Job ID = 11192562 sra ファイルのダウンロード中... Completed: 809036K bytes transferred in 9 seconds (703019K 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 25569550 spots for /home/okishinya/chipatlas/results/rn6/SRX2226576/SRR4374826.sra Written 25569550 spots for /home/okishinya/chipatlas/results/rn6/SRX2226576/SRR4374826.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: 00:00:01 Time loading forward index: 00:00:02 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:15:33 25569550 reads; of these: 25569550 (100.00%) were unpaired; of these: 5427062 (21.22%) aligned 0 times 15474484 (60.52%) aligned exactly 1 time 4668004 (18.26%) aligned >1 times 78.78% overall alignment rate Time searching: 00:15:37 Overall time: 00:15:37 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_sort_core] merging from 12 files... [bam_rmdupse_core] 9647037 / 20142488 = 0.4789 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 09:12:48: # Command line: callpeak -t SRX2226576.bam -f BAM -g 2.15e9 -n SRX2226576.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226576.20 # format = BAM # ChIP-seq file = ['SRX2226576.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 09:12:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:12:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:12:48: # Command line: callpeak -t SRX2226576.bam -f BAM -g 2.15e9 -n SRX2226576.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226576.10 # format = BAM # ChIP-seq file = ['SRX2226576.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 09:12:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:12:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:12:48: # Command line: callpeak -t SRX2226576.bam -f BAM -g 2.15e9 -n SRX2226576.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226576.05 # format = BAM # ChIP-seq file = ['SRX2226576.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 09:12:48: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:12:48: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:12:56: 1000000 INFO @ Sat, 15 Sep 2018 09:12:56: 1000000 INFO @ Sat, 15 Sep 2018 09:12:57: 1000000 INFO @ Sat, 15 Sep 2018 09:13:05: 2000000 INFO @ Sat, 15 Sep 2018 09:13:05: 2000000 INFO @ Sat, 15 Sep 2018 09:13:06: 2000000 INFO @ Sat, 15 Sep 2018 09:13:14: 3000000 INFO @ Sat, 15 Sep 2018 09:13:14: 3000000 INFO @ Sat, 15 Sep 2018 09:13:16: 3000000 INFO @ Sat, 15 Sep 2018 09:13:22: 4000000 INFO @ Sat, 15 Sep 2018 09:13:22: 4000000 INFO @ Sat, 15 Sep 2018 09:13:25: 4000000 INFO @ Sat, 15 Sep 2018 09:13:31: 5000000 INFO @ Sat, 15 Sep 2018 09:13:31: 5000000 INFO @ Sat, 15 Sep 2018 09:13:34: 5000000 INFO @ Sat, 15 Sep 2018 09:13:39: 6000000 INFO @ Sat, 15 Sep 2018 09:13:39: 6000000 INFO @ Sat, 15 Sep 2018 09:13:44: 6000000 INFO @ Sat, 15 Sep 2018 09:13:48: 7000000 INFO @ Sat, 15 Sep 2018 09:13:48: 7000000 INFO @ Sat, 15 Sep 2018 09:13:53: 7000000 INFO @ Sat, 15 Sep 2018 09:13:56: 8000000 INFO @ Sat, 15 Sep 2018 09:13:56: 8000000 INFO @ Sat, 15 Sep 2018 09:14:02: 8000000 INFO @ Sat, 15 Sep 2018 09:14:05: 9000000 INFO @ Sat, 15 Sep 2018 09:14:05: 9000000 INFO @ Sat, 15 Sep 2018 09:14:12: 9000000 INFO @ Sat, 15 Sep 2018 09:14:14: 10000000 INFO @ Sat, 15 Sep 2018 09:14:14: 10000000 INFO @ Sat, 15 Sep 2018 09:14:18: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:14:18: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:14:18: #1 total tags in treatment: 10495451 INFO @ Sat, 15 Sep 2018 09:14:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:14:18: #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 09:14:18: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:14:18: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:14:18: #1 total tags in treatment: 10495451 INFO @ Sat, 15 Sep 2018 09:14:18: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:14:18: #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 09:14:18: #1 tags after filtering in treatment: 10495276 INFO @ Sat, 15 Sep 2018 09:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:14:18: #1 finished! INFO @ Sat, 15 Sep 2018 09:14:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:14:18: #1 tags after filtering in treatment: 10495276 INFO @ Sat, 15 Sep 2018 09:14:18: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:14:18: #1 