Job ID = 11192552 sra ファイルのダウンロード中... Completed: 1418163K bytes transferred in 19 seconds (584753K 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... Read 43886470 spots for /home/okishinya/chipatlas/results/rn6/SRX2226567/SRR4374817.sra Written 43886470 spots for /home/okishinya/chipatlas/results/rn6/SRX2226567/SRR4374817.sra 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: 00:00:02 Time loading forward index: 00:00:03 Time loading mirror index: 00:00:02 Multiseed full-index search: 00:27:15 43886470 reads; of these: 43886470 (100.00%) were unpaired; of these: 10081081 (22.97%) aligned 0 times 26643989 (60.71%) aligned exactly 1 time 7161400 (16.32%) aligned >1 times 77.03% overall alignment rate Time searching: 00:27:22 Overall time: 00:27:22 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 16 files... [bam_rmdupse_core] 22242894 / 33805389 = 0.6580 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, 15 Sep 2018 09:17:08: # Command line: callpeak -t SRX2226567.bam -f BAM -g 2.15e9 -n SRX2226567.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226567.10 # format = BAM # ChIP-seq file = ['SRX2226567.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, 15 Sep 2018 09:17:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:17:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:17:08: # Command line: callpeak -t SRX2226567.bam -f BAM -g 2.15e9 -n SRX2226567.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226567.20 # format = BAM # ChIP-seq file = ['SRX2226567.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, 15 Sep 2018 09:17:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:17:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:17:08: # Command line: callpeak -t SRX2226567.bam -f BAM -g 2.15e9 -n SRX2226567.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226567.05 # format = BAM # ChIP-seq file = ['SRX2226567.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, 15 Sep 2018 09:17:08: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:17:08: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:17:17: 1000000 INFO @ Sat, 15 Sep 2018 09:17:18: 1000000 INFO @ Sat, 15 Sep 2018 09:17:18: 1000000 INFO @ Sat, 15 Sep 2018 09:17:26: 2000000 INFO @ Sat, 15 Sep 2018 09:17:27: 2000000 INFO @ Sat, 15 Sep 2018 09:17:27: 2000000 INFO @ Sat, 15 Sep 2018 09:17:35: 3000000 INFO @ Sat, 15 Sep 2018 09:17:36: 3000000 INFO @ Sat, 15 Sep 2018 09:17:36: 3000000 INFO @ Sat, 15 Sep 2018 09:17:43: 4000000 INFO @ Sat, 15 Sep 2018 09:17:45: 4000000 INFO @ Sat, 15 Sep 2018 09:17:45: 4000000 INFO @ Sat, 15 Sep 2018 09:17:52: 5000000 INFO @ Sat, 15 Sep 2018 09:17:54: 5000000 INFO @ Sat, 15 Sep 2018 09:17:54: 5000000 INFO @ Sat, 15 Sep 2018 09:18:02: 6000000 INFO @ Sat, 15 Sep 2018 09:18:02: 6000000 INFO @ Sat, 15 Sep 2018 09:18:02: 6000000 INFO @ Sat, 15 Sep 2018 09:18:11: 7000000 INFO @ Sat, 15 Sep 2018 09:18:11: 7000000 INFO @ Sat, 15 Sep 2018 09:18:11: 7000000 INFO @ Sat, 15 Sep 2018 09:18:20: 8000000 INFO @ Sat, 15 Sep 2018 09:18:20: 8000000 INFO @ Sat, 15 Sep 2018 09:18:20: 8000000 INFO @ Sat, 15 Sep 2018 09:18:28: 9000000 INFO @ Sat, 15 Sep 2018 09:18:28: 9000000 INFO @ Sat, 15 Sep 2018 09:18:29: 9000000 INFO @ Sat, 15 Sep 2018 09:18:37: 10000000 INFO @ Sat, 15 Sep 2018 09:18:38: 10000000 INFO @ Sat, 15 Sep 2018 09:18:38: 10000000 INFO @ Sat, 15 Sep 2018 09:18:45: 11000000 INFO @ Sat, 15 Sep 2018 09:18:47: 11000000 INFO @ Sat, 15 Sep 2018 09:18:47: 11000000 INFO @ Sat, 15 Sep 2018 09:18:50: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:18:50: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:18:50: #1 total tags in treatment: 11562495 INFO @ Sat, 15 Sep 2018 09:18:50: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:18:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:18:51: #1 tags after filtering in treatment: 11562319 INFO @ Sat, 15 Sep 2018 09:18:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:18:51: #1 finished! INFO @ Sat, 15 Sep 2018 09:18:51: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:18:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:18:52: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:18:52: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:18:52: #1 total tags in treatment: 11562495 INFO @ Sat, 15 Sep 2018 