Job ID = 10194787 sra ファイルのダウンロード中... Completed: 382944K bytes transferred in 6 seconds (481116K 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 16757152 spots for /home/okishinya/chipatlas/results/rn6/SRX1774919/SRR3544954.sra Written 16757152 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: 00:00:00 Multiseed full-index search: 00:12:10 16757152 reads; of these: 16757152 (100.00%) were unpaired; of these: 689877 (4.12%) aligned 0 times 12374006 (73.84%) aligned exactly 1 time 3693269 (22.04%) aligned >1 times 95.88% overall alignment rate Time searching: 00:12:13 Overall time: 00:12:13 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] 2232211 / 16067275 = 0.1389 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 17:23:24: # Command line: callpeak -t SRX1774919.bam -f BAM -g 2.15e9 -n SRX1774919.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1774919.05 # format = BAM # ChIP-seq file = ['SRX1774919.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 17:23:24: # Command line: callpeak -t SRX1774919.bam -f BAM -g 2.15e9 -n SRX1774919.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1774919.20 # format = BAM # ChIP-seq file = ['SRX1774919.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 17:23:24: # Command line: callpeak -t SRX1774919.bam -f BAM -g 2.15e9 -n SRX1774919.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1774919.10 # format = BAM # ChIP-seq file = ['SRX1774919.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 17:23:24: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:23:24: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:23:24: #1 read tag files... INFO @ Fri, 10 Nov 2017 17:23:24: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:23:24: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:23:24: #1 read treatment tags... INFO @ Fri, 10 Nov 2017 17:23:31: 1000000 INFO @ Fri, 10 Nov 2017 17:23:31: 1000000 INFO @ Fri, 10 Nov 2017 17:23:32: 1000000 INFO @ Fri, 10 Nov 2017 17:23:39: 2000000 INFO @ Fri, 10 Nov 2017 17:23:39: 2000000 INFO @ Fri, 10 Nov 2017 17:23:39: 2000000 INFO @ Fri, 10 Nov 2017 17:23:46: 3000000 INFO @ Fri, 10 Nov 2017 17:23:46: 3000000 INFO @ Fri, 10 Nov 2017 17:23:46: 3000000 INFO @ Fri, 10 Nov 2017 17:23:53: 4000000 INFO @ Fri, 10 Nov 2017 17:23:54: 4000000 INFO @ Fri, 10 Nov 2017 17:23:54: 4000000 INFO @ Fri, 10 Nov 2017 17:24:01: 5000000 INFO @ Fri, 10 Nov 2017 17:24:01: 5000000 INFO @ Fri, 10 Nov 2017 17:24:01: 5000000 INFO @ Fri, 10 Nov 2017 17:24:08: 6000000 INFO @ Fri, 10 Nov 2017 17:24:08: 6000000 INFO @ Fri, 10 Nov 2017 17:24:08: 6000000 INFO @ Fri, 10 Nov 2017 17:24:15: 7000000 INFO @ Fri, 10 Nov 2017 17:24:16: 7000000 INFO @ Fri, 10 Nov 2017 17:24:16: 7000000 INFO @ Fri, 10 Nov 2017 17:24:23: 8000000 INFO @ Fri, 10 Nov 2017 17:24:23: 8000000 INFO @ Fri, 10 Nov 2017 17:24:23: 8000000 INFO @ Fri, 10 Nov 2017 17:24:30: 9000000 INFO @ Fri, 10 Nov 2017 17:24:30: 9000000 INFO @ Fri, 10 Nov 2017 17:24:30: 9000000 INFO @ Fri, 10 Nov 2017 17:24:37: 10000000 INFO @ Fri, 10 Nov 2017 17:24:38: 10000000 INFO @ Fri, 10 Nov 2017 17:24:38: 10000000 INFO @ Fri, 10 Nov 2017 17:24:45: 11000000 INFO @ Fri, 10 Nov 2017 17:24:45: 11000000 INFO @ Fri, 10 Nov 2017 17:24:45: 11000000 INFO @ Fri, 10 Nov 2017 17:24:52: 12000000 INFO @ Fri, 10 Nov 2017 17:24:52: 12000000 INFO @ Fri, 10 Nov 2017 17:24:52: 12000000 INFO @ Fri, 10 Nov 2017 17:25:00: 13000000 INFO @ Fri, 10 Nov 2017 17:25:00: 13000000 INFO @ Fri, 10 Nov 2017 17:25:00: 13000000 INFO @ Fri, 10 Nov 2017 17:25:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:25:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:25:06: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:25:06: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:25:06: #1 total tags in treatment: 13835064 INFO @ Fri, 10 Nov 2017 17:25:06: #1 total tags in treatment: 13835064 INFO @ Fri, 10 Nov 2017 17:25:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:25:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:25:06: #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 17:25:06: #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 17:25:06: #1 tag size is determined as 50 bps INFO @ Fri, 10 Nov 2017 17:25:06: #1 tag size = 50 INFO @ Fri, 10 Nov 2017 17:25:06: #1 total tags in treatment: 13835064 INFO @ Fri, 10 Nov 2017 17:25:06: #1 user defined the