Job ID = 10194745 sra ファイルのダウンロード中... Completed: 404411K bytes transferred in 6 seconds (514812K 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 15517699 spots for /home/okishinya/chipatlas/results/rn6/SRX1068234/SRR2073193.sra Written 15517699 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: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:20:37 15517699 reads; of these: 15517699 (100.00%) were unpaired; of these: 355789 (2.29%) aligned 0 times 7918123 (51.03%) aligned exactly 1 time 7243787 (46.68%) aligned >1 times 97.71% overall alignment rate Time searching: 00:20:41 Overall time: 00:20:41 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] 1163755 / 15161910 = 0.0768 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 23:56:18: # Command line: callpeak -t SRX1068234.bam -f BAM -g 2.15e9 -n SRX1068234.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1068234.10 # format = BAM # ChIP-seq file = ['SRX1068234.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 23:56:18: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:56:18: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:56:18: # Command line: callpeak -t SRX1068234.bam -f BAM -g 2.15e9 -n SRX1068234.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1068234.20 # format = BAM # ChIP-seq file = ['SRX1068234.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 23:56:18: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:56:18: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:56:18: # Command line: callpeak -t SRX1068234.bam -f BAM -g 2.15e9 -n SRX1068234.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1068234.05 # format = BAM # ChIP-seq file = ['SRX1068234.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 23:56:18: #1 read tag files... INFO @ Fri, 10 Nov 2017 23:56:18: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 23:56:26: 1000000 INFO @ Fri, 10 Nov 2017 23:56:26: 1000000 INFO @ Fri, 10 Nov 2017 23:56:28: 1000000 INFO @ Fri, 10 Nov 2017 23:56:34: 2000000 INFO @ Fri, 10 Nov 2017 23:56:35: 2000000 INFO @ Fri, 10 Nov 2017 23:56:38: 2000000 INFO @ Fri, 10 Nov 2017 23:56:42: 3000000 INFO @ Fri, 10 Nov 2017 23:56:44: 3000000 INFO @ Fri, 10 Nov 2017 23:56:47: 3000000 INFO @ Fri, 10 Nov 2017 23:56:50: 4000000 INFO @ Fri, 10 Nov 2017 23:56:54: 4000000 INFO @ Fri, 10 Nov 2017 23:56:55: 4000000 INFO @ Fri, 10 Nov 2017 23:56:58: 5000000 INFO @ Fri, 10 Nov 2017 23:57:04: 5000000 INFO @ Fri, 10 Nov 2017 23:57:05: 5000000 INFO @ Fri, 10 Nov 2017 23:57:07: 6000000 INFO @ Fri, 10 Nov 2017 23:57:14: 6000000 INFO @ Fri, 10 Nov 2017 23:57:15: 6000000 INFO @ Fri, 10 Nov 2017 23:57:16: 7000000 INFO @ Fri, 10 Nov 2017 23:57:22: 7000000 INFO @ Fri, 10 Nov 2017 23:57:24: 7000000 INFO @ Fri, 10 Nov 2017 23:57:26: 8000000 INFO @ Fri, 10 Nov 2017 23:57:31: 8000000 INFO @ Fri, 10 Nov 2017 23:57:33: 8000000 INFO @ Fri, 10 Nov 2017 23:57:36: 9000000 INFO @ Fri, 10 Nov 2017 23:57:40: 9000000 INFO @ Fri, 10 Nov 2017 23:57:42: 9000000 INFO @ Fri, 10 Nov 2017 23:57:46: 10000000 INFO @ Fri, 10 Nov 2017 23:57:50: 10000000 INFO @ Fri, 10 Nov 2017 23:57:50: 10000000 INFO @ Fri, 10 Nov 2017 23:57:57: 11000000 INFO @ Fri, 10 Nov 2017 23:57:58: 11000000 INFO @ Fri, 10 Nov 2017 23:57:58: 11000000 INFO @ Fri, 10 Nov 2017 23:58:05: 12000000 INFO @ Fri, 10 Nov 2017 23:58:06: 12000000 INFO @ Fri, 10 Nov 2017 23:58:06: 12000000 INFO @ Fri, 10 Nov 2017 23:58:14: 13000000 INFO @ Fri, 10 Nov 2017 23:58:14: 13000000 INFO @ Fri, 10 Nov 2017 23:58:14: 13000000 INFO @ Fri, 10 Nov 2017 23:58:22: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:58:22: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:58:22: #1 total tags in treatment: 13998155 INFO @ Fri, 10 Nov 2017 23:58:22: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:58:22: #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 23:58:23: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:58:23: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:58:23: #1 total tags in treatment: 13998155 INFO @ Fri, 10 Nov 2017 23:58:23: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:58:23: #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 23:58:23: #1 tags after filtering in treatment: 13997975 INFO @ Fri, 10 Nov 2017 23:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:58:23: #1 finished! INFO @ Fri, 10 Nov 2017 23:58:23: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:58:23: #1 tag size is determined as 64 bps INFO @ Fri, 10 Nov 2017 23:58:23: #1 tag size = 64 INFO @ Fri, 10 Nov 2017 23:58:23: #1 total tags in treatment: 13998155 INFO @ Fri, 10 Nov 2017 23:58:23: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 23:58:23: #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 23:58:23: #1 tags after filtering in treatment: 13997975 INFO @ Fri, 10 Nov 2017 23:58:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:58:23: #1 finished! INFO @ Fri, 10 Nov 2017 23:58:23: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:58:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:58:24: #1 tags after filtering in treatment: 13997975 INFO @ Fri, 10 Nov 2017 23:58:24: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 23:58:24: #1 finished! INFO @ Fri, 10 Nov 2017 23:58:24: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 23:58:24: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 23:58:27: #2 number of paired peaks: 78893 INFO @ Fri, 10 Nov 2017 23:58:27: start model_add_line... INFO @ Fri, 10 Nov 2017 23:58:28: #2 number of paired peaks: 78893 INFO @ Fri, 10 Nov 2017 23:58:28: start model_add_line... INFO @ Fri, 10 Nov 2017 23:58:28: start X-correlation... INFO @ Fri, 10 Nov 2017 23:58:28: end of X-cor INFO @ Fri, 10 Nov 2017 23:58:28: #2 finished! INFO @ Fri, 10 Nov 2017 23:58:28: #2 predicted fragment length is 287 bps INFO @ Fri, 10 Nov 2017 23:58:28: #2 alternative fragment length(s) may be 287 bps INFO @ Fri, 10 Nov 2017 23:58:28: #2.2 Generate R script for model : SRX1068234.05_model.r INFO @ Fri, 10 Nov 2017 23:58:28: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:58:28: start X-correlation... INFO @ Fri, 10 Nov 2017 23:58:28: end of X-cor INFO @ Fri, 10 Nov 2017 23:58:28: #2 finished! INFO @ Fri, 10 Nov 2017 23:58:28: #2 predicted fragment length is 287 bps INFO @ Fri, 10 Nov 2017 23:58:28: #2 alternative fragment length(s) may be 287 bps INFO @ Fri, 10 Nov 2017 23:58:28: #2.2 Generate R script for model : SRX1068234.20_model.r INFO @ Fri, 10 Nov 2017 23:58:28: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:58:28: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:58:28: #2 number of paired peaks: 78893 INFO @ Fri, 10 Nov 2017 23:58:28: start model_add_line... INFO @ Fri, 10 Nov 2017 23:58:28: start X-correlation... INFO @ Fri, 10 Nov 2017 23:58:28: end of X-cor INFO @ Fri, 10 Nov 2017 23:58:28: #2 finished! INFO @ Fri, 10 Nov 2017 23:58:28: #2 predicted fragment length is 287 bps INFO @ Fri, 10 Nov 2017 23:58:28: #2 alternative fragment length(s) may be 287 bps INFO @ Fri, 10 Nov 2017 23:58:28: #2.2 Generate R script for model : SRX1068234.10_model.r INFO @ Fri, 10 Nov 2017 23:58:29: #3 Call peaks... INFO @ Fri, 10 Nov 2017 23:58:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 23:59:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:59:09: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:59:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 23:59:30: #4 Write output xls file... SRX1068234.20_peaks.xls INFO @ Fri, 10 Nov 2017 23:59:30: #4 Write peak in narrowPeak format file... SRX1068234.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:59:31: #4 Write summits bed file... SRX1068234.20_summits.bed INFO @ Fri, 10 Nov 2017 23:59:31: Done! INFO @ Fri, 10 Nov 2017 23:59:31: #4 Write output xls file... SRX1068234.10_peaks.xls INFO @ Fri, 10 Nov 2017 23:59:31: #4 Write peak in narrowPeak format file... SRX1068234.10_peaks.narrowPeak pass1 - making usageList (39 chroms): 1 millis INFO @ Fri, 10 Nov 2017 23:59:31: #4 Write summits bed file... SRX1068234.10_summits.bed pass2 - checking and writing primary data (496 records, 4 fields): 9 millis INFO @ Fri, 10 Nov 2017 23:59:31: Done! CompletedMACS2peakCalling pass1 - making usageList (48 chroms): 1 millis pass2 - checking and writing primary data (1155 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 23:59:33: #4 Write output xls file... SRX1068234.05_peaks.xls INFO @ Fri, 10 Nov 2017 23:59:33: #4 Write peak in narrowPeak format file... SRX1068234.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 23:59:33: #4 Write summits bed file... SRX1068234.05_summits.bed INFO @ Fri, 10 Nov 2017 23:59:33: Done! pass1 - making usageList (80 chroms): 1 millis pass2 - checking and writing primary data (5484 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。