Job ID = 11293655 sra ファイルのダウンロード中... Completed: 286824K bytes transferred in 9 seconds (239274K 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 13697497 spots for /home/okishinya/chipatlas/results/dm3/SRX3873736/SRR6927801.sra Written 13697497 spots for /home/okishinya/chipatlas/results/dm3/SRX3873736/SRR6927801.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: 00:03:35 13697497 reads; of these: 13697497 (100.00%) were unpaired; of these: 2699919 (19.71%) aligned 0 times 9116613 (66.56%) aligned exactly 1 time 1880965 (13.73%) aligned >1 times 80.29% overall alignment rate Time searching: 00:03:35 Overall time: 00:03:35 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_sort_core] merging from 8 files... [bam_rmdupse_core] 2371016 / 10997578 = 0.2156 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, 04 Nov 2018 17:53:59: # Command line: callpeak -t SRX3873736.bam -f BAM -g dm -n SRX3873736.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3873736.05 # format = BAM # ChIP-seq file = ['SRX3873736.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, 04 Nov 2018 17:53:59: # Command line: callpeak -t SRX3873736.bam -f BAM -g dm -n SRX3873736.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3873736.10 # format = BAM # ChIP-seq file = ['SRX3873736.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, 04 Nov 2018 17:53:59: # Command line: callpeak -t SRX3873736.bam -f BAM -g dm -n SRX3873736.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3873736.20 # format = BAM # ChIP-seq file = ['SRX3873736.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, 04 Nov 2018 17:53:59: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:59: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:59: #1 read tag files... INFO @ Sun, 04 Nov 2018 17:53:59: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:59: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:53:59: #1 read treatment tags... INFO @ Sun, 04 Nov 2018 17:54:05: 1000000 INFO @ Sun, 04 Nov 2018 17:54:05: 1000000 INFO @ Sun, 04 Nov 2018 17:54:06: 1000000 INFO @ Sun, 04 Nov 2018 17:54:12: 2000000 INFO @ Sun, 04 Nov 2018 17:54:12: 2000000 INFO @ Sun, 04 Nov 2018 17:54:13: 2000000 INFO @ Sun, 04 Nov 2018 17:54:19: 3000000 INFO @ Sun, 04 Nov 2018 17:54:19: 3000000 INFO @ Sun, 04 Nov 2018 17:54:20: 3000000 INFO @ Sun, 04 Nov 2018 17:54:26: 4000000 INFO @ Sun, 04 Nov 2018 17:54:26: 4000000 INFO @ Sun, 04 Nov 2018 17:54:27: 4000000 INFO @ Sun, 04 Nov 2018 17:54:32: 5000000 INFO @ Sun, 04 Nov 2018 17:54:33: 5000000 INFO @ Sun, 04 Nov 2018 17:54:34: 5000000 INFO @ Sun, 04 Nov 2018 17:54:40: 6000000 INFO @ Sun, 04 Nov 2018 17:54:40: 6000000 INFO @ Sun, 04 Nov 2018 17:54:41: 6000000 INFO @ Sun, 04 Nov 2018 17:54:47: 7000000 INFO @ Sun, 04 Nov 2018 17:54:47: 7000000 INFO @ Sun, 04 Nov 2018 17:54:49: 7000000 INFO @ Sun, 04 Nov 2018 17:54:54: 8000000 INFO @ Sun, 04 Nov 2018 17:54:55: 8000000 INFO @ Sun, 04 Nov 2018 17:54:56: 8000000 INFO @ Sun, 04 Nov 2018 17:54:59: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 17:54:59: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 17:54:59: #1 total tags in treatment: 8626562 INFO @ Sun, 04 Nov 2018 17:54:59: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:54:59: #1 tags after filtering in treatment: 8626562 INFO @ Sun, 04 Nov 2018 17:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:59: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:59: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:54:59: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 17:54:59: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 17:54:59: #1 total tags in treatment: 8626562 INFO @ Sun, 04 Nov 2018 17:54:59: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:54:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:54:59: #1 tags after filtering in treatment: 8626562 INFO @ Sun, 04 Nov 2018 17:54:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:54:59: #1 finished! INFO @ Sun, 04 Nov 2018 17:54:59: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:54:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:55:00: #2 number of paired peaks: 6889 INFO @ Sun, 04 Nov 2018 17:55:00: start model_add_line... INFO @ Sun, 04 Nov 2018 17:55:00: start X-correlation... INFO @ Sun, 04 Nov 2018 17:55:01: end of X-cor INFO @ Sun, 04 Nov 2018 17:55:01: #2 finished! INFO @ Sun, 04 Nov 2018 17:55:01: #2 predicted fragment length is 164 bps INFO @ Sun, 04 Nov 2018 17:55:01: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 04 Nov 2018 17:55:01: #2.2 Generate R script for model : SRX3873736.10_model.r INFO @ Sun, 04 Nov 2018 17:55:01: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:55:01: #2 number of paired peaks: 6889 INFO @ Sun, 04 Nov 2018 17:55:01: start model_add_line... INFO @ Sun, 04 Nov 2018 17:55:01: start X-correlation... INFO @ Sun, 04 Nov 2018 17:55:01: end of X-cor INFO @ Sun, 04 Nov 2018 17:55:01: #2 finished! INFO @ Sun, 04 Nov 2018 17:55:01: #2 predicted fragment length is 164 bps INFO @ Sun, 04 Nov 2018 17:55:01: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 04 Nov 2018 17:55:01: #2.2 Generate R script for model : SRX3873736.20_model.r INFO @ Sun, 04 Nov 2018 17:55:01: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:55:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:55:01: #1 tag size is determined as 49 bps INFO @ Sun, 04 Nov 2018 17:55:01: #1 tag size = 49 INFO @ Sun, 04 Nov 2018 17:55:01: #1 total tags in treatment: 8626562 INFO @ Sun, 04 Nov 2018 17:55:01: #1 user defined the maximum tags... INFO @ Sun, 04 Nov 2018 17:55:01: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 04 Nov 2018 17:55:01: #1 tags after filtering in treatment: 8626562 INFO @ Sun, 04 Nov 2018 17:55:01: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 04 Nov 2018 17:55:01: #1 finished! INFO @ Sun, 04 Nov 2018 17:55:01: #2 Build Peak Model... INFO @ Sun, 04 Nov 2018 17:55:01: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 04 Nov 2018 17:55:02: #2 number of paired peaks: 6889 INFO @ Sun, 04 Nov 2018 17:55:02: start model_add_line... INFO @ Sun, 04 Nov 2018 17:55:02: start X-correlation... INFO @ Sun, 04 Nov 2018 17:55:02: end of X-cor INFO @ Sun, 04 Nov 2018 17:55:02: #2 finished! INFO @ Sun, 04 Nov 2018 17:55:02: #2 predicted fragment length is 164 bps INFO @ Sun, 04 Nov 2018 17:55:02: #2 alternative fragment length(s) may be 164 bps INFO @ Sun, 04 Nov 2018 17:55:02: #2.2 Generate R script for model : SRX3873736.05_model.r INFO @ Sun, 04 Nov 2018 17:55:02: #3 Call peaks... INFO @ Sun, 04 Nov 2018 17:55:02: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 04 Nov 2018 17:55:28: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:55:30: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:55:32: #3 Call peaks for each chromosome... INFO @ Sun, 04 Nov 2018 17:55:40: #4 Write output xls file... SRX3873736.20_peaks.xls INFO @ Sun, 04 Nov 2018 17:55:40: #4 Write peak in narrowPeak format file... SRX3873736.20_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:55:40: #4 Write summits bed file... SRX3873736.20_summits.bed INFO @ Sun, 04 Nov 2018 17:55:40: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (4638 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:55:42: #4 Write output xls file... SRX3873736.10_peaks.xls INFO @ Sun, 04 Nov 2018 17:55:42: #4 Write peak in narrowPeak format file... SRX3873736.10_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:55:42: #4 Write summits bed file... SRX3873736.10_summits.bed INFO @ Sun, 04 Nov 2018 17:55:42: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (7012 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 04 Nov 2018 17:55:44: #4 Write output xls file... SRX3873736.05_peaks.xls INFO @ Sun, 04 Nov 2018 17:55:44: #4 Write peak in narrowPeak format file... SRX3873736.05_peaks.narrowPeak INFO @ Sun, 04 Nov 2018 17:55:44: #4 Write summits bed file... SRX3873736.05_summits.bed INFO @ Sun, 04 Nov 2018 17:55:44: Done! pass1 - making usageList (15 chroms): 2 millis pass2 - checking and writing primary data (9085 records, 4 fields): 21 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。