Job ID = 11240808 sra ファイルのダウンロード中... Completed: 529720K bytes transferred in 8 seconds (535664K 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 14042123 spots for /home/okishinya/chipatlas/results/dm3/SRX4798856/SRR7965213.sra Written 14042123 spots for /home/okishinya/chipatlas/results/dm3/SRX4798856/SRR7965213.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: 00:02:56 14042123 reads; of these: 14042123 (100.00%) were unpaired; of these: 5795551 (41.27%) aligned 0 times 7401108 (52.71%) aligned exactly 1 time 845464 (6.02%) aligned >1 times 58.73% overall alignment rate Time searching: 00:02:56 Overall time: 00:02:56 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] 1849790 / 8246572 = 0.2243 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, 07 Oct 2018 20:49:50: # Command line: callpeak -t SRX4798856.bam -f BAM -g dm -n SRX4798856.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX4798856.20 # format = BAM # ChIP-seq file = ['SRX4798856.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, 07 Oct 2018 20:49:50: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:49:50: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:49:50: # Command line: callpeak -t SRX4798856.bam -f BAM -g dm -n SRX4798856.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX4798856.05 # format = BAM # ChIP-seq file = ['SRX4798856.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, 07 Oct 2018 20:49:50: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:49:50: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:49:50: # Command line: callpeak -t SRX4798856.bam -f BAM -g dm -n SRX4798856.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX4798856.10 # format = BAM # ChIP-seq file = ['SRX4798856.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, 07 Oct 2018 20:49:50: #1 read tag files... INFO @ Sun, 07 Oct 2018 20:49:50: #1 read treatment tags... INFO @ Sun, 07 Oct 2018 20:49:58: 1000000 INFO @ Sun, 07 Oct 2018 20:49:59: 1000000 INFO @ Sun, 07 Oct 2018 20:49:59: 1000000 INFO @ Sun, 07 Oct 2018 20:50:06: 2000000 INFO @ Sun, 07 Oct 2018 20:50:08: 2000000 INFO @ Sun, 07 Oct 2018 20:50:08: 2000000 INFO @ Sun, 07 Oct 2018 20:50:14: 3000000 INFO @ Sun, 07 Oct 2018 20:50:16: 3000000 INFO @ Sun, 07 Oct 2018 20:50:16: 3000000 INFO @ Sun, 07 Oct 2018 20:50:21: 4000000 INFO @ Sun, 07 Oct 2018 20:50:25: 4000000 INFO @ Sun, 07 Oct 2018 20:50:25: 4000000 INFO @ Sun, 07 Oct 2018 20:50:29: 5000000 INFO @ Sun, 07 Oct 2018 20:50:34: 5000000 INFO @ Sun, 07 Oct 2018 20:50:34: 5000000 INFO @ Sun, 07 Oct 2018 20:50:37: 6000000 INFO @ Sun, 07 Oct 2018 20:50:40: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:50:40: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:50:40: #1 total tags in treatment: 6396782 INFO @ Sun, 07 Oct 2018 20:50:40: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:50:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:50:40: #1 tags after filtering in treatment: 6396782 INFO @ Sun, 07 Oct 2018 20:50:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:50:40: #1 finished! INFO @ Sun, 07 Oct 2018 20:50:40: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:50:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:50:40: #2 number of paired peaks: 1119 INFO @ Sun, 07 Oct 2018 20:50:40: start model_add_line... INFO @ Sun, 07 Oct 2018 20:50:40: start X-correlation... INFO @ Sun, 07 Oct 2018 20:50:40: end of X-cor INFO @ Sun, 07 Oct 2018 20:50:40: #2 finished! INFO @ Sun, 07 Oct 2018 20:50:40: #2 predicted fragment length is 181 bps INFO @ Sun, 07 Oct 2018 20:50:40: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 07 Oct 2018 20:50:40: #2.2 Generate R script for model : SRX4798856.10_model.r INFO @ Sun, 07 Oct 2018 20:50:40: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:50:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:50:42: 6000000 INFO @ Sun, 07 Oct 2018 20:50:43: 6000000 INFO @ Sun, 07 Oct 2018 