Job ID = 10194999 sra ファイルのダウンロード中... Completed: 753571K bytes transferred in 9 seconds (673835K 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 37609463 spots for /home/okishinya/chipatlas/results/rn6/SRX831350/SRR1743285.sra Written 37609463 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: 00:00:01 Multiseed full-index search: 00:14:21 37609463 reads; of these: 37609463 (100.00%) were unpaired; of these: 3289217 (8.75%) aligned 0 times 25487348 (67.77%) aligned exactly 1 time 8832898 (23.49%) aligned >1 times 91.25% overall alignment rate Time searching: 00:14:24 Overall time: 00:14:24 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] 20515381 / 34320246 = 0.5978 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 19:13:38: # Command line: callpeak -t SRX831350.bam -f BAM -g 2.15e9 -n SRX831350.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX831350.10 # format = BAM # ChIP-seq file = ['SRX831350.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 19:13:38: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:13:38: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:13:38: # Command line: callpeak -t SRX831350.bam -f BAM -g 2.15e9 -n SRX831350.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX831350.20 # format = BAM # ChIP-seq file = ['SRX831350.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 19:13:38: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:13:38: # Command line: callpeak -t SRX831350.bam -f BAM -g 2.15e9 -n SRX831350.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX831350.05 # format = BAM # ChIP-seq file = ['SRX831350.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 19:13:38: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:13:38: #1 read tag files... INFO @ Fri, 10 Nov 2017 19:13:38: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 19:13:44: 1000000 INFO @ Fri, 10 Nov 2017 19:13:44: 1000000 INFO @ Fri, 10 Nov 2017 19:13:44: 1000000 INFO @ Fri, 10 Nov 2017 19:13:49: 2000000 INFO @ Fri, 10 Nov 2017 19:13:50: 2000000 INFO @ Fri, 10 Nov 2017 19:13:50: 2000000 INFO @ Fri, 10 Nov 2017 19:13:55: 3000000 INFO @ Fri, 10 Nov 2017 19:13:56: 3000000 INFO @ Fri, 10 Nov 2017 19:13:57: 3000000 INFO @ Fri, 10 Nov 2017 19:14:01: 4000000 INFO @ Fri, 10 Nov 2017 19:14:03: 4000000 INFO @ Fri, 10 Nov 2017 19:14:04: 4000000 INFO @ Fri, 10 Nov 2017 19:14:07: 5000000 INFO @ Fri, 10 Nov 2017 19:14:10: 5000000 INFO @ Fri, 10 Nov 2017 19:14:11: 5000000 INFO @ Fri, 10 Nov 2017 19:14:12: 6000000 INFO @ Fri, 10 Nov 2017 19:14:16: 6000000 INFO @ Fri, 10 Nov 2017 19:14:18: 6000000 INFO @ Fri, 10 Nov 2017 19:14:18: 7000000 INFO @ Fri, 10 Nov 2017 19:14:22: 7000000 INFO @ Fri, 10 Nov 2017 19:14:24: 8000000 INFO @ Fri, 10 Nov 2017 19:14:24: 7000000 INFO @ Fri, 10 Nov 2017 19:14:29: 8000000 INFO @ Fri, 10 Nov 2017 19:14:30: 9000000 INFO @ Fri, 10 Nov 2017 19:14:30: 8000000 INFO @ Fri, 10 Nov 2017 19:14:35: 9000000 INFO @ Fri, 10 Nov 2017 19:14:36: 10000000 INFO @ Fri, 10 Nov 2017 19:14:37: 9000000 INFO @ Fri, 10 Nov 2017 19:14:41: 10000000 INFO @ Fri, 10 Nov 2017 19:14:42: 11000000 INFO @ Fri, 10 Nov 2017 19:14:43: 10000000 INFO @ Fri, 10 Nov 2017 19:14:47: 11000000 INFO @ Fri, 10 Nov 2017 19:14:47: 12000000 INFO @ Fri, 10 Nov 2017 19:14:50: 11000000 INFO @ Fri, 10 Nov 2017 19:14:53: 12000000 INFO @ Fri, 10 Nov 2017 19:14:54: 13000000 INFO @ Fri, 10 Nov 2017 19:14:56: 12000000 INFO @ Fri, 10 Nov 2017 19:14:58: #1 tag size is determined as 36 bps INFO @ Fri, 10 Nov 2017 19:14:58: #1 tag size = 36 INFO @ Fri, 10 Nov 2017 19:14:58: #1 total tags in treatment: 13804865 INFO @ Fri, 10 Nov 2017 19:14:58: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:14:58: #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 19:14:59: #1 tags after filtering in treatment: 13804735 INFO @ Fri, 10 Nov 2017 19:14:59: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:14:59: #1 finished! INFO @ Fri, 10 Nov 2017 19:14:59: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:14:59: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:15:00: 13000000 INFO @ Fri, 10 Nov 2017 19:15:01: #2 number of paired peaks: 17847 INFO @ Fri, 10 Nov 2017 19:15:01: start model_add_line... INFO @ Fri, 10 Nov 2017 19:15:01: start X-correlation... INFO @ Fri, 10 Nov 2017 19:15:01: end of X-cor INFO @ Fri, 10 Nov 2017 19:15:01: #2 finished! INFO @ Fri, 10 Nov 2017 19:15:01: #2 predicted fragment length is 117 bps INFO @ Fri, 10 Nov 2017 19:15:01: #2 alternative fragment length(s) may be 117 bps INFO @ Fri, 10 Nov 2017 19:15:01: #2.2 Generate R script for model : SRX831350.10_model.r INFO @ Fri, 10 Nov 2017 19:15:01: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:15:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:15:03: 13000000 INFO @ Fri, 10 Nov 2017 19:15:05: #1 tag size is determined as 36 bps INFO @ Fri, 10 Nov 2017 19:15:05: #1 tag size = 36 INFO @ Fri, 10 Nov 2017 19:15:05: #1 total tags in treatment: 13804865 INFO @ Fri, 10 Nov 2017 19:15:05: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:15:05: #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 19:15:05: #1 tags after filtering in treatment: 13804735 INFO @ Fri, 10 Nov 2017 19:15:05: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:15:05: #1 finished! INFO @ Fri, 10 Nov 2017 19:15:05: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:15:05: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:15:07: #2 number of paired peaks: 17847 INFO @ Fri, 10 Nov 2017 19:15:07: start model_add_line... INFO @ Fri, 10 Nov 2017 19:15:07: start X-correlation... INFO @ Fri, 10 Nov 2017 19:15:07: end of X-cor INFO @ Fri, 10 Nov 2017 19:15:07: #2 finished! INFO @ Fri, 10 Nov 2017 19:15:07: #2 predicted fragment length is 117 bps INFO @ Fri, 10 Nov 2017 19:15:07: #2 alternative fragment length(s) may be 117 bps INFO @ Fri, 10 Nov 2017 19:15:07: #2.2 Generate R script for model : SRX831350.05_model.r INFO @ Fri, 10 Nov 2017 19:15:07: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:15:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:15:08: #1 tag size is determined as 36 bps INFO @ Fri, 10 Nov 2017 19:15:08: #1 tag size = 36 INFO @ Fri, 10 Nov 2017 19:15:08: #1 total tags in treatment: 13804865 INFO @ Fri, 10 Nov 2017 19:15:08: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 19:15:08: #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 19:15:08: #1 tags after filtering in treatment: 13804735 INFO @ Fri, 10 Nov 2017 19:15:08: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 19:15:08: #1 finished! INFO @ Fri, 10 Nov 2017 19:15:08: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 19:15:08: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 19:15:10: #2 number of paired peaks: 17847 INFO @ Fri, 10 Nov 2017 19:15:10: start model_add_line... INFO @ Fri, 10 Nov 2017 19:15:10: start X-correlation... INFO @ Fri, 10 Nov 2017 19:15:10: end of X-cor INFO @ Fri, 10 Nov 2017 19:15:10: #2 finished! INFO @ Fri, 10 Nov 2017 19:15:10: #2 predicted fragment length is 117 bps INFO @ Fri, 10 Nov 2017 19:15:10: #2 alternative fragment length(s) may be 117 bps INFO @ Fri, 10 Nov 2017 19:15:10: #2.2 Generate R script for model : SRX831350.20_model.r INFO @ Fri, 10 Nov 2017 19:15:10: #3 Call peaks... INFO @ Fri, 10 Nov 2017 19:15:10: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 19:15:35: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:15:44: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:15:46: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 19:15:56: #4 Write output xls file... SRX831350.10_peaks.xls INFO @ Fri, 10 Nov 2017 19:15:56: #4 Write peak in narrowPeak format file... SRX831350.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:15:56: #4 Write summits bed file... SRX831350.10_summits.bed INFO @ Fri, 10 Nov 2017 19:15:56: Done! pass1 - making usageList (41 chroms): 1 millis pass2 - checking and writing primary data (2120 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:16:02: #4 Write output xls file... SRX831350.05_peaks.xls INFO @ Fri, 10 Nov 2017 19:16:02: #4 Write peak in narrowPeak format file... SRX831350.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:16:02: #4 Write summits bed file... SRX831350.05_summits.bed INFO @ Fri, 10 Nov 2017 19:16:02: Done! pass1 - making usageList (57 chroms): 1 millis pass2 - checking and writing primary data (5126 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 19:16:05: #4 Write output xls file... SRX831350.20_peaks.xls INFO @ Fri, 10 Nov 2017 19:16:05: #4 Write peak in narrowPeak format file... SRX831350.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 19:16:05: #4 Write summits bed file... SRX831350.20_summits.bed INFO @ Fri, 10 Nov 2017 19:16:05: Done! pass1 - making usageList (32 chroms): 1 millis pass2 - checking and writing primary data (564 records, 4 fields): 28 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。