Job ID = 10845176 sra ファイルのダウンロード中... Completed: 122316K bytes transferred in 12 seconds (82917K 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: SINGLE fastq に変換中... Read 2768361 spots for /home/okishinya/chipatlas/results/dm3/SRX2642392/SRR5345732.sra Written 2768361 spots for /home/okishinya/chipatlas/results/dm3/SRX2642392/SRR5345732.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: 00:01:32 2768361 reads; of these: 2768361 (100.00%) were unpaired; of these: 209506 (7.57%) aligned 0 times 1931105 (69.76%) aligned exactly 1 time 627750 (22.68%) aligned >1 times 92.43% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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_rmdupse_core] 38441 / 2558855 = 0.0150 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, 04 Jul 2018 09:28:59: # Command line: callpeak -t SRX2642392.bam -f BAM -g dm -n SRX2642392.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2642392.05 # format = BAM # ChIP-seq file = ['SRX2642392.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, 04 Jul 2018 09:28:59: # Command line: callpeak -t SRX2642392.bam -f BAM -g dm -n SRX2642392.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2642392.20 # format = BAM # ChIP-seq file = ['SRX2642392.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, 04 Jul 2018 09:28:59: # Command line: callpeak -t SRX2642392.bam -f BAM -g dm -n SRX2642392.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2642392.10 # format = BAM # ChIP-seq file = ['SRX2642392.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, 04 Jul 2018 09:28:59: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:59: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:59: #1 read tag files... INFO @ Wed, 04 Jul 2018 09:28:59: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:59: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:28:59: #1 read treatment tags... INFO @ Wed, 04 Jul 2018 09:29:07: 1000000 INFO @ Wed, 04 Jul 2018 09:29:07: 1000000 INFO @ Wed, 04 Jul 2018 09:29:07: 1000000 INFO @ Wed, 04 Jul 2018 09:29:15: 2000000 INFO @ Wed, 04 Jul 2018 09:29:15: 2000000 INFO @ Wed, 04 Jul 2018 09:29:15: 2000000 INFO @ Wed, 04 Jul 2018 09:29:19: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:29:19: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:29:19: #1 total tags in treatment: 2520414 INFO @ Wed, 04 Jul 2018 09:29:19: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:29:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:29:19: #1 tags after filtering in treatment: 2520414 INFO @ Wed, 04 Jul 2018 09:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:29:19: #1 finished! INFO @ Wed, 04 Jul 2018 09:29:19: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:29:19: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:29:19: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:29:19: #1 total tags in treatment: 2520414 INFO @ Wed, 04 Jul 2018 09:29:19: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:29:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:29:19: #1 tags after filtering in treatment: 2520414 INFO @ Wed, 04 Jul 2018 09:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:29:19: #1 finished! INFO @ Wed, 04 Jul 2018 09:29:19: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:29:19: #2 number of paired peaks: 1078 INFO @ Wed, 04 Jul 2018 09:29:19: start model_add_line... INFO @ Wed, 04 Jul 2018 09:29:19: start X-correlation... INFO @ Wed, 04 Jul 2018 09:29:19: #2 number of paired peaks: 1078 INFO @ Wed, 04 Jul 2018 09:29:19: start model_add_line... INFO @ Wed, 04 Jul 2018 09:29:19: start X-correlation... INFO @ Wed, 04 Jul 2018 09:29:19: #1 tag size is determined as 101 bps INFO @ Wed, 04 Jul 2018 09:29:19: #1 tag size = 101 INFO @ Wed, 04 Jul 2018 09:29:19: #1 total tags in treatment: 2520414 INFO @ Wed, 04 Jul 2018 09:29:19: #1 user defined the maximum tags... INFO @ Wed, 04 Jul 2018 09:29:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Wed, 04 Jul 2018 09:29:19: end of X-cor INFO @ Wed, 04 Jul 2018 