Job ID = 11632674 sra ファイルのダウンロード中... Completed: 970329K bytes transferred in 24 seconds (318076K 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 52022211 spots for /home/okishinya/chipatlas/results/rn6/SRX3360112/SRR6253218.sra Written 52022211 spots for /home/okishinya/chipatlas/results/rn6/SRX3360112/SRR6253218.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: 00:00:01 Time loading mirror index: 00:00:01 Multiseed full-index search: 00:18:28 52022211 reads; of these: 52022211 (100.00%) were unpaired; of these: 28121251 (54.06%) aligned 0 times 19587894 (37.65%) aligned exactly 1 time 4313066 (8.29%) aligned >1 times 45.94% overall alignment rate Time searching: 00:18:33 Overall time: 00:18:33 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] 10886711 / 23900960 = 0.4555 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 05:53:59: # Command line: callpeak -t SRX3360112.bam -f BAM -g 2.15e9 -n SRX3360112.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3360112.10 # format = BAM # ChIP-seq file = ['SRX3360112.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 05:53:59: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:53:59: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:53:59: # Command line: callpeak -t SRX3360112.bam -f BAM -g 2.15e9 -n SRX3360112.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3360112.05 # format = BAM # ChIP-seq file = ['SRX3360112.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 05:53:59: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:53:59: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:53:59: # Command line: callpeak -t SRX3360112.bam -f BAM -g 2.15e9 -n SRX3360112.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3360112.20 # format = BAM # ChIP-seq file = ['SRX3360112.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 05:53:59: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:53:59: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:54:06: 1000000 INFO @ Fri, 15 Feb 2019 05:54:06: 1000000 INFO @ Fri, 15 Feb 2019 05:54:06: 1000000 INFO @ Fri, 15 Feb 2019 05:54:12: 2000000 INFO @ Fri, 15 Feb 2019 05:54:12: 2000000 INFO @ Fri, 15 Feb 2019 05:54:12: 2000000 INFO @ Fri, 15 Feb 2019 05:54:18: 3000000 INFO @ Fri, 15 Feb 2019 05:54:19: 3000000 INFO @ Fri, 15 Feb 2019 05:54:19: 3000000 INFO @ Fri, 15 Feb 2019 05:54:25: 4000000 INFO @ Fri, 15 Feb 2019 05:54:25: 4000000 INFO @ Fri, 15 Feb 2019 05:54:25: 4000000 INFO @ Fri, 15 Feb 2019 05:54:31: 5000000 INFO @ Fri, 15 Feb 2019 05:54:32: 5000000 INFO @ Fri, 15 Feb 2019 05:54:32: 5000000 INFO @ Fri, 15 Feb 2019 05:54:38: 6000000 INFO @ Fri, 15 Feb 2019 05:54:38: 6000000 INFO @ Fri, 15 Feb 2019 05:54:38: 6000000 INFO @ Fri, 15 Feb 2019 05:54:44: 7000000 INFO @ Fri, 15 Feb 2019 05:54:45: 7000000 INFO @ Fri, 15 Feb 2019 05:54:45: 7000000 INFO @ Fri, 15 Feb 2019 05:54:50: 8000000 INFO @ Fri, 15 Feb 2019 05:54:51: 8000000 INFO @ Fri, 15 Feb 2019 05:54:51: 8000000 INFO @ Fri, 15 Feb 2019 05:54:57: 9000000 INFO @ Fri, 15 Feb 2019 05:54:58: 9000000 INFO @ Fri, 15 Feb 2019 05:54:58: 9000000 INFO @ Fri, 15 Feb 2019 05:55:03: 10000000 INFO @ Fri, 15 Feb 2019 05:55:04: 10000000 INFO @ Fri, 15 Feb 2019 05:55:05: 10000000 INFO @ Fri, 15 Feb 2019 05:55:09: 11000000 INFO @ Fri, 15 Feb 2019 05:55:11: 11000000 INFO @ Fri, 15 Feb 2019 05:55:11: 11000000 INFO @ Fri, 15 Feb 2019 05:55:16: 12000000 INFO @ Fri, 15 Feb 2019 05:55:17: 12000000 INFO @ Fri, 15 Feb 2019 05:55:18: 12000000 INFO @ Fri, 15 Feb 2019 05:55:22: 13000000 INFO @ Fri, 15 Feb 2019 05:55:22: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 05:55:22: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 05:55:22: #1 total tags in treatment: 13014249 INFO @ Fri, 15 Feb 2019 05:55:22: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:55:22: #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 05:55:23: #1 tags after filtering in treatment: 13014002 INFO @ Fri, 15 Feb 2019 05:55:23: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:55:23: #1 finished! INFO @ Fri, 15 Feb 2019 05:55:23: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:55:23: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:55:24: 13000000 INFO @ Fri, 15 Feb 2019 05:55:24: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 05:55:24: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 05:55:24: #1 total tags in treatment: 13014249 INFO @ Fri, 15 Feb 2019 05:55:24: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:55:24: #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 05:55:25: #1 tags after filtering in treatment: 13014002 INFO @ Fri, 15 Feb 2019 05:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:55:25: #1 finished! INFO @ Fri, 15 Feb 2019 05:55:25: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:55:25: 13000000 INFO @ Fri, 15 Feb 2019 05:55:25: #1 tag size is determined as 51 bps INFO @ Fri, 15 Feb 2019 05:55:25: #1 tag size = 51 INFO @ Fri, 15 Feb 2019 05:55:25: #1 total tags in treatment: 13014249 INFO @ Fri, 15 Feb 2019 05:55:25: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:55:25: #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 05:55:25: #1 tags after filtering in treatment: 13014002 INFO @ Fri, 15 Feb 2019 05:55:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:55:25: #1 finished! INFO @ Fri, 15 Feb 2019 05:55:25: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:55:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:55:26: #2 number of paired peaks: 34661 INFO @ Fri, 15 Feb 2019 05:55:26: start model_add_line... INFO @ Fri, 15 Feb 2019 05:55:26: start X-correlation... INFO @ Fri, 15 Feb 2019 05:55:26: end of X-cor INFO @ Fri, 15 Feb 2019 05:55:26: #2 finished! INFO @ Fri, 15 Feb 2019 05:55:26: #2 predicted fragment length is 165 bps INFO @ Fri, 15 Feb 2019 05:55:26: #2 alternative fragment length(s) may be 165 bps INFO @ Fri, 15 Feb 2019 05:55:26: #2.2 Generate R script for model : SRX3360112.10_model.r INFO @ Fri, 15 Feb 2019 05:55:26: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:55:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:55:27: #2 number of paired peaks: 34661 INFO @ Fri, 15 Feb 2019 05:55:27: start model_add_line... INFO @ Fri, 15 Feb 2019 05:55:27: start X-correlation... INFO @ Fri, 15 Feb 2019 05:55:27: end of X-cor INFO @ Fri, 15 Feb 2019 05:55:27: #2 finished! INFO @ Fri, 15 Feb 2019 05:55:27: #2 predicted fragment length is 165 bps INFO @ Fri, 15 Feb 2019 05:55:27: #2 alternative fragment length(s) may be 165 bps INFO @ Fri, 15 Feb 2019 05:55:27: #2.2 Generate R script for model : SRX3360112.05_model.r INFO @ Fri, 15 Feb 2019 05:55:27: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:55:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:55:28: #2 number of paired peaks: 34661 INFO @ Fri, 15 Feb 2019 05:55:28: start model_add_line... INFO @ Fri, 15 Feb 2019 05:55:28: start X-correlation... INFO @ Fri, 15 Feb 2019 05:55:28: end of X-cor INFO @ Fri, 15 Feb 2019 05:55:28: #2 finished! INFO @ Fri, 15 Feb 2019 05:55:28: #2 predicted fragment length is 165 bps INFO @ Fri, 15 Feb 2019 05:55:28: #2 alternative fragment length(s) may be 165 bps INFO @ Fri, 15 Feb 2019 05:55:28: #2.2 Generate R script for model : SRX3360112.20_model.r INFO @ Fri, 15 Feb 2019 05:55:29: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:55:29: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:56:00: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:56:01: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:56:01: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:56:20: #4 Write output xls file... SRX3360112.20_peaks.xls INFO @ Fri, 15 Feb 2019 05:56:20: #4 Write peak in narrowPeak format file... SRX3360112.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:56:20: #4 Write summits bed file... SRX3360112.20_summits.bed INFO @ Fri, 15 Feb 2019 05:56:20: Done! pass1 - making usageList (80 chroms): 10 millis pass2 - checking and writing primary data (14775 records, 4 fields): 24 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 05:56:21: #4 Write output xls file... SRX3360112.05_peaks.xls INFO @ Fri, 15 Feb 2019 05:56:21: #4 Write peak in narrowPeak format file... SRX3360112.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:56:21: #4 Write summits bed file... SRX3360112.05_summits.bed INFO @ Fri, 15 Feb 2019 05:56:21: Done! pass1 - making usageList (123 chroms): 9 millis pass2 - checking and writing primary data (23290 records, 4 fields): 36 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 05:56:24: #4 Write output xls file... SRX3360112.10_peaks.xls INFO @ Fri, 15 Feb 2019 05:56:25: #4 Write peak in narrowPeak format file... SRX3360112.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:56:25: #4 Write summits bed file... SRX3360112.10_summits.bed INFO @ Fri, 15 Feb 2019 05:56:25: Done! pass1 - making usageList (106 chroms): 9 millis pass2 - checking and writing primary data (19690 records, 4 fields): 33 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。