Job ID = 10609076 sra ファイルのダウンロード中... Completed: 147039K bytes transferred in 4 seconds (248502K bits/sec), in 1 file. 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... Read 2999817 spots for /home/okishinya/chipatlas/results/dm3/SRX2200901/SRR4309624.sra Written 2999817 spots for /home/okishinya/chipatlas/results/dm3/SRX2200901/SRR4309624.sra rm: cannot remove `[DSE]RX*': そのようなファイルやディレクトリはありません 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: 00:09:21 2999817 reads; of these: 2999817 (100.00%) were paired; of these: 894268 (29.81%) aligned concordantly 0 times 1457600 (48.59%) aligned concordantly exactly 1 time 647949 (21.60%) aligned concordantly >1 times ---- 894268 pairs aligned concordantly 0 times; of these: 42762 (4.78%) aligned discordantly 1 time ---- 851506 pairs aligned 0 times concordantly or discordantly; of these: 1703012 mates make up the pairs; of these: 1570873 (92.24%) aligned 0 times 66814 (3.92%) aligned exactly 1 time 65325 (3.84%) aligned >1 times 73.82% overall alignment rate Time searching: 00:09:21 Overall time: 00:09:21 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] 27940 / 2095384 = 0.0133 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 May 2018 07:14:59: # Command line: callpeak -t SRX2200901.bam -f BAM -g dm -n SRX2200901.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2200901.20 # format = BAM # ChIP-seq file = ['SRX2200901.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 May 2018 07:14:59: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:59: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:59: # Command line: callpeak -t SRX2200901.bam -f BAM -g dm -n SRX2200901.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2200901.05 # format = BAM # ChIP-seq file = ['SRX2200901.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 May 2018 07:14:59: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:59: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:14:59: # Command line: callpeak -t SRX2200901.bam -f BAM -g dm -n SRX2200901.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2200901.10 # format = BAM # ChIP-seq file = ['SRX2200901.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 May 2018 07:14:59: #1 read tag files... INFO @ Fri, 04 May 2018 07:14:59: #1 read treatment tags... INFO @ Fri, 04 May 2018 07:15:07: 1000000 INFO @ Fri, 04 May 2018 07:15:07: 1000000 INFO @ Fri, 04 May 2018 07:15:07: 1000000 INFO @ Fri, 04 May 2018 07:15:14: 2000000 INFO @ Fri, 04 May 2018 07:15:14: 2000000 INFO @ Fri, 04 May 2018 07:15:14: 2000000 INFO @ Fri, 04 May 2018 07:15:21: 3000000 INFO @ Fri, 04 May 2018 07:15:21: 3000000 INFO @ Fri, 04 May 2018 07:15:21: 3000000 INFO @ Fri, 04 May 2018 07:15:29: 4000000 INFO @ Fri, 04 May 2018 07:15:29: 4000000 INFO @ Fri, 04 May 2018 07:15:29: 4000000 INFO @ Fri, 04 May 2018 07:15:32: #1 tag size is determined as 82 bps INFO @ Fri, 04 May 2018 07:15:32: #1 tag size = 82 INFO @ Fri, 04 May 2018 07:15:32: #1 total tags in treatment: 2077639 INFO @ Fri, 04 May 2018 07:15:32: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:15:32: #1 tags after filtering in treatment: 1936117 INFO @ Fri, 04 May 2018 07:15:32: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 04 May 2018 07:15:32: #1 finished! INFO @ Fri, 04 May 2018 07:15:32: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:32: #1 tag size is determined as 82 bps INFO @ Fri, 04 May 2018 07:15:32: #1 tag size = 82 INFO @ Fri, 04 May 2018 07:15:32: #1 total tags in treatment: 2077639 INFO @ Fri, 04 May 2018 07:15:32: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:15:32: #1 tag size is determined as 82 bps INFO @ Fri, 04 May 2018 07:15:32: #1 tag size = 82 INFO @ Fri, 04 May 2018 07:15:32: #1 total tags in treatment: 2077639 INFO @ Fri, 04 May 2018 07:15:32: #1 user defined the maximum tags... INFO @ Fri, 04 May 2018 07:15:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 04 May 2018 07:15:32: #1 tags after filtering in treatment: 1936117 INFO @ Fri, 04 May 2018 07:15:32: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 04 May 2018 07:15:32: #1 finished! INFO @ Fri, 04 May 2018 07:15:32: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:32: #1 tags after filtering in treatment: 1936117 INFO @ Fri, 