09:18:52: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:18:52: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:18:53: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:18:53: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:18:53: #1 total tags in treatment: 11562495 INFO @ Sat, 15 Sep 2018 09:18:53: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:18:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 15 Sep 2018 09:18:53: #1 tags after filtering in treatment: 11562319 INFO @ Sat, 15 Sep 2018 09:18:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:18:53: #1 finished! INFO @ Sat, 15 Sep 2018 09:18:53: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:18:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:18:53: #1 tags after filtering in treatment: 11562319 INFO @ Sat, 15 Sep 2018 09:18:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:18:53: #1 finished! INFO @ Sat, 15 Sep 2018 09:18:53: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:18:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:18:54: #2 number of paired peaks: 58753 INFO @ Sat, 15 Sep 2018 09:18:54: start model_add_line... INFO @ Sat, 15 Sep 2018 09:18:54: start X-correlation... INFO @ Sat, 15 Sep 2018 09:18:54: end of X-cor INFO @ Sat, 15 Sep 2018 09:18:54: #2 finished! INFO @ Sat, 15 Sep 2018 09:18:54: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Sep 2018 09:18:54: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 15 Sep 2018 09:18:54: #2.2 Generate R script for model : SRX2226567.10_model.r INFO @ Sat, 15 Sep 2018 09:18:54: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:18:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:18:56: #2 number of paired peaks: 58753 INFO @ Sat, 15 Sep 2018 09:18:56: start model_add_line... INFO @ Sat, 15 Sep 2018 09:18:56: start X-correlation... INFO @ Sat, 15 Sep 2018 09:18:56: end of X-cor INFO @ Sat, 15 Sep 2018 09:18:56: #2 finished! INFO @ Sat, 15 Sep 2018 09:18:56: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Sep 2018 09:18:56: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 15 Sep 2018 09:18:56: #2.2 Generate R script for model : SRX2226567.05_model.r INFO @ Sat, 15 Sep 2018 09:18:56: #2 number of paired peaks: 58753 INFO @ Sat, 15 Sep 2018 09:18:56: start model_add_line... INFO @ Sat, 15 Sep 2018 09:18:56: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:18:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:18:56: start X-correlation... INFO @ Sat, 15 Sep 2018 09:18:56: end of X-cor INFO @ Sat, 15 Sep 2018 09:18:56: #2 finished! INFO @ Sat, 15 Sep 2018 09:18:56: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Sep 2018 09:18:56: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 15 Sep 2018 09:18:56: #2.2 Generate R script for model : SRX2226567.20_model.r INFO @ Sat, 15 Sep 2018 09:18:56: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:18:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:19:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:19:26: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:19:27: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:19:43: #4 Write output xls file... SRX2226567.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:19:43: #4 Write peak in narrowPeak format file... SRX2226567.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:19:43: #4 Write summits bed file... SRX2226567.10_summits.bed INFO @ Sat, 15 Sep 2018 09:19:43: Done! pass1 - making usageList (52 chroms): 1 millis pass2 - checking and writing primary data (2271 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:19:43: #4 Write output xls file... SRX2226567.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:19:43: #4 Write peak in narrowPeak format file... SRX2226567.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:19:43: #4 Write summits bed file... SRX2226567.20_summits.bed INFO @ Sat, 15 Sep 2018 09:19:43: Done! pass1 - making usageList (39 chroms): 1 millis pass2 - checking and writing primary data (875 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:19:45: #4 Write output xls file... SRX2226567.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:19:45: #4 Write peak in narrowPeak format file... SRX2226567.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:19:45: #4 Write summits bed file... SRX2226567.05_summits.bed INFO @ Sat, 15 Sep 2018 09:19:45: Done! pass1 - making usageList (73 chroms): 2 millis pass2 - checking and writing primary data (5699 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。