Job ID = 10175303 sra ファイルのダウンロード中... Completed: 131969K bytes transferred in 5 seconds (196785K 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... Written 8102745 spots for /home/okishinya/chipatlas/results/dm3/SRX3170976/SRR6019823.sra Written 8102745 spots total 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: 00:00:01 Multiseed full-index search: 00:04:03 8102745 reads; of these: 8102745 (100.00%) were unpaired; of these: 350728 (4.33%) aligned 0 times 6358850 (78.48%) aligned exactly 1 time 1393167 (17.19%) aligned >1 times 95.67% overall alignment rate Time searching: 00:04:04 Overall time: 00:04:04 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] 3657232 / 7752017 = 0.4718 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 @ Mon, 06 Nov 2017 12:29:15: # Command line: callpeak -t SRX3170976.bam -f BAM -g dm -n SRX3170976.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3170976.20 # format = BAM # ChIP-seq file = ['SRX3170976.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 @ Mon, 06 Nov 2017 12:29:15: # Command line: callpeak -t SRX3170976.bam -f BAM -g dm -n SRX3170976.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3170976.05 # format = BAM # ChIP-seq file = ['SRX3170976.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 @ Mon, 06 Nov 2017 12:29:15: # Command line: callpeak -t SRX3170976.bam -f BAM -g dm -n SRX3170976.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3170976.10 # format = BAM # ChIP-seq file = ['SRX3170976.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 @ Mon, 06 Nov 2017 12:29:15: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:29:15: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:29:15: #1 read tag files... INFO @ Mon, 06 Nov 2017 12:29:15: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:29:15: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:29:15: #1 read treatment tags... INFO @ Mon, 06 Nov 2017 12:29:30: 1000000 INFO @ Mon, 06 Nov 2017 12:29:30: 1000000 INFO @ Mon, 06 Nov 2017 12:29:32: 1000000 INFO @ Mon, 06 Nov 2017 12:29:43: 2000000 INFO @ Mon, 06 Nov 2017 12:29:43: 2000000 INFO @ Mon, 06 Nov 2017 12:29:44: 2000000 INFO @ Mon, 06 Nov 2017 12:29:53: 3000000 INFO @ Mon, 06 Nov 2017 12:29:54: 3000000 INFO @ Mon, 06 Nov 2017 12:29:57: 3000000 INFO @ Mon, 06 Nov 2017 12:30:09: 4000000 INFO @ Mon, 06 Nov 2017 12:30:09: 4000000 INFO @ Mon, 06 Nov 2017 12:30:10: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:30:10: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:30:10: #1 total tags in treatment: 4094785 INFO @ Mon, 06 Nov 2017 12:30:10: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:30:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:30:10: #1 tags after filtering in treatment: 4094785 INFO @ Mon, 06 Nov 2017 12:30:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:30:10: #1 finished! INFO @ Mon, 06 Nov 2017 12:30:10: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:30:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:30:10: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:30:10: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:30:10: #1 total tags in treatment: 4094785 INFO @ Mon, 06 Nov 2017 12:30:10: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:30:10: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:30:11: #1 tags after filtering in treatment: 4094785 INFO @ Mon, 06 Nov 2017 12:30:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:30:11: #1 finished! INFO @ Mon, 06 Nov 2017 12:30:11: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:30:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:30:11: #2 number of paired peaks: 978 WARNING @ Mon, 06 Nov 2017 12:30:11: Fewer paired peaks (978) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 978 pairs to build model! INFO @ Mon, 06 Nov 2017 12:30:11: start model_add_line... INFO @ Mon, 06 Nov 2017 12:30:11: start X-correlation... INFO @ Mon, 06 Nov 2017 12:30:11: end of X-cor INFO @ Mon, 06 Nov 2017 12:30:11: #2 finished! INFO @ Mon, 06 Nov 2017 12:30:11: #2 predicted fragment length is 