Job ID = 10195032 sra ファイルのダウンロード中... Completed: 63410K bytes transferred in 4 seconds (127098K bits/sec), in 1 file. Completed: 514178K bytes transferred in 12 seconds (350462K 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 2678847 spots for /home/okishinya/chipatlas/results/rn6/SRX913501/SRR1870939.sra Written 2678847 spots total Written 16176176 spots for /home/okishinya/chipatlas/results/rn6/SRX913501/SRR1870940.sra Written 16176176 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 fastq に変換しました。 bowtie でマッピング中... Time loading reference: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:11:10 18855023 reads; of these: 18855023 (100.00%) were unpaired; of these: 1814086 (9.62%) aligned 0 times 12653466 (67.11%) aligned exactly 1 time 4387471 (23.27%) aligned >1 times 90.38% overall alignment rate Time searching: 00:11:13 Overall time: 00:11:13 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 953 sequences. [bam_sort_core] merging from 8 files... [bam_rmdupse_core] 3261226 / 17040937 = 0.1914 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 @ Sat, 11 Nov 2017 06:54:50: # Command line: callpeak -t SRX913501.bam -f BAM -g 2.15e9 -n SRX913501.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913501.05 # format = BAM # ChIP-seq file = ['SRX913501.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 06:54:50: # Command line: callpeak -t SRX913501.bam -f BAM -g 2.15e9 -n SRX913501.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913501.20 # format = BAM # ChIP-seq file = ['SRX913501.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 06:54:50: # Command line: callpeak -t SRX913501.bam -f BAM -g 2.15e9 -n SRX913501.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913501.10 # format = BAM # ChIP-seq file = ['SRX913501.bam'] # control file = None # effective genome size = 2.15e+09 # 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 @ Sat, 11 Nov 2017 06:54:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:54:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:54:50: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:54:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:54:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:54:50: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:54:56: 1000000 INFO @ Sat, 11 Nov 2017 06:54:57: 1000000 INFO @ Sat, 11 Nov 2017 06:54:57: 1000000 INFO @ Sat, 11 Nov 2017 06:55:03: 2000000 INFO @ Sat, 11 Nov 2017 06:55:03: 2000000 INFO @ Sat, 11 Nov 2017 06:55:04: 2000000 INFO @ Sat, 11 Nov 2017 06:55:09: 3000000 INFO @ Sat, 11 Nov 2017 06:55:10: 3000000 INFO @ Sat, 11 Nov 2017 06:55:11: 3000000 INFO @ Sat, 11 Nov 2017 06:55:16: 4000000 INFO @ Sat, 11 Nov 2017 06:55:17: 4000000 INFO @ Sat, 11 Nov 2017 06:55:17: 4000000 INFO @ Sat, 11 Nov 2017 06:55:22: 5000000 INFO @ Sat, 11 Nov 2017 06:55:24: 5000000 INFO @ Sat, 11 Nov 2017 06:55:24: 5000000 INFO @ Sat, 11 Nov 2017 06:55:29: 6000000 INFO @ Sat, 11 Nov 2017 06:55:31: 6000000 INFO @ Sat, 11 Nov 2017 06:55:31: 6000000 INFO @ Sat, 11 Nov 2017 06:55:35: 7000000 INFO @ Sat, 11 Nov 2017 06:55:38: 7000000 INFO @ Sat, 11 Nov 2017 06:55:38: 7000000 INFO @ Sat, 11 Nov 2017 06:55:42: 8000000 INFO @ Sat, 11 Nov 2017 06:55:45: 8000000 INFO @ Sat, 11 Nov 2017 06:55:45: 8000000 INFO @ Sat, 11 Nov 2017 06:55:48: 9000000 INFO @ Sat, 11 Nov 2017 06:55:52: 9000000 INFO @ Sat, 11 Nov 2017 06:55:52: 9000000 INFO @ Sat, 11 Nov 2017 06:55:55: 10000000 INFO @ Sat, 11 Nov 2017 06:55:59: 10000000 INFO @ Sat, 11 Nov 2017 06:55:59: 10000000 INFO @ Sat, 11 Nov 2017 06:56:01: 11000000 INFO @ Sat, 11 Nov 2017 06:56:06: 11000000 INFO @ Sat, 11 Nov 2017 06:56:06: 11000000 INFO @ Sat, 11 Nov 2017 06:56:08: 12000000 INFO @ Sat, 11 Nov 2017 06:56:13: 12000000 INFO @ Sat, 11 Nov 2017 06:56:13: 12000000 INFO @ Sat, 11 Nov 2017 06:56:14: 13000000 INFO @ Sat, 11 Nov 2017 06:56:20: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:56:20: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:56:20: #1 total tags in treatment: 13779711 INFO @ Sat, 11 Nov 2017 06:56:20: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:56:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 06:56:20: 13000000 INFO @ Sat, 11 Nov 2017 06:56:20: #1 tags after filtering in treatment: 13779544 INFO @ Sat, 11 Nov 2017 06:56:20: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:56:20: #1 finished! INFO @ Sat, 11 Nov 2017 06:56:20: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:56:20: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:56:21: 13000000 