Job ID = 10194889 sra ファイルのダウンロード中... Completed: 131474K bytes transferred in 5 seconds (211883K bits/sec), in 1 file. Completed: 132102K bytes transferred in 5 seconds (194006K bits/sec), in 1 file. Completed: 124820K bytes transferred in 5 seconds (198578K bits/sec), in 1 file. Completed: 123206K bytes transferred in 4 seconds (238222K bits/sec), in 1 file. Completed: 145381K bytes transferred in 8 seconds (141791K bits/sec), in 1 file. Completed: 147143K bytes transferred in 6 seconds (193908K 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 2781456 spots for /home/okishinya/chipatlas/results/rn6/SRX2202884/SRR4319851.sra Written 2781456 spots total Written 2811228 spots for /home/okishinya/chipatlas/results/rn6/SRX2202884/SRR4319850.sra Written 2811228 spots total Written 2948927 spots for /home/okishinya/chipatlas/results/rn6/SRX2202884/SRR4319848.sra Written 2948927 spots total Written 2952525 spots for /home/okishinya/chipatlas/results/rn6/SRX2202884/SRR4319849.sra Written 2952525 spots total Written 3188069 spots for /home/okishinya/chipatlas/results/rn6/SRX2202884/SRR4319852.sra Written 3188069 spots total Written 3213887 spots for /home/okishinya/chipatlas/results/rn6/SRX2202884/SRR4319853.sra Written 3213887 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:13:00 17896092 reads; of these: 17896092 (100.00%) were unpaired; of these: 818379 (4.57%) aligned 0 times 12761479 (71.31%) aligned exactly 1 time 4316234 (24.12%) aligned >1 times 95.43% overall alignment rate Time searching: 00:13:02 Overall time: 00:13:02 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] 1826673 / 17077713 = 0.1070 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 @ Fri, 10 Nov 2017 18:10:34: # Command line: callpeak -t SRX2202884.bam -f BAM -g 2.15e9 -n SRX2202884.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202884.20 # format = BAM # ChIP-seq file = ['SRX2202884.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 @ Fri, 10 Nov 2017 18:10:34: # Command line: callpeak -t SRX2202884.bam -f BAM -g 2.15e9 -n SRX2202884.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202884.05 # format = BAM # ChIP-seq file = ['SRX2202884.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 @ Fri, 10 Nov 2017 18:10:34: # Command line: callpeak -t SRX2202884.bam -f BAM -g 2.15e9 -n SRX2202884.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202884.10 # format = BAM # ChIP-seq file = ['SRX2202884.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 @ Fri, 10 Nov 2017 18:10:34: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:10:34: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:10:34: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:10:34: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:10:34: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:10:34: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:10:41: 1000000 INFO @ Fri, 10 Nov 2017 18:10:41: 1000000 INFO @ Fri, 10 Nov 2017 18:10:42: 1000000 INFO @ Fri, 10 Nov 2017 18:10:49: 2000000 INFO @ Fri, 10 Nov 2017 18:10:49: 2000000 INFO @ Fri, 10 Nov 2017 18:10:49: 2000000 INFO @ Fri, 10 Nov 2017 18:10:56: 3000000 INFO @ Fri, 10 Nov 2017 18:10:56: 3000000 INFO @ Fri, 10 Nov 2017 18:10:56: 3000000 INFO @ Fri, 10 Nov 2017 18:11:03: 4000000 INFO @ Fri, 10 Nov 2017 18:11:03: 4000000 INFO @ Fri, 10 Nov 2017 18:11:04: 4000000 INFO @ Fri, 10 Nov 2017 18:11:11: 5000000 INFO @ Fri, 10 Nov 2017 18:11:11: 5000000 INFO @ Fri, 10 Nov 2017 18:11:11: 5000000 INFO @ Fri, 10 Nov 2017 18:11:18: 6000000 INFO @ Fri, 10 Nov 2017 18:11:18: 6000000 INFO @ Fri, 10 Nov 2017 18:11:19: 6000000 INFO @ Fri, 10 Nov 2017 18:11:26: 7000000 INFO @ Fri, 10 Nov 2017 18:11:26: 7000000 INFO @ Fri, 10 Nov 2017 18:11:26: 7000000 INFO @ Fri, 10 Nov 2017 18:11:33: 8000000 INFO @ Fri, 10 Nov 2017 18:11:33: 8000000 INFO @ Fri, 10 Nov 2017 18:11:34: 8000000 INFO @ Fri, 10 Nov 2017 18:11:41: 9000000 INFO @ Fri, 10 Nov 2017 18:11:41: 9000000 INFO @ Fri, 10 Nov 2017 18:11:41: 9000000 INFO @ Fri, 10 Nov 2017 18:11:48: 10000000 INFO @ Fri, 10 Nov 2017 18:11:48: 10000000 INFO @ Fri, 10 Nov 2017 18:11:49: 10000000 INFO @ Fri, 10 Nov 2017 18:11:56: 11000000 INFO @ Fri, 10 Nov 2017 18:11:56: 11000000 INFO @ Fri, 10 Nov 2017 18:11:57: 11000000 INFO @ Fri, 10 Nov 2017 18:12:03: 12000000 INFO @ Fri, 10 Nov 2017 18:12:03: 12000000 INFO @ Fri, 10 Nov 2017 18:12:04: 12000000 INFO @ Fri, 10 Nov 2017 18:12:11: 13000000 INFO @ Fri, 10 Nov 2017 18:12:11: 13000000 INFO @ Fri, 10 Nov 2017 18:12:11: 13000000 INFO @ Fri, 10 Nov 2017 18:12:18: 14000000 INFO @ Fri, 10 Nov 2017 18:12:18: 14000000 INFO @ Fri, 10 Nov 2017 18:12:19: 14000000 INFO @ Fri, 10 Nov 2017 18:12:25: 15000000 INFO @ Fri, 10 Nov 2017 18:12:25: 15000000 INFO @ Fri, 10 Nov 2017 18:12:27: 15000000 INFO @ Fri, 10 Nov 2017 18:12:27: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:12:27: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:12:27: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:12:27: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:12:27: #1 total tags in treatment: 15251040 INFO @ Fri, 10 Nov 2017 18:12:27: #1 total tags in treatment: 15251040 INFO @ Fri, 10 Nov 2017 18:12:27: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:12:27: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:12:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:12:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:12:28: #1 tags after filtering in treatment: 15250881 INFO @ Fri, 10 Nov 2017 18:12:28: #1 tags after filtering in treatment: 15250881 INFO @ Fri, 10 Nov 2017 18:12:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:12:28: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:12:28: #1 finished! INFO @ Fri, 10 Nov 2017 18:12:28: #1 finished! INFO @ Fri, 10 Nov 2017 18:12:28: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:12:28: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:12:28: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:12:29: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:12:29: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:12:29: #1 total tags in treatment: 15251040 INFO @ Fri, 10 Nov 2017 18:12:29: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:12:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Nov 2017 18:12:29: #1 tags after filtering in treatment: 15250881 INFO @ Fri, 10 Nov 2017 18:12:29: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:12:29: #1 finished! INFO @ Fri, 10 Nov 2017 18:12:29: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:12:29: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:12:30: #2 number of paired peaks: 23807 INFO @ Fri, 10 Nov 2017 18:12:30: start model_add_line... INFO @ Fri, 10 Nov 2017 18:12:30: #2 number of paired peaks: 23807 INFO @ Fri, 10 Nov 2017 18:12:30: start model_add_line... INFO @ Fri, 10 Nov 2017 18:12:30: start X-correlation... INFO @ Fri, 10 Nov 2017 18:12:30: end of X-cor INFO @ Fri, 10 Nov 2017 18:12:30: #2 finished! INFO @ Fri, 10 Nov 2017 18:12:30: #2 predicted fragment length is 124 bps INFO @ Fri, 10 Nov 2017 18:12:30: #2 alternative fragment length(s) may be 124 bps INFO @ Fri, 10 Nov 2017 18:12:30: #2.2 Generate R script for model : SRX2202884.10_model.r INFO @ Fri, 10 Nov 2017 18:12:30: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:12:30: start X-correlation... INFO @ Fri, 10 Nov 2017 18:12:30: end of X-cor INFO @ Fri, 10 Nov 2017 18:12:30: #2 finished! INFO @ Fri, 10 Nov 2017 18:12:30: #2 predicted fragment length is 124 bps INFO @ Fri, 10 Nov 2017 18:12:30: #2 alternative fragment length(s) may be 124 bps INFO @ Fri, 10 Nov 2017 18:12:30: #2.2 Generate R script for model : SRX2202884.05_model.r INFO @ Fri, 10 Nov 2017 18:12:30: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:12:30: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:12:31: #2 number of paired peaks: 23807 INFO @ Fri, 10 Nov 2017 18:12:31: start model_add_line... INFO @ Fri, 10 Nov 2017 18:12:32: start X-correlation... INFO @ Fri, 10 Nov 2017 18:12:32: end of X-cor INFO @ Fri, 10 Nov 2017 18:12:32: #2 finished! INFO @ Fri, 10 Nov 2017 18:12:32: #2 predicted fragment length is 124 bps INFO @ Fri, 10 Nov 2017 18:12:32: #2 alternative fragment length(s) may be 124 bps INFO @ Fri, 10 Nov 2017 18:12:32: #2.2 Generate R script for model : SRX2202884.20_model.r INFO @ Fri, 10 Nov 2017 18:12:32: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:12:32: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:13:08: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:13:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:13:12: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:13:28: #4 Write output xls file... SRX2202884.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:13:28: #4 Write peak in narrowPeak format file... SRX2202884.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:13:28: #4 Write summits bed file... SRX2202884.10_summits.bed INFO @ Fri, 10 Nov 2017 18:13:28: Done! pass1 - making usageList (38 chroms): 1 millis pass2 - checking and writing primary data (986 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:13:34: #4 Write output xls file... SRX2202884.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:13:34: #4 Write peak in narrowPeak format file... SRX2202884.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:13:34: #4 Write summits bed file... SRX2202884.20_summits.bed INFO @ Fri, 10 Nov 2017 18:13:34: Done! pass1 - making usageList (30 chroms): 0 millis pass2 - checking and writing primary data (296 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:13:34: #4 Write output xls file... SRX2202884.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:13:34: #4 Write peak in narrowPeak format file... SRX2202884.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:13:34: #4 Write summits bed file... SRX2202884.05_summits.bed INFO @ Fri, 10 Nov 2017 18:13:34: Done! pass1 - making usageList (58 chroms): 2 millis pass2 - checking and writing primary data (5157 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。