Job ID = 10195016 sra ファイルのダウンロード中... Completed: 168169K bytes transferred in 5 seconds (263757K 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 5418358 spots for /home/okishinya/chipatlas/results/rn6/SRX913485/SRR1870915.sra Written 5418358 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: 00:03:22 5418358 reads; of these: 5418358 (100.00%) were unpaired; of these: 323078 (5.96%) aligned 0 times 3550168 (65.52%) aligned exactly 1 time 1545112 (28.52%) aligned >1 times 94.04% overall alignment rate Time searching: 00:03:24 Overall time: 00:03:24 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_rmdupse_core] 241265 / 5095280 = 0.0474 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 @ Sat, 11 Nov 2017 05:58:15: # Command line: callpeak -t SRX913485.bam -f BAM -g 2.15e9 -n SRX913485.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913485.05 # format = BAM # ChIP-seq file = ['SRX913485.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 @ Sat, 11 Nov 2017 05:58:15: #1 read tag files... INFO @ Sat, 11 Nov 2017 05:58:15: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 05:58:15: # Command line: callpeak -t SRX913485.bam -f BAM -g 2.15e9 -n SRX913485.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913485.20 # format = BAM # ChIP-seq file = ['SRX913485.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 @ Sat, 11 Nov 2017 05:58:15: #1 read tag files... INFO @ Sat, 11 Nov 2017 05:58:15: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 05:58:15: # Command line: callpeak -t SRX913485.bam -f BAM -g 2.15e9 -n SRX913485.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913485.10 # format = BAM # ChIP-seq file = ['SRX913485.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 @ Sat, 11 Nov 2017 05:58:15: #1 read tag files... INFO @ Sat, 11 Nov 2017 05:58:15: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 05:58:22: 1000000 INFO @ Sat, 11 Nov 2017 05:58:23: 1000000 INFO @ Sat, 11 Nov 2017 05:58:23: 1000000 INFO @ Sat, 11 Nov 2017 05:58:29: 2000000 INFO @ Sat, 11 Nov 2017 05:58:30: 2000000 INFO @ Sat, 11 Nov 2017 05:58:30: 2000000 INFO @ Sat, 11 Nov 2017 05:58:37: 3000000 INFO @ Sat, 11 Nov 2017 05:58:37: 3000000 INFO @ Sat, 11 Nov 2017 05:58:38: 3000000 INFO @ Sat, 11 Nov 2017 05:58:44: 4000000 INFO @ Sat, 11 Nov 2017 05:58:45: 4000000 INFO @ Sat, 11 Nov 2017 05:58:45: 4000000 INFO @ Sat, 11 Nov 2017 05:58:50: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 05:58:50: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 05:58:50: #1 total tags in treatment: 4854015 INFO @ Sat, 11 Nov 2017 05:58:50: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 05:58:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 05:58:51: #1 tags after filtering in treatment: 4853723 INFO @ Sat, 11 Nov 2017 05:58:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 05:58:51: #1 finished! INFO @ Sat, 11 Nov 2017 05:58:51: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 05:58:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 05:58:51: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 05:58:51: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 05:58:51: #1 total tags in treatment: 4854015 INFO @ Sat, 11 Nov 2017 05:58:51: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 05:58:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 05:58:51: #1 tags after filtering in treatment: 4853723 INFO @ Sat, 11 Nov 2017 05:58:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 05:58:51: #1 finished! INFO @ Sat, 11 Nov 2017 05:58:51: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 05:58:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 05:58:52: #1 tag size is determined as 47 bps INFO @ Sat, 11 Nov 2017 05:58:52: #1 tag size = 47 INFO @ Sat, 11 Nov 2017 05:58:52: #1 total tags in treatment: 4854015 INFO @ Sat, 11 Nov 2017 05:58:52: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 