Job ID = 10487618 sra ファイルのダウンロード中... Completed: 600551K bytes transferred in 58 seconds (84750K 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 15323744 spots for /home/okishinya/chipatlas/results/rn6/SRX3358574/SRR6251633.sra Written 15323744 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: 00:22:13 15323744 reads; of these: 15323744 (100.00%) were unpaired; of these: 543191 (3.54%) aligned 0 times 12181518 (79.49%) aligned exactly 1 time 2599035 (16.96%) aligned >1 times 96.46% overall alignment rate Time searching: 00:22:17 Overall time: 00:22:17 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] 163875 / 14780553 = 0.0111 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 @ Sun, 18 Mar 2018 10:47:29: # Command line: callpeak -t SRX3358574.bam -f BAM -g 2.15e9 -n SRX3358574.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3358574.20 # format = BAM # ChIP-seq file = ['SRX3358574.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 @ Sun, 18 Mar 2018 10:47:29: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:47:29: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:47:29: # Command line: callpeak -t SRX3358574.bam -f BAM -g 2.15e9 -n SRX3358574.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3358574.05 # format = BAM # ChIP-seq file = ['SRX3358574.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 @ Sun, 18 Mar 2018 10:47:29: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:47:29: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:47:29: # Command line: callpeak -t SRX3358574.bam -f BAM -g 2.15e9 -n SRX3358574.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3358574.10 # format = BAM # ChIP-seq file = ['SRX3358574.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 @ Sun, 18 Mar 2018 10:47:29: #1 read tag files... INFO @ Sun, 18 Mar 2018 10:47:29: #1 read treatment tags... INFO @ Sun, 18 Mar 2018 10:47:36: 1000000 INFO @ Sun, 18 Mar 2018 10:47:36: 1000000 INFO @ Sun, 18 Mar 2018 10:47:36: 1000000 INFO @ Sun, 18 Mar 2018 10:47:43: 2000000 INFO @ Sun, 18 Mar 2018 10:47:43: 2000000 INFO @ Sun, 18 Mar 2018 10:47:43: 2000000 INFO @ Sun, 18 Mar 2018 10:47:49: 3000000 INFO @ Sun, 18 Mar 2018 10:47:50: 3000000 INFO @ Sun, 18 Mar 2018 10:47:50: 3000000 INFO @ Sun, 18 Mar 2018 10:47:56: 4000000 INFO @ Sun, 18 Mar 2018 10:47:58: 4000000 INFO @ Sun, 18 Mar 2018 10:47:58: 4000000 INFO @ Sun, 18 Mar 2018 10:48:02: 5000000 INFO @ Sun, 18 Mar 2018 10:48:05: 5000000 INFO @ Sun, 18 Mar 2018 10:48:05: 5000000 INFO @ Sun, 18 Mar 2018 10:48:09: 6000000 INFO @ Sun, 18 Mar 2018 10:48:12: 6000000 INFO @ Sun, 18 Mar 2018 10:48:13: 6000000 INFO @ Sun, 18 Mar 2018 10:48:16: 7000000 INFO @ Sun, 18 Mar 2018 10:48:20: 7000000 INFO @ Sun, 18 Mar 2018 10:48:20: 7000000 INFO @ Sun, 18 Mar 2018 10:48:22: 8000000 INFO @ Sun, 18 Mar 2018 10:48:27: 8000000 INFO @ Sun, 18 Mar 2018 10:48:28: 8000000 INFO @ Sun, 18 Mar 2018 10:48:29: 9000000 INFO @ Sun, 18 Mar 2018 10:48:35: 9000000 INFO @ Sun, 18 Mar 2018 10:48:35: 10000000 INFO @ Sun, 18 Mar 2018 10:48:36: 9000000 INFO @ Sun, 18 Mar 2018 10:48:42: 11000000 INFO @ Sun, 18 Mar 2018 10:48:43: 10000000 INFO @ Sun, 18 Mar 2018 10:48:43: 10000000 INFO @ Sun, 18 Mar 2018 10:48:49: 12000000 INFO @ Sun, 18 Mar 2018 10:48:50: 11000000 INFO @ Sun, 18 Mar 2018 10:48:51: 11000000 INFO @ Sun, 18 Mar 2018 10:48:56: 13000000 INFO @ Sun, 18 Mar 2018 10:48:58: 12000000 INFO @ Sun, 18 Mar 2018 10:48:58: 12000000 INFO @ Sun, 18 Mar 2018 10:49:03: 14000000 INFO @ Sun, 18 Mar 2018 10:49:05: 13000000 INFO @ Sun, 18 Mar 2018 10:49:05: 13000000 INFO @ Sun, 18 Mar 2018 10:49:08: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:49:08: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:49:08: #1 total tags in treatment: 14616678 INFO @ Sun, 18 Mar 2018 10:49:08: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:49:08: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 10:49:08: #1 tags after filtering in treatment: 14616475 INFO @ Sun, 18 Mar 2018 10:49:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:49:08: #1 finished! INFO @ Sun, 18 Mar 2018 10:49:08: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:49:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:49:12: #2 number of paired peaks: 70954 INFO @ Sun, 18 Mar 2018 10:49:12: start model_add_line... INFO @ Sun, 18 Mar 2018 10:49:12: 14000000 INFO @ Sun, 18 Mar 2018 10:49:12: start X-correlation... INFO @ Sun, 18 Mar 2018 10:49:12: end of X-cor INFO @ Sun, 18 Mar 2018 10:49:12: #2 finished! INFO @ Sun, 18 Mar 2018 10:49:12: #2 predicted fragment length is 195 bps INFO @ Sun, 18 Mar 2018 10:49:12: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 18 Mar 2018 10:49:12: #2.2 Generate R script for model : SRX3358574.10_model.r INFO @ Sun, 18 Mar 2018 10:49:12: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:49:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:49:12: 14000000 INFO @ Sun, 18 Mar 2018 10:49:17: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:49:17: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:49:17: #1 total tags in treatment: 14616678 INFO @ Sun, 18 Mar 2018 10:49:17: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 10:49:17: #1 tags after filtering in treatment: 14616475 INFO @ Sun, 18 Mar 2018 10:49:17: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:49:17: #1 finished! INFO @ Sun, 18 Mar 2018 10:49:17: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:49:17: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:49:17: #1 tag size is determined as 75 bps INFO @ Sun, 18 Mar 2018 10:49:17: #1 tag size = 75 INFO @ Sun, 18 Mar 2018 10:49:17: #1 total tags in treatment: 14616678 INFO @ Sun, 18 Mar 2018 10:49:17: #1 user defined the maximum tags... INFO @ Sun, 18 Mar 2018 10:49:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 18 Mar 2018 10:49:18: #1 tags after filtering in treatment: 14616475 INFO @ Sun, 18 Mar 2018 10:49:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 18 Mar 2018 10:49:18: #1 finished! INFO @ Sun, 18 Mar 2018 10:49:18: #2 Build Peak Model... INFO @ Sun, 18 Mar 2018 10:49:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 18 Mar 2018 10:49:21: #2 number of paired peaks: 70954 INFO @ Sun, 18 Mar 2018 10:49:21: start model_add_line... INFO @ Sun, 18 Mar 2018 10:49:21: start X-correlation... INFO @ Sun, 18 Mar 2018 10:49:21: end of X-cor INFO @ Sun, 18 Mar 2018 10:49:21: #2 finished! INFO @ Sun, 18 Mar 2018 10:49:21: #2 predicted fragment length is 195 bps INFO @ Sun, 18 Mar 2018 10:49:21: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 18 Mar 2018 10:49:21: #2.2 Generate R script for model : SRX3358574.20_model.r INFO @ Sun, 18 Mar 2018 10:49:21: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:49:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:49:22: #2 number of paired peaks: 70954 INFO @ Sun, 18 Mar 2018 10:49:22: start model_add_line... INFO @ Sun, 18 Mar 2018 10:49:22: start X-correlation... INFO @ Sun, 18 Mar 2018 10:49:22: end of X-cor INFO @ Sun, 18 Mar 2018 10:49:22: #2 finished! INFO @ Sun, 18 Mar 2018 10:49:22: #2 predicted fragment length is 195 bps INFO @ Sun, 18 Mar 2018 10:49:22: #2 alternative fragment length(s) may be 195 bps INFO @ Sun, 18 Mar 2018 10:49:22: #2.2 Generate R script for model : SRX3358574.05_model.r INFO @ Sun, 18 Mar 2018 10:49:22: #3 Call peaks... INFO @ Sun, 18 Mar 2018 10:49:22: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 18 Mar 2018 10:49:49: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:49:56: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:49:57: #3 Call peaks for each chromosome... INFO @ Sun, 18 Mar 2018 10:50:11: #4 Write output xls file... SRX3358574.10_peaks.xls INFO @ Sun, 18 Mar 2018 10:50:11: #4 Write peak in narrowPeak format file... SRX3358574.10_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:50:11: #4 Write summits bed file... SRX3358574.10_summits.bed INFO @ Sun, 18 Mar 2018 10:50:11: Done! pass1 - making usageList (30 chroms): 1 millis pass2 - checking and writing primary data (314 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 10:50:16: #4 Write output xls file... SRX3358574.20_peaks.xls INFO @ Sun, 18 Mar 2018 10:50:16: #4 Write peak in narrowPeak format file... SRX3358574.20_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:50:16: #4 Write summits bed file... SRX3358574.20_summits.bed INFO @ Sun, 18 Mar 2018 10:50:17: Done! pass1 - making usageList (21 chroms): 1 millis pass2 - checking and writing primary data (163 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 18 Mar 2018 10:50:21: #4 Write output xls file... SRX3358574.05_peaks.xls INFO @ Sun, 18 Mar 2018 10:50:21: #4 Write peak in narrowPeak format file... SRX3358574.05_peaks.narrowPeak INFO @ Sun, 18 Mar 2018 10:50:21: #4 Write summits bed file... SRX3358574.05_summits.bed INFO @ Sun, 18 Mar 2018 10:50:21: Done! pass1 - making usageList (43 chroms): 1 millis pass2 - checking and writing primary data (1753 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。