20:50:46: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:50:46: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:50:46: #1 total tags in treatment: 6396782 INFO @ Sun, 07 Oct 2018 20:50:46: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:50:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:50:46: #1 tags after filtering in treatment: 6396782 INFO @ Sun, 07 Oct 2018 20:50:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:50:46: #1 finished! INFO @ Sun, 07 Oct 2018 20:50:46: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:50:46: #1 tag size is determined as 51 bps INFO @ Sun, 07 Oct 2018 20:50:46: #1 tag size = 51 INFO @ Sun, 07 Oct 2018 20:50:46: #1 total tags in treatment: 6396782 INFO @ Sun, 07 Oct 2018 20:50:46: #1 user defined the maximum tags... INFO @ Sun, 07 Oct 2018 20:50:46: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 07 Oct 2018 20:50:46: #1 tags after filtering in treatment: 6396782 INFO @ Sun, 07 Oct 2018 20:50:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 07 Oct 2018 20:50:46: #1 finished! INFO @ Sun, 07 Oct 2018 20:50:46: #2 Build Peak Model... INFO @ Sun, 07 Oct 2018 20:50:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 07 Oct 2018 20:50:47: #2 number of paired peaks: 1119 INFO @ Sun, 07 Oct 2018 20:50:47: start model_add_line... INFO @ Sun, 07 Oct 2018 20:50:47: start X-correlation... INFO @ Sun, 07 Oct 2018 20:50:47: end of X-cor INFO @ Sun, 07 Oct 2018 20:50:47: #2 finished! INFO @ Sun, 07 Oct 2018 20:50:47: #2 predicted fragment length is 181 bps INFO @ Sun, 07 Oct 2018 20:50:47: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 07 Oct 2018 20:50:47: #2.2 Generate R script for model : SRX4798856.05_model.r INFO @ Sun, 07 Oct 2018 20:50:47: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:50:47: #2 number of paired peaks: 1119 INFO @ Sun, 07 Oct 2018 20:50:47: start model_add_line... INFO @ Sun, 07 Oct 2018 20:50:47: start X-correlation... INFO @ Sun, 07 Oct 2018 20:50:47: end of X-cor INFO @ Sun, 07 Oct 2018 20:50:47: #2 finished! INFO @ Sun, 07 Oct 2018 20:50:47: #2 predicted fragment length is 181 bps INFO @ Sun, 07 Oct 2018 20:50:47: #2 alternative fragment length(s) may be 181 bps INFO @ Sun, 07 Oct 2018 20:50:47: #2.2 Generate R script for model : SRX4798856.20_model.r INFO @ Sun, 07 Oct 2018 20:50:47: #3 Call peaks... INFO @ Sun, 07 Oct 2018 20:50:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 07 Oct 2018 20:50:56: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:51:04: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:51:04: #3 Call peaks for each chromosome... INFO @ Sun, 07 Oct 2018 20:51:06: #4 Write output xls file... SRX4798856.10_peaks.xls INFO @ Sun, 07 Oct 2018 20:51:06: #4 Write peak in narrowPeak format file... SRX4798856.10_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:51:06: #4 Write summits bed file... SRX4798856.10_summits.bed INFO @ Sun, 07 Oct 2018 20:51:06: Done! pass1 - making usageList (11 chroms): 2 millis pass2 - checking and writing primary data (3036 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:51:13: #4 Write output xls file... SRX4798856.05_peaks.xls INFO @ Sun, 07 Oct 2018 20:51:13: #4 Write peak in narrowPeak format file... SRX4798856.05_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:51:13: #4 Write summits bed file... SRX4798856.05_summits.bed INFO @ Sun, 07 Oct 2018 20:51:13: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (6725 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sun, 07 Oct 2018 20:51:14: #4 Write output xls file... SRX4798856.20_peaks.xls INFO @ Sun, 07 Oct 2018 20:51:14: #4 Write peak in narrowPeak format file... SRX4798856.20_peaks.narrowPeak INFO @ Sun, 07 Oct 2018 20:51:14: #4 Write summits bed file... SRX4798856.20_summits.bed INFO @ Sun, 07 Oct 2018 20:51:14: Done! pass1 - making usageList (11 chroms): 1 millis pass2 - checking and writing primary data (947 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。