Job ID = 10194818 sra ファイルのダウンロード中... Completed: 444651K bytes transferred in 15 seconds (231568K 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 15357525 spots for /home/okishinya/chipatlas/results/rn6/SRX1927032/SRR3831679.sra Written 15357525 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: 00:15:03 15357525 reads; of these: 15357525 (100.00%) were unpaired; of these: 2122126 (13.82%) aligned 0 times 11963265 (77.90%) aligned exactly 1 time 1272134 (8.28%) aligned >1 times 86.18% overall alignment rate Time searching: 00:15:06 Overall time: 00:15:06 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] 6445258 / 13235399 = 0.4870 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 22:15:39: # Command line: callpeak -t SRX1927032.bam -f BAM -g 2.15e9 -n SRX1927032.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1927032.10 # format = BAM # ChIP-seq file = ['SRX1927032.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 22:15:39: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:15:39: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:15:39: # Command line: callpeak -t SRX1927032.bam -f BAM -g 2.15e9 -n SRX1927032.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1927032.05 # format = BAM # ChIP-seq file = ['SRX1927032.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 22:15:39: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:15:39: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:15:39: # Command line: callpeak -t SRX1927032.bam -f BAM -g 2.15e9 -n SRX1927032.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1927032.20 # format = BAM # ChIP-seq file = ['SRX1927032.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 22:15:39: #1 read tag files... INFO @ Fri, 10 Nov 2017 22:15:39: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 22:15:56: 1000000 INFO @ Fri, 10 Nov 2017 22:15:56: 1000000 INFO @ Fri, 10 Nov 2017 22:15:59: 1000000 INFO @ Fri, 10 Nov 2017 22:16:13: 2000000 INFO @ Fri, 10 Nov 2017 22:16:13: 2000000 INFO @ Fri, 10 Nov 2017 22:16:17: 2000000 INFO @ Fri, 10 Nov 2017 22:16:32: 3000000 INFO @ Fri, 10 Nov 2017 22:16:32: 3000000 INFO @ Fri, 10 Nov 2017 22:16:36: 3000000 INFO @ Fri, 10 Nov 2017 22:16:52: 4000000 INFO @ Fri, 10 Nov 2017 22:16:52: 4000000 INFO @ Fri, 10 Nov 2017 22:16:56: 4000000 INFO @ Fri, 10 Nov 2017 22:17:12: 5000000 INFO @ Fri, 10 Nov 2017 22:17:12: 5000000 INFO @ Fri, 10 Nov 2017 22:17:16: 5000000 INFO @ Fri, 10 Nov 2017 22:17:30: 6000000 INFO @ Fri, 10 Nov 2017 22:17:30: 6000000 INFO @ Fri, 10 Nov 2017 22:17:35: 6000000 INFO @ Fri, 10 Nov 2017 22:17:44: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 22:17:44: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 22:17:44: #1 total tags in treatment: 6790141 INFO @ Fri, 10 Nov 2017 22:17:44: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:17:44: #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 22:17:44: #1 tags after filtering in treatment: 6789810 INFO @ Fri, 10 Nov 2017 22:17:44: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:17:44: #1 finished! INFO @ Fri, 10 Nov 2017 22:17:44: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:17:44: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:17:45: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 22:17:45: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 22:17:45: #1 total tags in treatment: 6790141 INFO @ Fri, 10 Nov 2017 22:17:45: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:17:45: #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 22:17:45: #1 tags after filtering in treatment: 6789810 INFO @ Fri, 10 Nov 2017 22:17:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:17:45: #1 finished! INFO @ Fri, 10 Nov 2017 22:17:45: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:17:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:17:47: #2 number of paired peaks: 35620 INFO @ Fri, 10 Nov 2017 22:17:47: start model_add_line... INFO @ Fri, 10 Nov 2017 22:17:47: start X-correlation... INFO @ Fri, 10 