Job ID = 10194784 sra ファイルのダウンロード中... Completed: 465423K bytes transferred in 6 seconds (564383K 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 19927473 spots for /home/okishinya/chipatlas/results/rn6/SRX1774916/SRR3544949.sra Written 19927473 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 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: 00:00:01 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:14:14 19927473 reads; of these: 19927473 (100.00%) were unpaired; of these: 658283 (3.30%) aligned 0 times 15581720 (78.19%) aligned exactly 1 time 3687470 (18.50%) aligned >1 times 96.70% overall alignment rate Time searching: 00:14:18 Overall time: 00:14:18 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] 2958291 / 19269190 = 0.1535 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 17:21:23: # Command line: callpeak -t SRX1774916.bam -f BAM -g 2.15e9 -n SRX1774916.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774916.05 # format = BAM # ChIP-seq file = ['SRX1774916.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 17:21:23: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:21:23: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:21:23: # Command line: callpeak -t SRX1774916.bam -f BAM -g 2.15e9 -n SRX1774916.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774916.10 # format = BAM # ChIP-seq file = ['SRX1774916.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 17:21:23: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:21:23: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:21:23: # Command line: callpeak -t SRX1774916.bam -f BAM -g 2.15e9 -n SRX1774916.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774916.20 # format = BAM # ChIP-seq file = ['SRX1774916.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 17:21:23: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:21:23: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:21:30: 1000000 INFO @ Fri, 10 Nov 2017 17:21:30: 1000000 INFO @ Fri, 10 Nov 2017 17:21:30: 1000000 INFO @ Fri, 10 Nov 2017 17:21:36: 2000000 INFO @ Fri, 10 Nov 2017 17:21:36: 2000000 INFO @ Fri, 10 Nov 2017 17:21:36: 2000000 INFO @ Fri, 10 Nov 2017 17:21:43: 3000000 INFO @ Fri, 10 Nov 2017 17:21:43: 3000000 INFO @ Fri, 10 Nov 2017 17:21:43: 3000000 INFO @ Fri, 10 Nov 2017 17:21:50: 4000000 INFO @ Fri, 10 Nov 2017 17:21:50: 4000000 INFO @ Fri, 10 Nov 2017 17:21:50: 4000000 INFO @ Fri, 10 Nov 2017 17:21:56: 5000000 INFO @ Fri, 10 Nov 2017 17:21:56: 5000000 INFO @ Fri, 10 Nov 2017 17:21:56: 5000000 INFO @ Fri, 10 Nov 2017 17:22:03: 6000000 INFO @ Fri, 10 Nov 2017 17:22:03: 6000000 INFO @ Fri, 10 Nov 2017 17:22:03: 6000000 INFO @ Fri, 10 Nov 2017 17:22:09: 7000000 INFO @ Fri, 10 Nov 2017 17:22:10: 7000000 INFO @ Fri, 10 Nov 2017 17:22:10: 7000000 INFO @ Fri, 10 Nov 2017 17:22:16: 8000000 INFO @ Fri, 10 Nov 2017 17:22:17: 8000000 INFO @ Fri, 10 Nov 2017 17:22:17: 8000000 INFO @ Fri, 10 Nov 2017 17:22:22: 9000000 INFO @ Fri, 10 Nov 2017 17:22:24: 9000000 INFO @ Fri, 10 Nov 2017 17:22:24: 9000000 INFO @ Fri, 10 Nov 2017 17:22:29: 10000000 INFO @ Fri, 10 Nov 2017 17:22:32: 10000000 INFO @ Fri, 10 Nov 2017 17:22:32: 10000000 INFO @ Fri, 10 Nov 2017 17:22:35: 11000000 INFO @ Fri, 10 Nov 2017 17:22:39: 11000000 INFO @ Fri, 10 Nov 2017 17:22:39: 11000000 INFO @ Fri, 10 Nov 2017 17:22:42: 12000000 INFO @ Fri, 10 Nov 2017 17:22:46: 12000000 INFO @ Fri, 10 Nov 2017 17:22:46: 12000000 INFO @ Fri, 10 Nov 2017 17:22:48: 13000000 INFO @ Fri, 10 Nov 2017 17:22:53: 13000000 INFO @ Fri, 10 Nov 2017 17:22:53: 13000000 INFO @ Fri, 10 Nov 2017 17:22:54: 14000000 INFO @ Fri, 10 Nov 2017 17:23:00: 14000000 INFO @ Fri, 10 Nov 2017 17:23:00: 14000000 INFO @ Fri, 10 Nov 2017 17:23:01: 15000000 INFO @ Fri, 10 Nov 2017 17:23:07: 15000000 INFO @ Fri, 10 Nov 2017 17:23:07: 15000000 INFO @ Fri, 10 Nov 2017 17:23:08: 16000000 INFO @ Fri, 10 Nov 2017 17:23:10: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:23:10: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:23:10: #1 total tags in treatment: 16310899 INFO @ Fri, 10 Nov 2017 17:23:10: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:23:10: #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 17:23:10: #1 tags after filtering in treatment: 16310709 INFO @ Fri, 10 Nov 2017 17:23:10: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:23:10: #1 finished! INFO @ Fri, 10 Nov 2017 17:23:10: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:23:10: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:23:14: #2 number of paired peaks: 54401 INFO @ Fri, 10 Nov 2017 17:23:14: start model_add_line... INFO @ Fri, 10 