Job ID = 10714580 sra ファイルのダウンロード中... Completed: 129717K bytes transferred in 4 seconds (249961K 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 8893050 spots for /home/okishinya/chipatlas/results/dm3/SRX4053334/SRR7132379.sra Written 8893050 spots for /home/okishinya/chipatlas/results/dm3/SRX4053334/SRR7132379.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: 00:02:15 8893050 reads; of these: 8893050 (100.00%) were unpaired; of these: 635599 (7.15%) aligned 0 times 7732817 (86.95%) aligned exactly 1 time 524634 (5.90%) aligned >1 times 92.85% overall alignment rate Time searching: 00:02:15 Overall time: 00:02:15 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] 2681385 / 8257451 = 0.3247 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 @ Sun, 03 Jun 2018 13:39:15: # Command line: callpeak -t SRX4053334.bam -f BAM -g dm -n SRX4053334.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4053334.20 # format = BAM # ChIP-seq file = ['SRX4053334.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 @ Sun, 03 Jun 2018 13:39:15: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:39:15: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:39:15: # Command line: callpeak -t SRX4053334.bam -f BAM -g dm -n SRX4053334.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4053334.10 # format = BAM # ChIP-seq file = ['SRX4053334.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 @ Sun, 03 Jun 2018 13:39:15: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:39:15: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:39:15: # Command line: callpeak -t SRX4053334.bam -f BAM -g dm -n SRX4053334.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4053334.05 # format = BAM # ChIP-seq file = ['SRX4053334.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 @ Sun, 03 Jun 2018 13:39:15: #1 read tag files... INFO @ Sun, 03 Jun 2018 13:39:15: #1 read treatment tags... INFO @ Sun, 03 Jun 2018 13:39:21: 1000000 INFO @ Sun, 03 Jun 2018 13:39:21: 1000000 INFO @ Sun, 03 Jun 2018 13:39:22: 1000000 INFO @ Sun, 03 Jun 2018 13:39:27: 2000000 INFO @ Sun, 03 Jun 2018 13:39:27: 2000000 INFO @ Sun, 03 Jun 2018 13:39:28: 2000000 INFO @ Sun, 03 Jun 2018 13:39:33: 3000000 INFO @ Sun, 03 Jun 2018 13:39:33: 3000000 INFO @ Sun, 03 Jun 2018 13:39:34: 3000000 INFO @ Sun, 03 Jun 2018 13:39:39: 4000000 INFO @ Sun, 03 Jun 2018 13:39:39: 4000000 INFO @ Sun, 03 Jun 2018 13:39:40: 4000000 INFO @ Sun, 03 Jun 2018 13:39:45: 5000000 INFO @ Sun, 03 Jun 2018 13:39:46: 5000000 INFO @ Sun, 03 Jun 2018 13:39:46: 5000000 INFO @ Sun, 03 Jun 2018 13:39:48: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:39:48: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:39:48: #1 total tags in treatment: 5576066 INFO @ Sun, 03 Jun 2018 13:39:48: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:39:48: #1 tags after filtering in treatment: 5576066 INFO @ Sun, 03 Jun 2018 13:39:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:39:48: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:48: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:49: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:39:49: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:39:49: #1 total tags in treatment: 5576066 INFO @ Sun, 03 Jun 2018 13:39:49: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:49: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:39:49: #1 tags after filtering in treatment: 5576066 INFO @ Sun, 03 Jun 2018 13:39:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:39:49: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:49: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:49: #2 number of paired peaks: 10064 INFO @ Sun, 03 Jun 2018 13:39:49: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:50: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:50: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:50: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:50: #2 predicted fragment length is 153 bps INFO @ Sun, 03 Jun 2018 13:39:50: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 03 Jun 2018 13:39:50: #2.2 Generate R script for model : SRX4053334.05_model.r INFO @ Sun, 03 Jun 2018 13:39:50: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:50: #1 tag size is determined as 50 bps INFO @ Sun, 03 Jun 2018 13:39:50: #1 tag size = 50 INFO @ Sun, 03 Jun 2018 13:39:50: #1 total tags in treatment: 5576066 INFO @ Sun, 03 Jun 2018 13:39:50: #1 user defined the maximum tags... INFO @ Sun, 03 Jun 2018 13:39:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 03 Jun 2018 13:39:50: #1 tags after filtering in treatment: 5576066 INFO @ Sun, 03 Jun 2018 13:39:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 03 Jun 2018 13:39:50: #1 finished! INFO @ Sun, 03 Jun 2018 13:39:50: #2 Build Peak Model... INFO @ Sun, 03 Jun 2018 13:39:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 03 Jun 2018 13:39:50: #2 number of paired peaks: 10064 INFO @ Sun, 03 Jun 2018 13:39:50: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:51: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:51: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:51: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:51: #2 predicted fragment length is 153 bps INFO @ Sun, 03 Jun 2018 13:39:51: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 03 Jun 2018 13:39:51: #2.2 Generate R script for model : SRX4053334.10_model.r INFO @ Sun, 03 Jun 2018 13:39:51: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:39:51: #2 number of paired peaks: 10064 INFO @ Sun, 03 Jun 2018 13:39:51: start model_add_line... INFO @ Sun, 03 Jun 2018 13:39:51: start X-correlation... INFO @ Sun, 03 Jun 2018 13:39:51: end of X-cor INFO @ Sun, 03 Jun 2018 13:39:51: #2 finished! INFO @ Sun, 03 Jun 2018 13:39:51: #2 predicted fragment length is 153 bps INFO @ Sun, 03 Jun 2018 13:39:51: #2 alternative fragment length(s) may be 153 bps INFO @ Sun, 03 Jun 2018 13:39:51: #2.2 Generate R script for model : SRX4053334.20_model.r INFO @ Sun, 03 Jun 2018 13:39:51: #3 Call peaks... INFO @ Sun, 03 Jun 2018 13:39:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 03 Jun 2018 13:40:06: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:08: #3 Call peaks for each chromosome... INFO @ Sun, 03 Jun 2018 13:40:14: #4 Write output xls file... SRX4053334.05_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:14: #4 Write peak in narrowPeak format file... SRX4053334.05_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:14: #4 Write summits bed file... SRX4053334.05_summits.bed INFO @ Sun, 03 Jun 2018 13:40:14: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (6201 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:40:15: #4 Write output xls file... SRX4053334.10_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:15: #4 Write peak in narrowPeak format file... SRX4053334.10_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:15: #4 Write summits bed file... SRX4053334.10_summits.bed INFO @ Sun, 03 Jun 2018 13:40:15: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (5974 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 03 Jun 2018 13:40:16: #4 Write output xls file... SRX4053334.20_peaks.xls INFO @ Sun, 03 Jun 2018 13:40:16: #4 Write peak in narrowPeak format file... SRX4053334.20_peaks.narrowPeak INFO @ Sun, 03 Jun 2018 13:40:16: #4 Write summits bed file... SRX4053334.20_summits.bed INFO @ Sun, 03 Jun 2018 13:40:16: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (5504 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。