maximum tags... INFO @ Fri, 10 Nov 2017 17:25:06: #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 17:25:06: #1 tags after filtering in treatment: 13834867 INFO @ Fri, 10 Nov 2017 17:25:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:25:06: #1 finished! INFO @ Fri, 10 Nov 2017 17:25:06: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:25:06: #1 tags after filtering in treatment: 13834867 INFO @ Fri, 10 Nov 2017 17:25:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:25:06: #1 finished! INFO @ Fri, 10 Nov 2017 17:25:06: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:25:06: #1 tags after filtering in treatment: 13834867 INFO @ Fri, 10 Nov 2017 17:25:06: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Nov 2017 17:25:06: #1 finished! INFO @ Fri, 10 Nov 2017 17:25:06: #2 Build Peak Model... INFO @ Fri, 10 Nov 2017 17:25:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Nov 2017 17:25:08: #2 number of paired peaks: 12321 INFO @ Fri, 10 Nov 2017 17:25:08: start model_add_line... INFO @ Fri, 10 Nov 2017 17:25:08: #2 number of paired peaks: 12321 INFO @ Fri, 10 Nov 2017 17:25:08: start model_add_line... INFO @ Fri, 10 Nov 2017 17:25:08: #2 number of paired peaks: 12321 INFO @ Fri, 10 Nov 2017 17:25:08: start model_add_line... INFO @ Fri, 10 Nov 2017 17:25:09: start X-correlation... INFO @ Fri, 10 Nov 2017 17:25:09: end of X-cor INFO @ Fri, 10 Nov 2017 17:25:09: #2 finished! INFO @ Fri, 10 Nov 2017 17:25:09: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Nov 2017 17:25:09: #2 alternative fragment length(s) may be 56,158,179 bps INFO @ Fri, 10 Nov 2017 17:25:09: #2.2 Generate R script for model : SRX1774919.05_model.r INFO @ Fri, 10 Nov 2017 17:25:09: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:25:09: start X-correlation... INFO @ Fri, 10 Nov 2017 17:25:09: end of X-cor INFO @ Fri, 10 Nov 2017 17:25:09: #2 finished! INFO @ Fri, 10 Nov 2017 17:25:09: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Nov 2017 17:25:09: #2 alternative fragment length(s) may be 56,158,179 bps INFO @ Fri, 10 Nov 2017 17:25:09: #2.2 Generate R script for model : SRX1774919.10_model.r INFO @ Fri, 10 Nov 2017 17:25:09: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:25:09: start X-correlation... INFO @ Fri, 10 Nov 2017 17:25:09: end of X-cor INFO @ Fri, 10 Nov 2017 17:25:09: #2 finished! INFO @ Fri, 10 Nov 2017 17:25:09: #2 predicted fragment length is 158 bps INFO @ Fri, 10 Nov 2017 17:25:09: #2 alternative fragment length(s) may be 56,158,179 bps INFO @ Fri, 10 Nov 2017 17:25:09: #2.2 Generate R script for model : SRX1774919.20_model.r INFO @ Fri, 10 Nov 2017 17:25:09: #3 Call peaks... INFO @ Fri, 10 Nov 2017 17:25:09: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Nov 2017 17:25:42: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:25:43: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:25:45: #3 Call peaks for each chromosome... INFO @ Fri, 10 Nov 2017 17:26:01: #4 Write output xls file... SRX1774919.05_peaks.xls INFO @ Fri, 10 Nov 2017 17:26:01: #4 Write peak in narrowPeak format file... SRX1774919.05_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:26:01: #4 Write summits bed file... SRX1774919.05_summits.bed INFO @ Fri, 10 Nov 2017 17:26:01: Done! pass1 - making usageList (35 chroms): 1 millis pass2 - checking and writing primary data (533 records, 4 fields): 20 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:26:06: #4 Write output xls file... SRX1774919.20_peaks.xls INFO @ Fri, 10 Nov 2017 17:26:06: #4 Write peak in narrowPeak format file... SRX1774919.20_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:26:06: #4 Write summits bed file... SRX1774919.20_summits.bed INFO @ Fri, 10 Nov 2017 17:26:06: Done! pass1 - making usageList (22 chroms): 1 millis pass2 - checking and writing primary data (166 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Fri, 10 Nov 2017 17:26:08: #4 Write output xls file... SRX1774919.10_peaks.xls INFO @ Fri, 10 Nov 2017 17:26:08: #4 Write peak in narrowPeak format file... SRX1774919.10_peaks.narrowPeak INFO @ Fri, 10 Nov 2017 17:26:08: #4 Write summits bed file... SRX1774919.10_summits.bed INFO @ Fri, 10 Nov 2017 17:26:08: Done! pass1 - making usageList (31 chroms): 1 millis pass2 - checking and writing primary data (318 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。