115 bps INFO @ Mon, 06 Nov 2017 12:30:11: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 06 Nov 2017 12:30:11: #2.2 Generate R script for model : SRX3170976.20_model.r INFO @ Mon, 06 Nov 2017 12:30:11: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:30:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:30:11: #2 number of paired peaks: 978 WARNING @ Mon, 06 Nov 2017 12:30:11: Fewer paired peaks (978) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 978 pairs to build model! INFO @ Mon, 06 Nov 2017 12:30:11: start model_add_line... INFO @ Mon, 06 Nov 2017 12:30:11: start X-correlation... INFO @ Mon, 06 Nov 2017 12:30:11: end of X-cor INFO @ Mon, 06 Nov 2017 12:30:11: #2 finished! INFO @ Mon, 06 Nov 2017 12:30:11: #2 predicted fragment length is 115 bps INFO @ Mon, 06 Nov 2017 12:30:11: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 06 Nov 2017 12:30:11: #2.2 Generate R script for model : SRX3170976.05_model.r INFO @ Mon, 06 Nov 2017 12:30:12: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:30:12: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:30:14: 4000000 INFO @ Mon, 06 Nov 2017 12:30:16: #1 tag size is determined as 49 bps INFO @ Mon, 06 Nov 2017 12:30:16: #1 tag size = 49 INFO @ Mon, 06 Nov 2017 12:30:16: #1 total tags in treatment: 4094785 INFO @ Mon, 06 Nov 2017 12:30:16: #1 user defined the maximum tags... INFO @ Mon, 06 Nov 2017 12:30:16: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 06 Nov 2017 12:30:16: #1 tags after filtering in treatment: 4094785 INFO @ Mon, 06 Nov 2017 12:30:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 06 Nov 2017 12:30:16: #1 finished! INFO @ Mon, 06 Nov 2017 12:30:16: #2 Build Peak Model... INFO @ Mon, 06 Nov 2017 12:30:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 06 Nov 2017 12:30:17: #2 number of paired peaks: 978 WARNING @ Mon, 06 Nov 2017 12:30:17: Fewer paired peaks (978) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 978 pairs to build model! INFO @ Mon, 06 Nov 2017 12:30:17: start model_add_line... INFO @ Mon, 06 Nov 2017 12:30:17: start X-correlation... INFO @ Mon, 06 Nov 2017 12:30:17: end of X-cor INFO @ Mon, 06 Nov 2017 12:30:17: #2 finished! INFO @ Mon, 06 Nov 2017 12:30:17: #2 predicted fragment length is 115 bps INFO @ Mon, 06 Nov 2017 12:30:17: #2 alternative fragment length(s) may be 115 bps INFO @ Mon, 06 Nov 2017 12:30:17: #2.2 Generate R script for model : SRX3170976.10_model.r INFO @ Mon, 06 Nov 2017 12:30:17: #3 Call peaks... INFO @ Mon, 06 Nov 2017 12:30:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 06 Nov 2017 12:30:32: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:30:34: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:30:39: #3 Call peaks for each chromosome... INFO @ Mon, 06 Nov 2017 12:30:43: #4 Write output xls file... SRX3170976.20_peaks.xls INFO @ Mon, 06 Nov 2017 12:30:43: #4 Write peak in narrowPeak format file... SRX3170976.20_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:30:43: #4 Write summits bed file... SRX3170976.20_summits.bed INFO @ Mon, 06 Nov 2017 12:30:43: Done! pass1 - making usageList (10 chroms): 1 millis pass2 - checking and writing primary data (139 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:30:45: #4 Write output xls file... SRX3170976.05_peaks.xls INFO @ Mon, 06 Nov 2017 12:30:45: #4 Write peak in narrowPeak format file... SRX3170976.05_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:30:45: #4 Write summits bed file... SRX3170976.05_summits.bed INFO @ Mon, 06 Nov 2017 12:30:45: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (938 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Mon, 06 Nov 2017 12:30:51: #4 Write output xls file... SRX3170976.10_peaks.xls INFO @ Mon, 06 Nov 2017 12:30:51: #4 Write peak in narrowPeak format file... SRX3170976.10_peaks.narrowPeak INFO @ Mon, 06 Nov 2017 12:30:51: #4 Write summits bed file... SRX3170976.10_summits.bed INFO @ Mon, 06 Nov 2017 12:30:51: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (308 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。