Job ID = 10195037 sra ファイルのダウンロード中... Completed: 133615K bytes transferred in 5 seconds (217955K bits/sec), in 1 file. Completed: 46272K bytes transferred in 3 seconds (98693K 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 1264058 spots for /home/okishinya/chipatlas/results/rn6/SRX913506/SRR1870948.sra Written 1264058 spots total Written 3685162 spots for /home/okishinya/chipatlas/results/rn6/SRX913506/SRR1870949.sra Written 3685162 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 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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:02:35 4949220 reads; of these: 4949220 (100.00%) were unpaired; of these: 1185015 (23.94%) aligned 0 times 2673777 (54.02%) aligned exactly 1 time 1090428 (22.03%) aligned >1 times 76.06% overall alignment rate Time searching: 00:02:37 Overall time: 00:02:37 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] 559861 / 3764205 = 0.1487 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 06:41:37: # Command line: callpeak -t SRX913506.bam -f BAM -g 2.15e9 -n SRX913506.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX913506.20 # format = BAM # ChIP-seq file = ['SRX913506.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 06:41:37: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:41:37: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:41:37: # Command line: callpeak -t SRX913506.bam -f BAM -g 2.15e9 -n SRX913506.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX913506.10 # format = BAM # ChIP-seq file = ['SRX913506.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 06:41:37: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:41:37: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:41:37: # Command line: callpeak -t SRX913506.bam -f BAM -g 2.15e9 -n SRX913506.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX913506.05 # format = BAM # ChIP-seq file = ['SRX913506.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 06:41:37: #1 read tag files... INFO @ Sat, 11 Nov 2017 06:41:37: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 06:41:44: 1000000 INFO @ Sat, 11 Nov 2017 06:41:44: 1000000 INFO @ Sat, 11 Nov 2017 06:41:44: 1000000 INFO @ Sat, 11 Nov 2017 06:41:51: 2000000 INFO @ Sat, 11 Nov 2017 06:41:51: 2000000 INFO @ Sat, 11 Nov 2017 06:41:51: 2000000 INFO @ Sat, 11 Nov 2017 06:41:59: 3000000 INFO @ Sat, 11 Nov 2017 06:41:59: 3000000 INFO @ Sat, 11 Nov 2017 06:42:00: 3000000 INFO @ Sat, 11 Nov 2017 06:42:01: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 06:42:01: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 06:42:01: #1 total tags in treatment: 3204344 INFO @ Sat, 11 Nov 2017 06:42:01: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:42:01: #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 06:42:01: #1 tags after filtering in treatment: 3204030 INFO @ Sat, 11 Nov 2017 06:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:42:01: #1 finished! INFO @ Sat, 11 Nov 2017 06:42:01: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:42:01: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 06:42:01: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 06:42:01: #1 total tags in treatment: 3204344 INFO @ Sat, 11 Nov 2017 06:42:01: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:42:01: #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 06:42:01: #1 tag size is determined as 46 bps INFO @ Sat, 11 Nov 2017 06:42:01: #1 tag size = 46 INFO @ Sat, 11 Nov 2017 06:42:01: #1 total tags in treatment: 3204344 INFO @ Sat, 11 Nov 2017 06:42:01: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 06:42:01: #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 06:42:01: #1 tags after filtering in treatment: 3204030 INFO @ Sat, 11 Nov 2017 06:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:42:01: #1 finished! INFO @ Sat, 11 Nov 2017 06:42:01: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:42:01: #1 tags after filtering in treatment: 3204030 INFO @ Sat, 11 Nov 2017 06:42:01: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 06:42:01: #1 finished! INFO @ Sat, 11 Nov 2017 06:42:01: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 06:42:01: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 06:42:07: #2 number of paired peaks: 63749 INFO @ Sat, 11 Nov 2017 06:42:07: start model_add_line... INFO @ Sat, 11 Nov 2017 06:42:07: start X-correlation... INFO @ Sat, 11 Nov 2017 06:42:07: end of X-cor INFO @ Sat, 11 Nov 2017 06:42:07: #2 finished! INFO @ Sat, 11 Nov 2017 06:42:07: #2 predicted fragment length is 291 bps INFO @ Sat, 11 Nov 2017 06:42:07: #2 alternative fragment length(s) may be 159,258,291 bps INFO @ Sat, 11 Nov 2017 06:42:07: #2.2 Generate R script for model : SRX913506.10_model.r INFO @ Sat, 11 Nov 2017 06:42:07: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:42:07: #2 number of paired peaks: 63749 INFO @ Sat, 11 Nov 2017 06:42:07: start model_add_line... INFO @ Sat, 11 Nov 2017 06:42:07: start X-correlation... INFO @ Sat, 11 Nov 2017 06:42:07: end of X-cor INFO @ Sat, 11 Nov 2017 06:42:07: #2 finished! INFO @ Sat, 11 Nov 2017 06:42:07: #2 predicted fragment length is 291 bps INFO @ Sat, 11 Nov 2017 06:42:07: #2 alternative fragment length(s) may be 159,258,291 bps INFO @ Sat, 11 Nov 2017 06:42:07: #2.2 Generate R script for model : SRX913506.20_model.r INFO @ Sat, 11 Nov 2017 06:42:07: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:42:07: #2 number of paired peaks: 63749 INFO @ Sat, 11 Nov 2017 06:42:07: start model_add_line... INFO @ Sat, 11 Nov 2017 06:42:07: start X-correlation... INFO @ Sat, 11 Nov 2017 06:42:07: end of X-cor INFO @ Sat, 11 Nov 2017 06:42:07: #2 finished! INFO @ Sat, 11 Nov 2017 06:42:07: #2 predicted fragment length is 291 bps INFO @ Sat, 11 Nov 2017 06:42:07: #2 alternative fragment length(s) may be 159,258,291 bps INFO @ Sat, 11 Nov 2017 06:42:07: #2.2 Generate R script for model : SRX913506.05_model.r INFO @ Sat, 11 Nov 2017 06:42:07: #3 Call peaks... INFO @ Sat, 11 Nov 2017 06:42:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 06:42:15: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:42:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:42:16: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 06:42:19: #4 Write output xls file... SRX913506.10_peaks.xls INFO @ Sat, 11 Nov 2017 06:42:19: #4 Write peak in narrowPeak format file... SRX913506.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:42:19: #4 Write summits bed file... SRX913506.10_summits.bed INFO @ Sat, 11 Nov 2017 06:42:19: Done! pass1 - making usageList (19 chroms): 1 millis pass2 - checking and writing primary data (78 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:42:20: #4 Write output xls file... SRX913506.20_peaks.xls INFO @ Sat, 11 Nov 2017 06:42:20: #4 Write peak in narrowPeak format file... SRX913506.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:42:20: #4 Write summits bed file... SRX913506.20_summits.bed INFO @ Sat, 11 Nov 2017 06:42:20: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (29 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 06:42:21: #4 Write output xls file... SRX913506.05_peaks.xls INFO @ Sat, 11 Nov 2017 06:42:21: #4 Write peak in narrowPeak format file... SRX913506.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 06:42:21: #4 Write summits bed file... SRX913506.05_summits.bed INFO @ Sat, 11 Nov 2017 06:42:21: Done! pass1 - making usageList (28 chroms): 1 millis pass2 - checking and writing primary data (168 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。