Nov 2017 17:23:14: start X-correlation... INFO @ Fri, 10 Nov 2017 17:23:14: end of X-cor INFO @ Fri, 10 Nov 2017 17:23:14: #2 finished! INFO @ Fri, 10 Nov 2017 17:23:14: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Nov 2017 17:23:14: #2 alternative fragment length(s) may be 177 bps INFO @ Fri, 10 Nov 2017 17:23:14: #2.2 Generate R script for model : SRX1774916.20_model.r INFO @ Fri, 10 Nov 2017 17:23:14: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:23:14: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:23:15: 16000000 INFO @ Fri, 10 Nov 2017 17:23:15: 16000000 INFO @ Fri, 10 Nov 2017 17:23:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:23:17: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:23:17: #1 total tags in treatment: 16310899 INFO @ Fri, 10 Nov 2017 17:23:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:23:17: #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 17:23:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:23:17: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:23:17: #1 total tags in treatment: 16310899 INFO @ Fri, 10 Nov 2017 17:23:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:23:17: #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 17:23:18: #1 tags after filtering in treatment: 16310709 INFO @ Fri, 10 Nov 2017 17:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:23:18: #1 finished! INFO @ Fri, 10 Nov 2017 17:23:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:23:18: #1 tags after filtering in treatment: 16310709 INFO @ Fri, 10 Nov 2017 17:23:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:23:18: #1 finished! INFO @ Fri, 10 Nov 2017 17:23:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:23:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:23:21: #2 number of paired peaks: 54401 INFO @ Fri, 10 Nov 2017 17:23:21: start model_add_line... INFO @ Fri, 10 Nov 2017 17:23:21: #2 number of paired peaks: 54401 INFO @ Fri, 10 Nov 2017 17:23:21: start model_add_line... INFO @ Fri, 10 Nov 2017 17:23:21: start X-correlation... INFO @ Fri, 10 Nov 2017 17:23:21: end of X-cor INFO @ Fri, 10 Nov 2017 17:23:21: #2 finished! INFO @ Fri, 10 Nov 2017 17:23:21: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Nov 2017 17:23:21: #2 alternative fragment length(s) may be 177 bps INFO @ Fri, 10 Nov 2017 17:23:21: #2.2 Generate R script for model : SRX1774916.10_model.r INFO @ Fri, 10 Nov 2017 17:23:21: start X-correlation... INFO @ Fri, 10 Nov 2017 17:23:21: end of X-cor INFO @ Fri, 10 Nov 2017 17:23:21: #2 finished! INFO @ Fri, 10 Nov 2017 17:23:21: #2 predicted fragment length is 177 bps INFO @ Fri, 10 Nov 2017 17:23:21: #2 alternative fragment length(s) may be 177 bps INFO @ Fri, 10 Nov 2017 17:23:21: #2.2 Generate R script for model : SRX1774916.05_model.r INFO @ Fri, 10 Nov 2017 17:23:21: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:23:21: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:23:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:23:56: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:24:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:24:04: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:24:24: #4 Write output xls file... SRX1774916.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:24:24: #4 Write peak in narrowPeak format file... SRX1774916.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:24:24: #4 Write summits bed file... SRX1774916.20_summits.bed INFO @ Fri, 10 Nov 2017 17:24:24: Done! pass1 - making usageList (63 chroms): 3 millis pass2 - checking and writing primary data (14383 records, 4 fields): 19 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:24:32: #4 Write output xls file... SRX1774916.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:24:32: #4 Write peak in narrowPeak format file... SRX1774916.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:24:32: #4 Write output xls file... SRX1774916.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:24:32: #4 Write summits bed file... SRX1774916.10_summits.bed INFO @ Fri, 10 Nov 2017 17:24:32: Done! INFO @ Fri, 10 Nov 2017 17:24:32: #4 Write peak in narrowPeak format file... SRX1774916.05_peaks.narrowPeak pass1 - making usageList (90 chroms): 5 millis INFO @ Fri, 10 Nov 2017 17:24:33: #4 Write summits bed file... SRX1774916.05_summits.bed pass2 - checking and writing primary data (24432 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:24:33: Done! pass1 - making usageList (115 chroms): 7 millis pass2 - checking and writing primary data (37149 records, 4 fields): 47 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。