05:58:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 11 Nov 2017 05:58:52: #1 tags after filtering in treatment: 4853723 INFO @ Sat, 11 Nov 2017 05:58:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 05:58:52: #1 finished! INFO @ Sat, 11 Nov 2017 05:58:52: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 05:58:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 05:58:54: #2 number of paired peaks: 20267 INFO @ Sat, 11 Nov 2017 05:58:54: start model_add_line... INFO @ Sat, 11 Nov 2017 05:58:54: start X-correlation... INFO @ Sat, 11 Nov 2017 05:58:54: end of X-cor INFO @ Sat, 11 Nov 2017 05:58:54: #2 finished! INFO @ Sat, 11 Nov 2017 05:58:54: #2 predicted fragment length is 215 bps INFO @ Sat, 11 Nov 2017 05:58:54: #2 alternative fragment length(s) may be 215,270 bps INFO @ Sat, 11 Nov 2017 05:58:54: #2.2 Generate R script for model : SRX913485.05_model.r INFO @ Sat, 11 Nov 2017 05:58:54: #3 Call peaks... INFO @ Sat, 11 Nov 2017 05:58:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 05:58:55: #2 number of paired peaks: 20267 INFO @ Sat, 11 Nov 2017 05:58:55: start model_add_line... INFO @ Sat, 11 Nov 2017 05:58:55: start X-correlation... INFO @ Sat, 11 Nov 2017 05:58:55: end of X-cor INFO @ Sat, 11 Nov 2017 05:58:55: #2 finished! INFO @ Sat, 11 Nov 2017 05:58:55: #2 predicted fragment length is 215 bps INFO @ Sat, 11 Nov 2017 05:58:55: #2 alternative fragment length(s) may be 215,270 bps INFO @ Sat, 11 Nov 2017 05:58:55: #2.2 Generate R script for model : SRX913485.10_model.r INFO @ Sat, 11 Nov 2017 05:58:55: #3 Call peaks... INFO @ Sat, 11 Nov 2017 05:58:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 05:58:56: #2 number of paired peaks: 20267 INFO @ Sat, 11 Nov 2017 05:58:56: start model_add_line... INFO @ Sat, 11 Nov 2017 05:58:56: start X-correlation... INFO @ Sat, 11 Nov 2017 05:58:56: end of X-cor INFO @ Sat, 11 Nov 2017 05:58:56: #2 finished! INFO @ Sat, 11 Nov 2017 05:58:56: #2 predicted fragment length is 215 bps INFO @ Sat, 11 Nov 2017 05:58:56: #2 alternative fragment length(s) may be 215,270 bps INFO @ Sat, 11 Nov 2017 05:58:56: #2.2 Generate R script for model : SRX913485.20_model.r INFO @ Sat, 11 Nov 2017 05:58:56: #3 Call peaks... INFO @ Sat, 11 Nov 2017 05:58:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 05:59:06: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 05:59:07: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 05:59:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 05:59:13: #4 Write output xls file... SRX913485.05_peaks.xls INFO @ Sat, 11 Nov 2017 05:59:13: #4 Write peak in narrowPeak format file... SRX913485.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 05:59:13: #4 Write summits bed file... SRX913485.05_summits.bed INFO @ Sat, 11 Nov 2017 05:59:13: Done! pass1 - making usageList (29 chroms): 1 millis pass2 - checking and writing primary data (354 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 05:59:13: #4 Write output xls file... SRX913485.10_peaks.xls INFO @ Sat, 11 Nov 2017 05:59:13: #4 Write peak in narrowPeak format file... SRX913485.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 05:59:13: #4 Write summits bed file... SRX913485.10_summits.bed INFO @ Sat, 11 Nov 2017 05:59:13: Done! pass1 - making usageList (24 chroms): 1 millis pass2 - checking and writing primary data (200 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 05:59:15: #4 Write output xls file... SRX913485.20_peaks.xls INFO @ Sat, 11 Nov 2017 05:59:15: #4 Write peak in narrowPeak format file... SRX913485.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 05:59:15: #4 Write summits bed file... SRX913485.20_summits.bed INFO @ Sat, 11 Nov 2017 05:59:15: Done! pass1 - making usageList (19 chroms): 0 millis pass2 - checking and writing primary data (58 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。