Job ID = 11632672 sra ファイルのダウンロード中... Completed: 1056192K bytes transferred in 16 seconds (512771K 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 56459536 spots for /home/okishinya/chipatlas/results/rn6/SRX3360110/SRR6253216.sra Written 56459536 spots for /home/okishinya/chipatlas/results/rn6/SRX3360110/SRR6253216.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: 00:00:00 Multiseed full-index search: 00:18:53 56459536 reads; of these: 56459536 (100.00%) were unpaired; of these: 33876566 (60.00%) aligned 0 times 18940552 (33.55%) aligned exactly 1 time 3642418 (6.45%) aligned >1 times 40.00% overall alignment rate Time searching: 00:18:56 Overall time: 00:18:56 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] 11577638 / 22582970 = 0.5127 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 @ Fri, 15 Feb 2019 07:11:12: # Command line: callpeak -t SRX3360110.bam -f BAM -g 2.15e9 -n SRX3360110.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360110.20 # format = BAM # ChIP-seq file = ['SRX3360110.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 @ Fri, 15 Feb 2019 07:11:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:11:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:11:12: # Command line: callpeak -t SRX3360110.bam -f BAM -g 2.15e9 -n SRX3360110.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360110.10 # format = BAM # ChIP-seq file = ['SRX3360110.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 @ Fri, 15 Feb 2019 07:11:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:11:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:11:12: # Command line: callpeak -t SRX3360110.bam -f BAM -g 2.15e9 -n SRX3360110.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360110.05 # format = BAM # ChIP-seq file = ['SRX3360110.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 @ Fri, 15 Feb 2019 07:11:12: #1 read tag files... INFO @ Fri, 15 Feb 2019 07:11:12: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 07:11:20: 1000000 INFO @ Fri, 15 Feb 2019 07:11:20: 1000000 INFO @ Fri, 15 Feb 2019 07:11:20: 1000000 INFO @ Fri, 15 Feb 2019 07:11:27: 2000000 INFO @ Fri, 15 Feb 2019 07:11:29: 2000000 INFO @ Fri, 15 Feb 2019 07:11:29: 2000000 INFO @ Fri, 15 Feb 2019 07:11:34: 3000000 INFO @ Fri, 15 Feb 2019 07:11:37: 3000000 INFO @ Fri, 15 Feb 2019 07:11:37: 3000000 INFO @ Fri, 15 Feb 2019 07:11:41: 4000000 INFO @ Fri, 15 Feb 2019 07:11:45: 4000000 INFO @ Fri, 15 Feb 2019 07:11:45: 4000000 INFO @ Fri, 15 Feb 2019 07:11:49: 5000000 INFO @ Fri, 15 Feb 2019 07:11:54: 5000000 INFO @ Fri, 15 Feb 2019 07:11:54: 5000000 INFO @ Fri, 15 Feb 2019 07:11:56: 6000000 INFO @ Fri, 15 Feb 2019 07:12:02: 6000000 INFO @ Fri, 15 Feb 2019 07:12:02: 6000000 INFO @ Fri, 15 Feb 2019 07:12:03: 7000000 INFO @ Fri, 15 Feb 2019 07:12:10: 7000000 INFO @ Fri, 15 Feb 2019 07:12:10: 7000000 INFO @ Fri, 15 Feb 2019 07:12:10: 8000000 INFO @ Fri, 15 Feb 2019 07:12:18: 9000000 INFO @ Fri, 15 Feb 2019 07:12:18: 8000000 INFO @ Fri, 15 Feb 2019 07:12:18: 8000000 INFO @ Fri, 15 Feb 2019 07:12:25: 10000000 INFO @ Fri, 15 Feb 2019 07:12:27: 9000000 INFO @ Fri, 15 Feb 2019 07:12:27: 9000000 INFO @ Fri, 15 Feb 2019 07:12:32: 11000000 INFO @ Fri, 15 Feb 2019 07:12:32: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:12:32: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:12:32: #1 total tags in treatment: 11005332 INFO @ Fri, 15 Feb 2019 07:12:32: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:12:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:12:33: #1 tags after filtering in treatment: 11005063 INFO @ Fri, 15 Feb 2019 07:12:33: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:12:33: #1 finished! INFO @ Fri, 15 Feb 2019 07:12:33: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:12:33: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:12:35: 10000000 INFO @ Fri, 15 Feb 2019 07:12:35: 10000000 INFO @ Fri, 15 Feb 2019 07:12:35: #2 number of paired peaks: 40499 INFO @ Fri, 15 Feb 2019 07:12:35: start model_add_line... INFO @ Fri, 15 Feb 2019 07:12:36: start X-correlation... INFO @ Fri, 15 Feb 2019 07:12:36: end of X-cor INFO @ Fri, 15 Feb 2019 07:12:36: #2 finished! INFO @ Fri, 15 Feb 2019 07:12:36: #2 predicted fragment length is 184 bps INFO @ Fri, 15 Feb 2019 07:12:36: #2 alternative fragment length(s) may be 184 bps INFO @ Fri, 15 Feb 2019 07:12:36: #2.2 