finished! INFO @ Sat, 15 Sep 2018 09:14:18: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:14:18: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:14:21: #2 number of paired peaks: 34889 INFO @ Sat, 15 Sep 2018 09:14:21: start model_add_line... INFO @ Sat, 15 Sep 2018 09:14:21: start X-correlation... INFO @ Sat, 15 Sep 2018 09:14:21: end of X-cor INFO @ Sat, 15 Sep 2018 09:14:21: #2 finished! INFO @ Sat, 15 Sep 2018 09:14:21: #2 predicted fragment length is 223 bps INFO @ Sat, 15 Sep 2018 09:14:21: #2 alternative fragment length(s) may be 223 bps INFO @ Sat, 15 Sep 2018 09:14:21: #2.2 Generate R script for model : SRX2226576.20_model.r INFO @ Sat, 15 Sep 2018 09:14:21: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:14:21: #2 number of paired peaks: 34889 INFO @ Sat, 15 Sep 2018 09:14:21: start model_add_line... INFO @ Sat, 15 Sep 2018 09:14:21: 10000000 INFO @ Sat, 15 Sep 2018 09:14:21: start X-correlation... INFO @ Sat, 15 Sep 2018 09:14:21: end of X-cor INFO @ Sat, 15 Sep 2018 09:14:21: #2 finished! INFO @ Sat, 15 Sep 2018 09:14:21: #2 predicted fragment length is 223 bps INFO @ Sat, 15 Sep 2018 09:14:21: #2 alternative fragment length(s) may be 223 bps INFO @ Sat, 15 Sep 2018 09:14:21: #2.2 Generate R script for model : SRX2226576.10_model.r INFO @ Sat, 15 Sep 2018 09:14:21: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:14:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:14:26: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:14:26: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:14:26: #1 total tags in treatment: 10495451 INFO @ Sat, 15 Sep 2018 09:14:26: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:14:26: #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 09:14:26: #1 tags after filtering in treatment: 10495276 INFO @ Sat, 15 Sep 2018 09:14:26: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:14:26: #1 finished! INFO @ Sat, 15 Sep 2018 09:14:26: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:14:26: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:14:28: #2 number of paired peaks: 34889 INFO @ Sat, 15 Sep 2018 09:14:28: start model_add_line... INFO @ Sat, 15 Sep 2018 09:14:29: start X-correlation... INFO @ Sat, 15 Sep 2018 09:14:29: end of X-cor INFO @ Sat, 15 Sep 2018 09:14:29: #2 finished! INFO @ Sat, 15 Sep 2018 09:14:29: #2 predicted fragment length is 223 bps INFO @ Sat, 15 Sep 2018 09:14:29: #2 alternative fragment length(s) may be 223 bps INFO @ Sat, 15 Sep 2018 09:14:29: #2.2 Generate R script for model : SRX2226576.05_model.r INFO @ Sat, 15 Sep 2018 09:14:29: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:14:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:14:47: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:14:49: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:14:55: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:15:05: #4 Write output xls file... SRX2226576.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:15:05: #4 Write peak in narrowPeak format file... SRX2226576.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:15:05: #4 Write summits bed file... SRX2226576.10_summits.bed INFO @ Sat, 15 Sep 2018 09:15:05: Done! pass1 - making usageList (56 chroms): 2 millis pass2 - checking and writing primary data (4481 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:15:07: #4 Write output xls file... SRX2226576.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:15:07: #4 Write peak in narrowPeak format file... SRX2226576.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:15:07: #4 Write summits bed file... SRX2226576.20_summits.bed INFO @ Sat, 15 Sep 2018 09:15:07: Done! pass1 - making usageList (40 chroms): 1 millis pass2 - checking and writing primary data (1799 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:15:11: #4 Write output xls file... SRX2226576.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:15:11: #4 Write peak in narrowPeak format file... SRX2226576.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:15:11: #4 Write summits bed file... SRX2226576.05_summits.bed INFO @ Sat, 15 Sep 2018 09:15:11: Done! pass1 - making usageList (77 chroms): 2 millis pass2 - checking and writing primary data (7703 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。