Job ID = 10194776 sra ファイルのダウンロード中... Completed: 596182K bytes transferred in 7 seconds (612275K 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 26109213 spots for /home/okishinya/chipatlas/results/rn6/SRX1774909/SRR3544939.sra Written 26109213 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: 00:00:00 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:47 26109213 reads; of these: 26109213 (100.00%) were unpaired; of these: 972052 (3.72%) aligned 0 times 19430616 (74.42%) aligned exactly 1 time 5706545 (21.86%) aligned >1 times 96.28% overall alignment rate Time searching: 00:20:50 Overall time: 00:20:50 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 12 files... [bam_rmdupse_core] 3704502 / 25137161 = 0.1474 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 17:16:38: # Command line: callpeak -t SRX1774909.bam -f BAM -g 2.15e9 -n SRX1774909.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774909.20 # format = BAM # ChIP-seq file = ['SRX1774909.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 17:16:38: # Command line: callpeak -t SRX1774909.bam -f BAM -g 2.15e9 -n SRX1774909.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774909.10 # format = BAM # ChIP-seq file = ['SRX1774909.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 17:16:38: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:16:38: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:16:38: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:16:38: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:16:38: # Command line: callpeak -t SRX1774909.bam -f BAM -g 2.15e9 -n SRX1774909.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774909.05 # format = BAM # ChIP-seq file = ['SRX1774909.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 17:16:38: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:16:38: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:16:46: 1000000 INFO @ Fri, 10 Nov 2017 17:16:46: 1000000 INFO @ Fri, 10 Nov 2017 17:16:46: 1000000 INFO @ Fri, 10 Nov 2017 17:16:53: 2000000 INFO @ Fri, 10 Nov 2017 17:16:53: 2000000 INFO @ Fri, 10 Nov 2017 17:16:53: 2000000 INFO @ Fri, 10 Nov 2017 17:17:01: 3000000 INFO @ Fri, 10 Nov 2017 17:17:01: 3000000 INFO @ Fri, 10 Nov 2017 17:17:01: 3000000 INFO @ Fri, 10 Nov 2017 17:17:09: 4000000 INFO @ Fri, 10 Nov 2017 17:17:09: 4000000 INFO @ Fri, 10 Nov 2017 17:17:09: 4000000 INFO @ Fri, 10 Nov 2017 17:17:16: 5000000 INFO @ Fri, 10 Nov 2017 17:17:16: 5000000 INFO @ Fri, 10 Nov 2017 17:17:16: 5000000 INFO @ Fri, 10 Nov 2017 17:17:24: 6000000 INFO @ Fri, 10 Nov 2017 17:17:24: 6000000 INFO @ Fri, 10 Nov 2017 17:17:24: 6000000 INFO @ Fri, 10 Nov 2017 17:17:31: 7000000 INFO @ Fri, 10 Nov 2017 17:17:31: 7000000 INFO @ Fri, 10 Nov 2017 17:17:31: 7000000 INFO @ Fri, 10 Nov 2017 17:17:39: 8000000 INFO @ Fri, 10 Nov 2017 17:17:39: 8000000 INFO @ Fri, 10 Nov 2017 17:17:39: 8000000 INFO @ Fri, 10 Nov 2017 17:17:46: 9000000 INFO @ Fri, 10 Nov 2017 17:17:46: 9000000 INFO @ Fri, 10 Nov 2017 17:17:46: 9000000 INFO @ Fri, 10 Nov 2017 17:17:54: 10000000 INFO @ Fri, 10 Nov 2017 17:17:54: 10000000 INFO @ Fri, 10 Nov 2017 17:17:54: 10000000 INFO @ Fri, 10 Nov 2017 17:18:01: 11000000 INFO @ Fri, 10 Nov 2017 17:18:01: 11000000 INFO @ Fri, 10 Nov 2017 17:18:01: 11000000 INFO @ Fri, 10 Nov 2017 17:18:09: 12000000 INFO @ Fri, 10 Nov 2017 17:18:09: 12000000 INFO @ Fri, 10 Nov 2017 17:18:09: 12000000 INFO @ Fri, 10 Nov 2017 17:18:16: 13000000 INFO @ Fri, 10 Nov 2017 17:18:16: 13000000 INFO @ Fri, 10 Nov 2017 17:18:16: 13000000 INFO @ Fri, 10 Nov 2017 17:18:24: 14000000 INFO @ Fri, 10 Nov 2017 17:18:24: 14000000 INFO @ Fri, 10 Nov 2017 17:18:24: 14000000 INFO @ Fri, 10 Nov 2017 17:18:31: 15000000 INFO @ Fri, 10 Nov 2017 17:18:31: 15000000 INFO @ Fri, 10 Nov 2017 17:18:31: 15000000 INFO @ Fri, 10 Nov 2017 17:18:39: 16000000 INFO @ Fri, 10 Nov 2017 17:18:39: 16000000 INFO @ Fri, 10 Nov 2017 17:18:39: 16000000 INFO @ Fri, 10 Nov 2017 17:18:46: 17000000 INFO @ Fri, 10 Nov 2017 17:18:46: 17000000 INFO @ Fri, 10 Nov 2017 17:18:46: 17000000 INFO @ Fri, 10 Nov 2017 17:18:53: 18000000 INFO @ Fri, 10 Nov 2017 17:18:53: 18000000 INFO @ Fri, 10 Nov 2017 17:18:53: 18000000 INFO @ Fri, 10 Nov 2017 17:19:00: 19000000 INFO @ Fri, 10 Nov 2017 17:19:00: 19000000 INFO @ Fri, 10 Nov 2017 17:19:00: 19000000 INFO @ Fri, 10 Nov 2017 17:19:07: 20000000 INFO @ Fri, 10 Nov 2017 17:19:07: 20000000 INFO @ Fri, 10 Nov 2017 17:19:07: 20000000 INFO @ Fri, 10 Nov 2017 17:19:14: 21000000 INFO @ Fri, 10 Nov 2017 17:19:14: 21000000 INFO @ Fri, 10 Nov 2017 17:19:14: 21000000 INFO @ Fri, 10 Nov 2017 17:19:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:19:17: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:19:17: #1 total tags in treatment: 21432659 INFO @ Fri, 10 Nov 2017 17:19:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:19:17: #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 17:19:17: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:19:17: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:19:17: #1 total tags in treatment: 21432659 INFO @ Fri, 10 Nov 2017 17:19:17: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:19:17: #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 17:19:18: #1 tags after filtering in treatment: 21432502 INFO @ Fri, 10 Nov 2017 17:19:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:19:18: #1 finished! INFO @ Fri, 10 Nov 2017 17:19:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:19:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:19:18: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:19:18: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:19:18: #1 total tags in treatment: 21432659 INFO @ Fri, 10 Nov 2017 17:19:18: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:19:18: #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 17:19:18: #1 tags after filtering in treatment: 21432502 INFO @ Fri, 10 Nov 2017 17:19:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:19:18: #1 finished! INFO @ Fri, 10 Nov 2017 17:19:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:19:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:19:18: #1 tags after filtering in treatment: 21432502 INFO @ Fri, 10 Nov 2017 17:19:18: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:19:18: #1 finished! INFO @ Fri, 10 Nov 2017 17:19:18: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:19:18: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:19:21: #2 number of paired peaks: 33183 INFO @ Fri, 10 Nov 2017 17:19:21: start model_add_line... INFO @ Fri, 10 Nov 2017 17:19:21: start X-correlation... INFO @ Fri, 10 Nov 2017 17:19:21: end of X-cor INFO @ Fri, 10 Nov 2017 17:19:21: #2 finished! INFO @ Fri, 10 Nov 2017 17:19:21: #2 predicted fragment length is 171 bps INFO @ Fri, 10 Nov 2017 17:19:21: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 10 Nov 2017 17:19:21: #2.2 Generate R script for model : SRX1774909.20_model.r INFO @ Fri, 10 Nov 2017 17:19:21: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:19:21: #2 number of paired peaks: 33183 INFO @ Fri, 10 Nov 2017 17:19:21: start model_add_line... INFO @ Fri, 10 Nov 2017 17:19:21: start X-correlation... INFO @ Fri, 10 Nov 2017 17:19:21: end of X-cor INFO @ Fri, 10 Nov 2017 17:19:21: #2 finished! INFO @ Fri, 10 Nov 2017 17:19:21: #2 predicted fragment length is 171 bps INFO @ Fri, 10 Nov 2017 17:19:21: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 10 Nov 2017 17:19:21: #2.2 Generate R script for model : SRX1774909.10_model.r INFO @ Fri, 10 Nov 2017 17:19:21: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:19:21: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:19:22: #2 number of paired peaks: 33183 INFO @ Fri, 10 Nov 2017 17:19:22: start model_add_line... INFO @ Fri, 10 Nov 2017 17:19:22: start X-correlation... INFO @ Fri, 10 Nov 2017 17:19:22: end of X-cor INFO @ Fri, 10 Nov 2017 17:19:22: #2 finished! INFO @ Fri, 10 Nov 2017 17:19:22: #2 predicted fragment length is 171 bps INFO @ Fri, 10 Nov 2017 17:19:22: #2 alternative fragment length(s) may be 171 bps INFO @ Fri, 10 Nov 2017 17:19:22: #2.2 Generate R script for model : SRX1774909.05_model.r INFO @ Fri, 10 Nov 2017 17:19:22: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:19:22: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:20:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:20:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:20:16: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:20:45: #4 Write output xls file... SRX1774909.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:20:45: #4 Write output xls file... SRX1774909.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:20:45: #4 Write peak in narrowPeak format file... SRX1774909.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:20:45: #4 Write peak in narrowPeak format file... SRX1774909.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:20:45: #4 Write summits bed file... SRX1774909.10_summits.bed INFO @ Fri, 10 Nov 2017 17:20:45: Done! INFO @ Fri, 10 Nov 2017 17:20:45: #4 Write summits bed file... SRX1774909.05_summits.bed INFO @ Fri, 10 Nov 2017 17:20:45: Done! pass1 - making usageList (62 chroms): 2 millis pass2 - checking and writing primary data (10095 records, 4 fields): 15 millis CompletedMACS2peakCalling pass1 - making usageList (79 chroms): 4 millis pass2 - checking and writing primary data (19183 records, 4 fields): 25 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:20:46: #4 Write output xls file... SRX1774909.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:20:46: #4 Write peak in narrowPeak format file... SRX1774909.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:20:46: #4 Write summits bed file... SRX1774909.20_summits.bed INFO @ Fri, 10 Nov 2017 17:20:46: Done! pass1 - making usageList (39 chroms): 2 millis pass2 - checking and writing primary data (4157 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。