Nov 2017 22:17:47: end of X-cor INFO @ Fri, 10 Nov 2017 22:17:47: #2 finished! INFO @ Fri, 10 Nov 2017 22:17:47: #2 predicted fragment length is 136 bps INFO @ Fri, 10 Nov 2017 22:17:47: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 10 Nov 2017 22:17:47: #2.2 Generate R script for model : SRX1927032.20_model.r INFO @ Fri, 10 Nov 2017 22:17:47: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:17:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:17:48: #2 number of paired peaks: 35620 INFO @ Fri, 10 Nov 2017 22:17:48: start model_add_line... INFO @ Fri, 10 Nov 2017 22:17:48: start X-correlation... INFO @ Fri, 10 Nov 2017 22:17:48: end of X-cor INFO @ Fri, 10 Nov 2017 22:17:48: #2 finished! INFO @ Fri, 10 Nov 2017 22:17:48: #2 predicted fragment length is 136 bps INFO @ Fri, 10 Nov 2017 22:17:48: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 10 Nov 2017 22:17:48: #2.2 Generate R script for model : SRX1927032.05_model.r INFO @ Fri, 10 Nov 2017 22:17:48: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:17:48: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:17:50: #1 tag size is determined as 51 bps INFO @ Fri, 10 Nov 2017 22:17:50: #1 tag size = 51 INFO @ Fri, 10 Nov 2017 22:17:50: #1 total tags in treatment: 6790141 INFO @ Fri, 10 Nov 2017 22:17:50: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 22:17:50: #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 22:17:50: #1 tags after filtering in treatment: 6789810 INFO @ Fri, 10 Nov 2017 22:17:50: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 22:17:50: #1 finished! INFO @ Fri, 10 Nov 2017 22:17:50: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 22:17:50: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 22:17:53: #2 number of paired peaks: 35620 INFO @ Fri, 10 Nov 2017 22:17:53: start model_add_line... INFO @ Fri, 10 Nov 2017 22:17:53: start X-correlation... INFO @ Fri, 10 Nov 2017 22:17:53: end of X-cor INFO @ Fri, 10 Nov 2017 22:17:53: #2 finished! INFO @ Fri, 10 Nov 2017 22:17:53: #2 predicted fragment length is 136 bps INFO @ Fri, 10 Nov 2017 22:17:53: #2 alternative fragment length(s) may be 136 bps INFO @ Fri, 10 Nov 2017 22:17:53: #2.2 Generate R script for model : SRX1927032.10_model.r INFO @ Fri, 10 Nov 2017 22:17:53: #3 Call peaks... INFO @ Fri, 10 Nov 2017 22:17:53: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 22:18:10: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:18:11: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:18:19: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 22:18:25: #4 Write output xls file... SRX1927032.05_peaks.xls INFO @ Fri, 10 Nov 2017 22:18:26: #4 Write peak in narrowPeak format file... SRX1927032.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:18:26: #4 Write summits bed file... SRX1927032.05_summits.bed INFO @ Fri, 10 Nov 2017 22:18:26: Done! pass1 - making usageList (116 chroms): 9 millis pass2 - checking and writing primary data (31285 records, 4 fields): 73 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:18:31: #4 Write output xls file... SRX1927032.20_peaks.xls INFO @ Fri, 10 Nov 2017 22:18:31: #4 Write peak in narrowPeak format file... SRX1927032.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:18:31: #4 Write summits bed file... SRX1927032.20_summits.bed INFO @ Fri, 10 Nov 2017 22:18:31: Done! pass1 - making usageList (67 chroms): 4 millis pass2 - checking and writing primary data (13050 records, 4 fields): 41 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 22:18:36: #4 Write output xls file... SRX1927032.10_peaks.xls INFO @ Fri, 10 Nov 2017 22:18:36: #4 Write peak in narrowPeak format file... SRX1927032.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 22:18:36: #4 Write summits bed file... SRX1927032.10_summits.bed INFO @ Fri, 10 Nov 2017 22:18:37: Done! pass1 - making usageList (93 chroms): 7 millis pass2 - checking and writing primary data (23319 records, 4 fields): 62 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。