Job ID = 10194821 sra ファイルのダウンロード中... Completed: 482732K bytes transferred in 12 seconds (304330K 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 16895994 spots for /home/okishinya/chipatlas/results/rn6/SRX1927035/SRR3831682.sra Written 16895994 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: 00:00:00 Time loading forward index: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:07:56 16895994 reads; of these: 16895994 (100.00%) were unpaired; of these: 2160728 (12.79%) aligned 0 times 13289660 (78.66%) aligned exactly 1 time 1445606 (8.56%) aligned >1 times 87.21% overall alignment rate Time searching: 00:07:58 Overall time: 00:07:58 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] 7475471 / 14735266 = 0.5073 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 01:12:03: # Command line: callpeak -t SRX1927035.bam -f BAM -g 2.15e9 -n SRX1927035.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX1927035.10 # format = BAM # ChIP-seq file = ['SRX1927035.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 01:12:03: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:12:03: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:12:03: # Command line: callpeak -t SRX1927035.bam -f BAM -g 2.15e9 -n SRX1927035.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX1927035.05 # format = BAM # ChIP-seq file = ['SRX1927035.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 01:12:03: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:12:03: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:12:03: # Command line: callpeak -t SRX1927035.bam -f BAM -g 2.15e9 -n SRX1927035.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX1927035.20 # format = BAM # ChIP-seq file = ['SRX1927035.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 01:12:03: #1 read tag files... INFO @ Sat, 11 Nov 2017 01:12:03: #1 read treatment tags... INFO @ Sat, 11 Nov 2017 01:12:09: 1000000 INFO @ Sat, 11 Nov 2017 01:12:09: 1000000 INFO @ Sat, 11 Nov 2017 01:12:09: 1000000 INFO @ Sat, 11 Nov 2017 01:12:15: 2000000 INFO @ Sat, 11 Nov 2017 01:12:15: 2000000 INFO @ Sat, 11 Nov 2017 01:12:16: 2000000 INFO @ Sat, 11 Nov 2017 01:12:22: 3000000 INFO @ Sat, 11 Nov 2017 01:12:22: 3000000 INFO @ Sat, 11 Nov 2017 01:12:23: 3000000 INFO @ Sat, 11 Nov 2017 01:12:28: 4000000 INFO @ Sat, 11 Nov 2017 01:12:29: 4000000 INFO @ Sat, 11 Nov 2017 01:12:30: 4000000 INFO @ Sat, 11 Nov 2017 01:12:34: 5000000 INFO @ Sat, 11 Nov 2017 01:12:35: 5000000 INFO @ Sat, 11 Nov 2017 01:12:37: 5000000 INFO @ Sat, 11 Nov 2017 01:12:40: 6000000 INFO @ Sat, 11 Nov 2017 01:12:42: 6000000 INFO @ Sat, 11 Nov 2017 01:12:43: 6000000 INFO @ Sat, 11 Nov 2017 01:12:47: 7000000 INFO @ Sat, 11 Nov 2017 01:12:48: 7000000 INFO @ Sat, 11 Nov 2017 01:12:48: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 01:12:48: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 01:12:48: #1 total tags in treatment: 7259795 INFO @ Sat, 11 Nov 2017 01:12:48: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:12:48: #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 01:12:49: #1 tags after filtering in treatment: 7259519 INFO @ Sat, 11 Nov 2017 01:12:49: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:12:49: #1 finished! INFO @ Sat, 11 Nov 2017 01:12:49: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:12:49: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:12:50: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 01:12:50: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 01:12:50: #1 total tags in treatment: 7259795 INFO @ Sat, 11 Nov 2017 01:12:50: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:12:50: #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 01:12:50: #1 tags after filtering in treatment: 7259519 INFO @ Sat, 11 Nov 2017 01:12:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:12:50: #1 finished! INFO @ Sat, 11 Nov 2017 01:12:50: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:12:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:12:50: 7000000 INFO @ Sat, 11 Nov 2017 01:12:51: #2 number of paired peaks: 39634 INFO @ Sat, 11 Nov 2017 01:12:51: