Job ID = 10194892 sra ファイルのダウンロード中... Completed: 129768K bytes transferred in 8 seconds (119268K bits/sec), in 1 file. Completed: 130032K bytes transferred in 5 seconds (204733K bits/sec), in 1 file. Completed: 123779K bytes transferred in 5 seconds (180504K bits/sec), in 1 file. Completed: 122470K bytes transferred in 5 seconds (197615K bits/sec), in 1 file. Completed: 141811K bytes transferred in 6 seconds (192571K bits/sec), in 1 file. Completed: 143388K bytes transferred in 5 seconds (208692K 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 2755644 spots for /home/okishinya/chipatlas/results/rn6/SRX2202887/SRR4319869.sra Written 2755644 spots total Written 2778562 spots for /home/okishinya/chipatlas/results/rn6/SRX2202887/SRR4319868.sra Written 2778562 spots total Written 2901655 spots for /home/okishinya/chipatlas/results/rn6/SRX2202887/SRR4319866.sra Written 2901655 spots total Written 2897751 spots for /home/okishinya/chipatlas/results/rn6/SRX2202887/SRR4319867.sra Written 2897751 spots total Written 3100291 spots for /home/okishinya/chipatlas/results/rn6/SRX2202887/SRR4319870.sra Written 3100291 spots total Written 3123104 spots for /home/okishinya/chipatlas/results/rn6/SRX2202887/SRR4319871.sra Written 3123104 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: 00:00:00 Multiseed full-index search: 00:11:56 17557007 reads; of these: 17557007 (100.00%) were unpaired; of these: 1939135 (11.04%) aligned 0 times 11798804 (67.20%) aligned exactly 1 time 3819068 (21.75%) aligned >1 times 88.96% overall alignment rate Time searching: 00:11:58 Overall time: 00:11:58 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] 4216134 / 15617872 = 0.2700 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 18:16:54: # Command line: callpeak -t SRX2202887.bam -f BAM -g 2.15e9 -n SRX2202887.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2202887.05 # format = BAM # ChIP-seq file = ['SRX2202887.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 18:16:54: # Command line: callpeak -t SRX2202887.bam -f BAM -g 2.15e9 -n SRX2202887.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2202887.10 # format = BAM # ChIP-seq file = ['SRX2202887.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 18:16:54: # Command line: callpeak -t SRX2202887.bam -f BAM -g 2.15e9 -n SRX2202887.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2202887.20 # format = BAM # ChIP-seq file = ['SRX2202887.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 18:16:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:16:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:16:54: #1 read tag files... INFO @ Fri, 10 Nov 2017 18:16:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:16:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:16:54: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 18:17:00: 1000000 INFO @ Fri, 10 Nov 2017 18:17:01: 1000000 INFO @ Fri, 10 Nov 2017 18:17:01: 1000000 INFO @ Fri, 10 Nov 2017 18:17:07: 2000000 INFO @ Fri, 10 Nov 2017 18:17:08: 2000000 INFO @ Fri, 10 Nov 2017 18:17:08: 2000000 INFO @ Fri, 10 Nov 2017 18:17:14: 3000000 INFO @ Fri, 10 Nov 2017 18:17:15: 3000000 INFO @ Fri, 10 Nov 2017 18:17:16: 3000000 INFO @ Fri, 10 Nov 2017 18:17:20: 4000000 INFO @ Fri, 10 Nov 2017 18:17:23: 4000000 INFO @ Fri, 10 Nov 2017 18:17:23: 4000000 INFO @ Fri, 10 Nov 2017 18:17:27: 5000000 INFO @ Fri, 10 Nov 2017 18:17:30: 5000000 INFO @ Fri, 10 Nov 2017 18:17:31: 5000000 INFO @ Fri, 10 Nov 2017 18:17:33: 6000000 INFO @ Fri, 10 Nov 2017 18:17:38: 6000000 INFO @ Fri, 10 Nov 2017 18:17:38: 6000000 INFO @ Fri, 10 Nov 2017 18:17:39: 7000000 INFO @ Fri, 10 Nov 2017 18:17:45: 7000000 INFO @ Fri, 10 Nov 2017 18:17:46: 7000000 INFO @ Fri, 10 Nov 2017 18:17:46: 8000000 INFO @ Fri, 10 Nov 2017 18:17:52: 9000000 INFO @ Fri, 10 Nov 2017 18:17:53: 8000000 INFO @ Fri, 10 Nov 2017 18:17:53: 8000000 INFO @ Fri, 10 Nov 2017 18:17:59: 10000000 INFO @ Fri, 10 Nov 2017 18:18:00: 9000000 INFO @ Fri, 10 Nov 2017 18:18:00: 9000000 INFO @ Fri, 10 Nov 2017 18:18:05: 11000000 INFO @ Fri, 10 Nov 2017 18:18:08: 10000000 INFO @ Fri, 10 Nov 2017 18:18:08: 10000000 INFO @ Fri, 10 Nov 2017 18:18:08: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:18:08: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:18:08: #1 total tags in treatment: 11401738 INFO @ Fri, 10 Nov 2017 18:18:08: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:18:08: #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 18:18:08: #1 tags after filtering in treatment: 11401558 INFO @ Fri, 10 Nov 2017 18:18:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:18:08: #1 finished! INFO @ Fri, 10 Nov 2017 