04 May 2018 07:15:32: #1 Redundant rate of treatment: 0.07 INFO @ Fri, 04 May 2018 07:15:32: #1 finished! INFO @ Fri, 04 May 2018 07:15:32: #2 Build Peak Model... INFO @ Fri, 04 May 2018 07:15:32: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 04 May 2018 07:15:32: #2 number of paired peaks: 3797 INFO @ Fri, 04 May 2018 07:15:32: start model_add_line... INFO @ Fri, 04 May 2018 07:15:32: start X-correlation... INFO @ Fri, 04 May 2018 07:15:32: end of X-cor INFO @ Fri, 04 May 2018 07:15:32: #2 finished! INFO @ Fri, 04 May 2018 07:15:32: #2 predicted fragment length is 154 bps INFO @ Fri, 04 May 2018 07:15:32: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 04 May 2018 07:15:32: #2.2 Generate R script for model : SRX2200901.10_model.r WARNING @ Fri, 04 May 2018 07:15:32: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:15:32: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 04 May 2018 07:15:32: #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 May 2018 07:15:32: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:32: #2 number of paired peaks: 3797 INFO @ Fri, 04 May 2018 07:15:32: start model_add_line... INFO @ Fri, 04 May 2018 07:15:32: #2 number of paired peaks: 3797 INFO @ Fri, 04 May 2018 07:15:32: start model_add_line... INFO @ Fri, 04 May 2018 07:15:32: start X-correlation... INFO @ Fri, 04 May 2018 07:15:32: end of X-cor INFO @ Fri, 04 May 2018 07:15:32: #2 finished! INFO @ Fri, 04 May 2018 07:15:32: start X-correlation... INFO @ Fri, 04 May 2018 07:15:32: #2 predicted fragment length is 154 bps INFO @ Fri, 04 May 2018 07:15:32: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 04 May 2018 07:15:32: #2.2 Generate R script for model : SRX2200901.05_model.r INFO @ Fri, 04 May 2018 07:15:32: end of X-cor INFO @ Fri, 04 May 2018 07:15:32: #2 finished! INFO @ Fri, 04 May 2018 07:15:32: #2 predicted fragment length is 154 bps INFO @ Fri, 04 May 2018 07:15:32: #2 alternative fragment length(s) may be 154 bps INFO @ Fri, 04 May 2018 07:15:32: #2.2 Generate R script for model : SRX2200901.20_model.r WARNING @ Fri, 04 May 2018 07:15:32: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:15:32: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 04 May 2018 07:15:32: #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 May 2018 07:15:32: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:32: #3 Pre-compute pvalue-qvalue table... WARNING @ Fri, 04 May 2018 07:15:32: #2 Since the d (154) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Fri, 04 May 2018 07:15:32: #2 You may need to consider one of the other alternative d(s): 154 WARNING @ Fri, 04 May 2018 07:15:32: #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 May 2018 07:15:32: #3 Call peaks... INFO @ Fri, 04 May 2018 07:15:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 04 May 2018 07:15:37: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:37: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:37: #3 Call peaks for each chromosome... INFO @ Fri, 04 May 2018 07:15:40: #4 Write output xls file... SRX2200901.05_peaks.xls INFO @ Fri, 04 May 2018 07:15:40: #4 Write peak in narrowPeak format file... SRX2200901.05_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:40: #4 Write summits bed file... SRX2200901.05_summits.bed INFO @ Fri, 04 May 2018 07:15:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (3505 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:15:40: #4 Write output xls file... SRX2200901.20_peaks.xls INFO @ Fri, 04 May 2018 07:15:40: #4 Write peak in narrowPeak format file... SRX2200901.20_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:40: #4 Write summits bed file... SRX2200901.20_summits.bed INFO @ Fri, 04 May 2018 07:15:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (1297 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 04 May 2018 07:15:40: #4 Write output xls file... SRX2200901.10_peaks.xls INFO @ Fri, 04 May 2018 07:15:40: #4 Write peak in narrowPeak format file... SRX2200901.10_peaks.narrowPeak INFO @ Fri, 04 May 2018 07:15:40: #4 Write summits bed file... SRX2200901.10_summits.bed INFO @ Fri, 04 May 2018 07:15:40: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2309 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。