INFO @ Sat, 11 Nov 2017 06:56:22: #2 number of paired peaks: 9604 INFO @ Sat, 11 Nov 2017 06:56:22: start model_add_line... INFO @ Sat, 11 Nov 2017 06:56:22: start X-correlation... INFO @ Sat, 11 Nov 2017 06:56:22: end of X-cor INFO @ Sat, 11 Nov 2017 06:56:22: #2 finished! INFO @ Sat, 11 Nov 2017 06:56:22: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Nov 2017 06:56:22: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 11 Nov 2017 06:56:22: #2.2 Generate R script for model : SRX913501.10_model.r INFO @ Sat, 11 Nov 2017 06:56:22: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:56:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:56:26: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:56:26: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:56:26: #1 total tags in treatment: 13779711 INFO @ Sat, 11 Nov 2017 06:56:26: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:56:26: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 06:56:27: #1 tags after filtering in treatment: 13779544 INFO @ Sat, 11 Nov 2017 06:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:56:27: #1 finished! INFO @ Sat, 11 Nov 2017 06:56:27: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:56:27: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 06:56:27: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 06:56:27: #1 total tags in treatment: 13779711 INFO @ Sat, 11 Nov 2017 06:56:27: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:56:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 06:56:27: #1 tags after filtering in treatment: 13779544 INFO @ Sat, 11 Nov 2017 06:56:27: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:56:27: #1 finished! INFO @ Sat, 11 Nov 2017 06:56:27: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:56:27: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:56:28: #2 number of paired peaks: 9604 INFO @ Sat, 11 Nov 2017 06:56:28: start model_add_line... INFO @ Sat, 11 Nov 2017 06:56:29: start X-correlation... INFO @ Sat, 11 Nov 2017 06:56:29: end of X-cor INFO @ Sat, 11 Nov 2017 06:56:29: #2 finished! INFO @ Sat, 11 Nov 2017 06:56:29: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Nov 2017 06:56:29: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 11 Nov 2017 06:56:29: #2.2 Generate R script for model : SRX913501.20_model.r INFO @ Sat, 11 Nov 2017 06:56:29: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:56:29: #2 number of paired peaks: 9604 INFO @ Sat, 11 Nov 2017 06:56:29: start model_add_line... INFO @ Sat, 11 Nov 2017 06:56:29: start X-correlation... INFO @ Sat, 11 Nov 2017 06:56:29: end of X-cor INFO @ Sat, 11 Nov 2017 06:56:29: #2 finished! INFO @ Sat, 11 Nov 2017 06:56:29: #2 predicted fragment length is 106 bps INFO @ Sat, 11 Nov 2017 06:56:29: #2 alternative fragment length(s) may be 106 bps INFO @ Sat, 11 Nov 2017 06:56:29: #2.2 Generate R script for model : SRX913501.05_model.r INFO @ Sat, 11 Nov 2017 06:56:29: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:56:57: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:57:00: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:57:02: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:57:18: #4 Write output xls file... SRX913501.10_peaks.xls INFO @ Sat, 11 Nov 2017 06:57:18: #4 Write peak in narrowPeak format file... SRX913501.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:57:18: #4 Write summits bed file... SRX913501.10_summits.bed INFO @ Sat, 11 Nov 2017 06:57:18: Done! pass1 - making usageList (31 chroms): 3 millis pass2 - checking and writing primary data (298 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:57:20: #4 Write output xls file... SRX913501.20_peaks.xls INFO @ Sat, 11 Nov 2017 06:57:20: #4 Write peak in narrowPeak format file... SRX913501.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:57:20: #4 Write summits bed file... SRX913501.20_summits.bed INFO @ Sat, 11 Nov 2017 06:57:20: Done! pass1 - making usageList (19 chroms): 3 millis pass2 - checking and writing primary data (93 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:57:20: #4 Write output xls file... SRX913501.05_peaks.xls INFO @ Sat, 11 Nov 2017 06:57:20: #4 Write peak in narrowPeak format file... SRX913501.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:57:20: #4 Write summits bed file... SRX913501.05_summits.bed INFO @ Sat, 11 Nov 2017 06:57:20: Done! pass1 - making usageList (44 chroms): 1 millis pass2 - checking and writing primary data (606 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。