start model_add_line... INFO @ Sat, 11 Nov 2017 01:12:51: start X-correlation... INFO @ Sat, 11 Nov 2017 01:12:51: end of X-cor INFO @ Sat, 11 Nov 2017 01:12:51: #2 finished! INFO @ Sat, 11 Nov 2017 01:12:51: #2 predicted fragment length is 119 bps INFO @ Sat, 11 Nov 2017 01:12:51: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 11 Nov 2017 01:12:51: #2.2 Generate R script for model : SRX1927035.05_model.r INFO @ Sat, 11 Nov 2017 01:12:51: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:12:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:12:52: #1 tag size is determined as 51 bps INFO @ Sat, 11 Nov 2017 01:12:52: #1 tag size = 51 INFO @ Sat, 11 Nov 2017 01:12:52: #1 total tags in treatment: 7259795 INFO @ Sat, 11 Nov 2017 01:12:52: #1 user defined the maximum tags... INFO @ Sat, 11 Nov 2017 01:12:52: #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 01:12:52: #1 tags after filtering in treatment: 7259519 INFO @ Sat, 11 Nov 2017 01:12:52: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 11 Nov 2017 01:12:52: #1 finished! INFO @ Sat, 11 Nov 2017 01:12:52: #2 Build Peak Model... INFO @ Sat, 11 Nov 2017 01:12:52: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 11 Nov 2017 01:12:52: #2 number of paired peaks: 39634 INFO @ Sat, 11 Nov 2017 01:12:52: start model_add_line... INFO @ Sat, 11 Nov 2017 01:12:53: start X-correlation... INFO @ Sat, 11 Nov 2017 01:12:53: end of X-cor INFO @ Sat, 11 Nov 2017 01:12:53: #2 finished! INFO @ Sat, 11 Nov 2017 01:12:53: #2 predicted fragment length is 119 bps INFO @ Sat, 11 Nov 2017 01:12:53: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 11 Nov 2017 01:12:53: #2.2 Generate R script for model : SRX1927035.10_model.r INFO @ Sat, 11 Nov 2017 01:12:53: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:12:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:12:55: #2 number of paired peaks: 39634 INFO @ Sat, 11 Nov 2017 01:12:55: start model_add_line... INFO @ Sat, 11 Nov 2017 01:12:55: start X-correlation... INFO @ Sat, 11 Nov 2017 01:12:55: end of X-cor INFO @ Sat, 11 Nov 2017 01:12:55: #2 finished! INFO @ Sat, 11 Nov 2017 01:12:55: #2 predicted fragment length is 119 bps INFO @ Sat, 11 Nov 2017 01:12:55: #2 alternative fragment length(s) may be 119 bps INFO @ Sat, 11 Nov 2017 01:12:55: #2.2 Generate R script for model : SRX1927035.20_model.r INFO @ Sat, 11 Nov 2017 01:12:55: #3 Call peaks... INFO @ Sat, 11 Nov 2017 01:12:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 11 Nov 2017 01:13:08: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:13:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:13:11: #3 Call peaks for each chromosome... INFO @ Sat, 11 Nov 2017 01:13:19: #4 Write output xls file... SRX1927035.05_peaks.xls INFO @ Sat, 11 Nov 2017 01:13:19: #4 Write peak in narrowPeak format file... SRX1927035.05_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:13:20: #4 Write summits bed file... SRX1927035.05_summits.bed INFO @ Sat, 11 Nov 2017 01:13:20: Done! pass1 - making usageList (113 chroms): 6 millis pass2 - checking and writing primary data (32470 records, 4 fields): 42 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:13:22: #4 Write output xls file... SRX1927035.10_peaks.xls INFO @ Sat, 11 Nov 2017 01:13:22: #4 Write peak in narrowPeak format file... SRX1927035.10_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:13:22: #4 Write summits bed file... SRX1927035.10_summits.bed INFO @ Sat, 11 Nov 2017 01:13:22: Done! INFO @ Sat, 11 Nov 2017 01:13:23: #4 Write output xls file... SRX1927035.20_peaks.xls pass1 - making usageList (93 chroms): 5 millis pass2 - checking and writing primary data (23697 records, 4 fields): 31 millis CompletedMACS2peakCalling INFO @ Sat, 11 Nov 2017 01:13:23: #4 Write peak in narrowPeak format file... SRX1927035.20_peaks.narrowPeak INFO @ Sat, 11 Nov 2017 01:13:23: #4 Write summits bed file... SRX1927035.20_summits.bed INFO @ Sat, 11 Nov 2017 01:13:23: Done! pass1 - making usageList (61 chroms): 3 millis pass2 - checking and writing primary data (12344 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。