09:29:19: #2 finished! INFO @ Wed, 04 Jul 2018 09:29:19: #2 predicted fragment length is 129 bps INFO @ Wed, 04 Jul 2018 09:29:19: #2 alternative fragment length(s) may be 129 bps INFO @ Wed, 04 Jul 2018 09:29:19: #2.2 Generate R script for model : SRX2642392.20_model.r INFO @ Wed, 04 Jul 2018 09:29:19: end of X-cor INFO @ Wed, 04 Jul 2018 09:29:19: #2 finished! INFO @ Wed, 04 Jul 2018 09:29:19: #2 predicted fragment length is 129 bps INFO @ Wed, 04 Jul 2018 09:29:19: #2 alternative fragment length(s) may be 129 bps INFO @ Wed, 04 Jul 2018 09:29:19: #2.2 Generate R script for model : SRX2642392.10_model.r WARNING @ Wed, 04 Jul 2018 09:29:19: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:29:19: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Wed, 04 Jul 2018 09:29:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:29:19: #3 Call peaks... WARNING @ Wed, 04 Jul 2018 09:29:19: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:29:19: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Wed, 04 Jul 2018 09:29:19: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:29:19: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:29:19: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:29:19: #1 tags after filtering in treatment: 2520414 INFO @ Wed, 04 Jul 2018 09:29:19: #1 Redundant rate of treatment: 0.00 INFO @ Wed, 04 Jul 2018 09:29:19: #1 finished! INFO @ Wed, 04 Jul 2018 09:29:19: #2 Build Peak Model... INFO @ Wed, 04 Jul 2018 09:29:19: #2 looking for paired plus/minus strand peaks... INFO @ Wed, 04 Jul 2018 09:29:20: #2 number of paired peaks: 1078 INFO @ Wed, 04 Jul 2018 09:29:20: start model_add_line... INFO @ Wed, 04 Jul 2018 09:29:20: start X-correlation... INFO @ Wed, 04 Jul 2018 09:29:20: end of X-cor INFO @ Wed, 04 Jul 2018 09:29:20: #2 finished! INFO @ Wed, 04 Jul 2018 09:29:20: #2 predicted fragment length is 129 bps INFO @ Wed, 04 Jul 2018 09:29:20: #2 alternative fragment length(s) may be 129 bps INFO @ Wed, 04 Jul 2018 09:29:20: #2.2 Generate R script for model : SRX2642392.05_model.r WARNING @ Wed, 04 Jul 2018 09:29:20: #2 Since the d (129) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Wed, 04 Jul 2018 09:29:20: #2 You may need to consider one of the other alternative d(s): 129 WARNING @ Wed, 04 Jul 2018 09:29:20: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Wed, 04 Jul 2018 09:29:20: #3 Call peaks... INFO @ Wed, 04 Jul 2018 09:29:20: #3 Pre-compute pvalue-qvalue table... INFO @ Wed, 04 Jul 2018 09:29:25: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:29:26: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:29:26: #3 Call peaks for each chromosome... INFO @ Wed, 04 Jul 2018 09:29:29: #4 Write output xls file... SRX2642392.05_peaks.xls INFO @ Wed, 04 Jul 2018 09:29:29: #4 Write peak in narrowPeak format file... SRX2642392.05_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:29:29: #4 Write summits bed file... SRX2642392.05_summits.bed INFO @ Wed, 04 Jul 2018 09:29:29: Done! INFO @ Wed, 04 Jul 2018 09:29:29: #4 Write output xls file... SRX2642392.10_peaks.xls INFO @ Wed, 04 Jul 2018 09:29:29: #4 Write peak in narrowPeak format file... SRX2642392.10_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:29:29: #4 Write summits bed file... SRX2642392.10_summits.bed INFO @ Wed, 04 Jul 2018 09:29:29: Done! pass1 - making usageList (8 chroms)pass1 - making usageList (6 chroms): 2 millis : 1 millis pass2 - checking and writing primary data (110 records, 4 fields): 5 millis pass2 - checking and writing primary data (216 records, 4 fields): 7 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Wed, 04 Jul 2018 09:29:30: #4 Write output xls file... SRX2642392.20_peaks.xls INFO @ Wed, 04 Jul 2018 09:29:30: #4 Write peak in narrowPeak format file... SRX2642392.20_peaks.narrowPeak INFO @ Wed, 04 Jul 2018 09:29:30: #4 Write summits bed file... SRX2642392.20_summits.bed INFO @ Wed, 04 Jul 2018 09:29:30: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (44 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。