18:18:08: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:18:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:18:10: #2 number of paired peaks: 27484 INFO @ Fri, 10 Nov 2017 18:18:10: start model_add_line... INFO @ Fri, 10 Nov 2017 18:18:10: start X-correlation... INFO @ Fri, 10 Nov 2017 18:18:10: end of X-cor INFO @ Fri, 10 Nov 2017 18:18:10: #2 finished! INFO @ Fri, 10 Nov 2017 18:18:10: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 18:18:10: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 18:18:10: #2.2 Generate R script for model : SRX2202887.20_model.r INFO @ Fri, 10 Nov 2017 18:18:10: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:18:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:18:15: 11000000 INFO @ Fri, 10 Nov 2017 18:18:15: 11000000 INFO @ Fri, 10 Nov 2017 18:18:18: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:18:18: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:18:18: #1 total tags in treatment: 11401738 INFO @ Fri, 10 Nov 2017 18:18:18: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:18:18: #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 18:18:18: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 18:18:18: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 18:18:18: #1 total tags in treatment: 11401738 INFO @ Fri, 10 Nov 2017 18:18:18: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 18:18:18: #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 18:18:18: #1 tags after filtering in treatment: 11401558 INFO @ Fri, 10 Nov 2017 18:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:18:18: #1 finished! INFO @ Fri, 10 Nov 2017 18:18:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:18:18: #1 tags after filtering in treatment: 11401558 INFO @ Fri, 10 Nov 2017 18:18:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 18:18:18: #1 finished! INFO @ Fri, 10 Nov 2017 18:18:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 18:18:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 18:18:21: #2 number of paired peaks: 27484 INFO @ Fri, 10 Nov 2017 18:18:21: start model_add_line... INFO @ Fri, 10 Nov 2017 18:18:21: #2 number of paired peaks: 27484 INFO @ Fri, 10 Nov 2017 18:18:21: start model_add_line... INFO @ Fri, 10 Nov 2017 18:18:21: start X-correlation... INFO @ Fri, 10 Nov 2017 18:18:21: end of X-cor INFO @ Fri, 10 Nov 2017 18:18:21: #2 finished! INFO @ Fri, 10 Nov 2017 18:18:21: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 18:18:21: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 18:18:21: #2.2 Generate R script for model : SRX2202887.05_model.r INFO @ Fri, 10 Nov 2017 18:18:21: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:18:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:18:21: start X-correlation... INFO @ Fri, 10 Nov 2017 18:18:21: end of X-cor INFO @ Fri, 10 Nov 2017 18:18:21: #2 finished! INFO @ Fri, 10 Nov 2017 18:18:21: #2 predicted fragment length is 127 bps INFO @ Fri, 10 Nov 2017 18:18:21: #2 alternative fragment length(s) may be 127 bps INFO @ Fri, 10 Nov 2017 18:18:21: #2.2 Generate R script for model : SRX2202887.10_model.r INFO @ Fri, 10 Nov 2017 18:18:21: #3 Call peaks... INFO @ Fri, 10 Nov 2017 18:18:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 18:18:40: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:18:48: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:18:50: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 18:18:56: #4 Write output xls file... SRX2202887.20_peaks.xls INFO @ Fri, 10 Nov 2017 18:18:56: #4 Write peak in narrowPeak format file... SRX2202887.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:18:56: #4 Write summits bed file... SRX2202887.20_summits.bed INFO @ Fri, 10 Nov 2017 18:18:56: Done! pass1 - making usageList (25 chroms): 1 millis pass2 - checking and writing primary data (247 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:19:04: #4 Write output xls file... SRX2202887.05_peaks.xls INFO @ Fri, 10 Nov 2017 18:19:04: #4 Write peak in narrowPeak format file... SRX2202887.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:19:04: #4 Write summits bed file... SRX2202887.05_summits.bed INFO @ Fri, 10 Nov 2017 18:19:04: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1958 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 18:19:06: #4 Write output xls file... SRX2202887.10_peaks.xls INFO @ Fri, 10 Nov 2017 18:19:06: #4 Write peak in narrowPeak format file... SRX2202887.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 18:19:06: #4 Write summits bed file... SRX2202887.10_summits.bed INFO @ Fri, 10 Nov 2017 18:19:06: Done! pass1 - making usageList (34 chroms): 1 millis pass2 - checking and writing primary data (509 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。