bytes transferred in 14 seconds (213013K 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 2624911 spots for /home/okishinya/chipatlas/results/dm3/SRX1958589/SRR3928903.sra Written 2624911 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: 00:00:01 Multiseed full-index search: 00:06:21 2624911 reads; of these: 2624911 (100.00%) were paired; of these: 1501864 (57.22%) aligned concordantly 0 times 897008 (34.17%) aligned concordantly exactly 1 time 226039 (8.61%) aligned concordantly >1 times ---- 1501864 pairs aligned concordantly 0 times; of these: 160532 (10.69%) aligned discordantly 1 time ---- 1341332 pairs aligned 0 times concordantly or discordantly; of these: 2682664 mates make up the pairs; of these: 2588338 (96.48%) aligned 0 times 20758 (0.77%) aligned exactly 1 time 73568 (2.74%) aligned >1 times 50.70% overall alignment rate Time searching: 00:06:22 Overall time: 00:06:22 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] 544269 / 1271941 = 0.4279 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 @ Fri, 04 Aug 2017 14:57:20: # Command line: callpeak -t SRX1958589.bam -f BAM -g dm -n SRX1958589.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1958589.05 # format = BAM # ChIP-seq file = ['SRX1958589.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 @ Fri, 04 Aug 2017 14:57:20: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:57:20: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:57:20: # Command line: callpeak -t SRX1958589.bam -f BAM -g dm -n SRX1958589.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1958589.10 # format = BAM # ChIP-seq file = ['SRX1958589.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 @ Fri, 04 Aug 2017 14:57:20: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:57:20: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:57:20: # Command line: callpeak -t SRX1958589.bam -f BAM -g dm -n SRX1958589.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1958589.20 # format = BAM # ChIP-seq file = ['SRX1958589.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 @ Fri, 04 Aug 2017 14:57:20: #1 read tag files... INFO @ Fri, 04 Aug 2017 14:57:20: #1 read treatment tags... INFO @ Fri, 04 Aug 2017 14:57:33: 1000000 INFO @ Fri, 04 Aug 2017 14:57:35: 1000000 INFO @ Fri, 04 Aug 2017 14:57:35: 1000000 INFO @ Fri, 04 Aug 2017 14:57:40: #1 tag size is determined as 151 bps INFO @ Fri, 04 Aug 2017 14:57:40: #1 tag size = 151 INFO @ Fri, 04 Aug 2017 14:57:40: #1 total tags in treatment: 641842 INFO @ Fri, 04 Aug 2017 14:57:40: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:57:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 14:57:40: #1 tags after filtering in treatment: 633118 INFO @ Fri, 04 Aug 2017 14:57:40: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 04 Aug 2017 14:57:40: #1 finished! INFO @ Fri, 04 Aug 2017 14:57:40: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:57:40: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:57:40: #2 number of paired peaks: 390 WARNING @ Fri, 04 Aug 2017 14:57:40: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Fri, 04 Aug 2017 14:57:40: start model_add_line... INFO @ Fri, 04 Aug 2017 14:57:40: start X-correlation... INFO @ Fri, 04 Aug 2017 14:57:40: end of X-cor INFO @ Fri, 04 Aug 2017 14:57:40: #2 finished! INFO @ Fri, 04 Aug 2017 14:57:40: #2 predicted fragment length is 174 bps INFO @ Fri, 04 Aug 2017 14:57:40: #2 alternative fragment length(s) may be 174 bps INFO @ Fri, 04 Aug 2017 14:57:40: #2.2 Generate R script for model : SRX1958589.05_model.r WARNING @ Fri, 04 Aug 2017 14:57:40: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:57:40: #2 You may need to consider one of the other alternative d(s): 174 WARNING @ Fri, 04 Aug 2017 14:57:40: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 14:57:40: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:57:40: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:57:42: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:57:42: #4 Write output xls file... SRX1958589.05_peaks.xls INFO @ Fri, 04 Aug 2017 14:57:42: #4 Write peak in narrowPeak format file... SRX1958589.05_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:57:42: #4 Write summits bed file... SRX1958589.05_summits.bed INFO @ Fri, 04 Aug 2017 14:57:42: Done! pass1 - making usageList (5 chroms): 13 millis pass2 - checking and writing primary data (191 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:57:43: #1 tag size is determined as 151 bps INFO @ Fri, 04 Aug 2017 14:57:43: #1 tag size = 151 INFO @ Fri, 04 Aug 2017 14:57:43: #1 total tags in treatment: 641842 INFO @ Fri, 04 Aug 2017 14:57:43: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:57:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 14:57:43: #1 tags after filtering in treatment: 633118 INFO @ Fri, 04 Aug 2017 14:57:43: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 04 Aug 2017 14:57:43: #1 finished! INFO @ Fri, 04 Aug 2017 14:57:43: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:57:43: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:57:44: #2 number of paired peaks: 390 WARNING @ Fri, 04 Aug 2017 14:57:44: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Fri, 04 Aug 2017 14:57:44: start model_add_line... INFO @ Fri, 04 Aug 2017 14:57:44: start X-correlation... INFO @ Fri, 04 Aug 2017 14:57:44: end of X-cor INFO @ Fri, 04 Aug 2017 14:57:44: #2 finished! INFO @ Fri, 04 Aug 2017 14:57:44: #2 predicted fragment length is 174 bps INFO @ Fri, 04 Aug 2017 14:57:44: #2 alternative fragment length(s) may be 174 bps INFO @ Fri, 04 Aug 2017 14:57:44: #2.2 Generate R script for model : SRX1958589.10_model.r WARNING @ Fri, 04 Aug 2017 14:57:44: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:57:44: #2 You may need to consider one of the other alternative d(s): 174 WARNING @ Fri, 04 Aug 2017 14:57:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 14:57:44: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:57:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:57:44: #1 tag size is determined as 151 bps INFO @ Fri, 04 Aug 2017 14:57:44: #1 tag size = 151 INFO @ Fri, 04 Aug 2017 14:57:44: #1 total tags in treatment: 641842 INFO @ Fri, 04 Aug 2017 14:57:44: #1 user defined the maximum tags... INFO @ Fri, 04 Aug 2017 14:57:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 Aug 2017 14:57:44: #1 tags after filtering in treatment: 633118 INFO @ Fri, 04 Aug 2017 14:57:44: #1 Redundant rate of treatment: 0.01 INFO @ Fri, 04 Aug 2017 14:57:44: #1 finished! INFO @ Fri, 04 Aug 2017 14:57:44: #2 Build Peak Model... INFO @ Fri, 04 Aug 2017 14:57:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 Aug 2017 14:57:44: #2 number of paired peaks: 390 WARNING @ Fri, 04 Aug 2017 14:57:44: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Fri, 04 Aug 2017 14:57:44: start model_add_line... INFO @ Fri, 04 Aug 2017 14:57:44: start X-correlation... INFO @ Fri, 04 Aug 2017 14:57:44: end of X-cor INFO @ Fri, 04 Aug 2017 14:57:44: #2 finished! INFO @ Fri, 04 Aug 2017 14:57:44: #2 predicted fragment length is 174 bps INFO @ Fri, 04 Aug 2017 14:57:44: #2 alternative fragment length(s) may be 174 bps INFO @ Fri, 04 Aug 2017 14:57:44: #2.2 Generate R script for model : SRX1958589.20_model.r WARNING @ Fri, 04 Aug 2017 14:57:44: #2 Since the d (174) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 Aug 2017 14:57:44: #2 You may need to consider one of the other alternative d(s): 174 WARNING @ Fri, 04 Aug 2017 14:57:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Fri, 04 Aug 2017 14:57:44: #3 Call peaks... INFO @ Fri, 04 Aug 2017 14:57:44: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 Aug 2017 14:57:45: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:57:45: #3 Call peaks for each chromosome... INFO @ Fri, 04 Aug 2017 14:57:46: #4 Write output xls file... SRX1958589.10_peaks.xls INFO @ Fri, 04 Aug 2017 14:57:46: #4 Write peak in narrowPeak format file... SRX1958589.10_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:57:46: #4 Write summits bed file... SRX1958589.10_summits.bed INFO @ Fri, 04 Aug 2017 14:57:46: Done! pass1 - making usageList (5 chroms): 2 millis pass2 - checking and writing primary data (116 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 04 Aug 2017 14:57:46: #4 Write output xls file... SRX1958589.20_peaks.xls INFO @ Fri, 04 Aug 2017 14:57:46: #4 Write peak in narrowPeak format file... SRX1958589.20_peaks.narrowPeak INFO @ Fri, 04 Aug 2017 14:57:46: #4 Write summits bed file... SRX1958589.20_summits.bed INFO @ Fri, 04 Aug 2017 14:57:46: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (58 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。