Generate R script for model : SRX3360110.20_model.r INFO @ Fri, 15 Feb 2019 07:12:36: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:12:36: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:12:44: 11000000 INFO @ Fri, 15 Feb 2019 07:12:44: 11000000 INFO @ Fri, 15 Feb 2019 07:12:44: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:12:44: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:12:44: #1 total tags in treatment: 11005332 INFO @ Fri, 15 Feb 2019 07:12:44: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 07:12:44: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:12:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:12:44: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 07:12:44: #1 total tags in treatment: 11005332 INFO @ Fri, 15 Feb 2019 07:12:44: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 07:12:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 15 Feb 2019 07:12:45: #1 tags after filtering in treatment: 11005063 INFO @ Fri, 15 Feb 2019 07:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:12:45: #1 finished! INFO @ Fri, 15 Feb 2019 07:12:45: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:12:45: #1 tags after filtering in treatment: 11005063 INFO @ Fri, 15 Feb 2019 07:12:45: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 07:12:45: #1 finished! INFO @ Fri, 15 Feb 2019 07:12:45: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 07:12:45: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 07:12:47: #2 number of paired peaks: 40499 INFO @ Fri, 15 Feb 2019 07:12:47: start model_add_line... INFO @ Fri, 15 Feb 2019 07:12:47: #2 number of paired peaks: 40499 INFO @ Fri, 15 Feb 2019 07:12:47: start model_add_line... INFO @ Fri, 15 Feb 2019 07:12:47: start X-correlation... INFO @ Fri, 15 Feb 2019 07:12:47: end of X-cor INFO @ Fri, 15 Feb 2019 07:12:47: #2 finished! INFO @ Fri, 15 Feb 2019 07:12:47: #2 predicted fragment length is 184 bps INFO @ Fri, 15 Feb 2019 07:12:47: #2 alternative fragment length(s) may be 184 bps INFO @ Fri, 15 Feb 2019 07:12:47: #2.2 Generate R script for model : SRX3360110.05_model.r INFO @ Fri, 15 Feb 2019 07:12:47: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:12:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:12:47: start X-correlation... INFO @ Fri, 15 Feb 2019 07:12:47: end of X-cor INFO @ Fri, 15 Feb 2019 07:12:47: #2 finished! INFO @ Fri, 15 Feb 2019 07:12:47: #2 predicted fragment length is 184 bps INFO @ Fri, 15 Feb 2019 07:12:47: #2 alternative fragment length(s) may be 184 bps INFO @ Fri, 15 Feb 2019 07:12:47: #2.2 Generate R script for model : SRX3360110.10_model.r INFO @ Fri, 15 Feb 2019 07:12:47: #3 Call peaks... INFO @ Fri, 15 Feb 2019 07:12:47: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 07:13:04: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:13:18: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:13:19: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 07:13:21: #4 Write output xls file... SRX3360110.20_peaks.xls INFO @ Fri, 15 Feb 2019 07:13:21: #4 Write peak in narrowPeak format file... SRX3360110.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:13:21: #4 Write summits bed file... SRX3360110.20_summits.bed INFO @ Fri, 15 Feb 2019 07:13:21: Done! pass1 - making usageList (92 chroms): 6 millis pass2 - checking and writing primary data (13896 records, 4 fields): 22 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:13:36: #4 Write output xls file... SRX3360110.05_peaks.xls INFO @ Fri, 15 Feb 2019 07:13:36: #4 Write peak in narrowPeak format file... SRX3360110.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:13:36: #4 Write summits bed file... SRX3360110.05_summits.bed INFO @ Fri, 15 Feb 2019 07:13:36: Done! pass1 - making usageList (135 chroms): 7 millis pass2 - checking and writing primary data (24529 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 07:13:38: #4 Write output xls file... SRX3360110.10_peaks.xls INFO @ Fri, 15 Feb 2019 07:13:38: #4 Write peak in narrowPeak format file... SRX3360110.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 07:13:38: #4 Write summits bed file... SRX3360110.10_summits.bed INFO @ Fri, 15 Feb 2019 07:13:38: Done! pass1 - making usageList (119 chroms): 6 millis pass2 - checking and writing primary data (20071 records, 4 fields): 31 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。