Job ID = 11632702 sra ファイルのダウンロード中... Completed: 1444136K bytes transferred in 17 seconds (687885K 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 57457269 spots for /home/okishinya/chipatlas/results/rn6/SRX3782461/SRR6826279.sra Written 57457269 spots for /home/okishinya/chipatlas/results/rn6/SRX3782461/SRR6826279.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: 00:00:03 Time loading mirror index: 00:00:03 Multiseed full-index search: 00:23:46 57457269 reads; of these: 57457269 (100.00%) were unpaired; of these: 20093943 (34.97%) aligned 0 times 29739878 (51.76%) aligned exactly 1 time 7623448 (13.27%) aligned >1 times 65.03% overall alignment rate Time searching: 00:23:53 Overall time: 00:23:53 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] 27345226 / 37363326 = 0.7319 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 06:39:51: # Command line: callpeak -t SRX3782461.bam -f BAM -g 2.15e9 -n SRX3782461.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3782461.10 # format = BAM # ChIP-seq file = ['SRX3782461.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 06:39:51: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:39:51: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:39:51: # Command line: callpeak -t SRX3782461.bam -f BAM -g 2.15e9 -n SRX3782461.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3782461.05 # format = BAM # ChIP-seq file = ['SRX3782461.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 06:39:51: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:39:51: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:39:51: # Command line: callpeak -t SRX3782461.bam -f BAM -g 2.15e9 -n SRX3782461.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3782461.20 # format = BAM # ChIP-seq file = ['SRX3782461.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 06:39:51: #1 read tag files... INFO @ Fri, 15 Feb 2019 06:39:51: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 06:39:57: 1000000 INFO @ Fri, 15 Feb 2019 06:39:58: 1000000 INFO @ Fri, 15 Feb 2019 06:39:58: 1000000 INFO @ Fri, 15 Feb 2019 06:40:04: 2000000 INFO @ Fri, 15 Feb 2019 06:40:04: 2000000 INFO @ Fri, 15 Feb 2019 06:40:05: 2000000 INFO @ Fri, 15 Feb 2019 06:40:11: 3000000 INFO @ Fri, 15 Feb 2019 06:40:11: 3000000 INFO @ Fri, 15 Feb 2019 06:40:12: 3000000 INFO @ Fri, 15 Feb 2019 06:40:17: 4000000 INFO @ Fri, 15 Feb 2019 06:40:18: 4000000 INFO @ Fri, 15 Feb 2019 06:40:19: 4000000 INFO @ Fri, 15 Feb 2019 06:40:24: 5000000 INFO @ Fri, 15 Feb 2019 06:40:25: 5000000 INFO @ Fri, 15 Feb 2019 06:40:27: 5000000 INFO @ Fri, 15 Feb 2019 06:40:30: 6000000 INFO @ Fri, 15 Feb 2019 06:40:32: 6000000 INFO @ Fri, 15 Feb 2019 06:40:34: 6000000 INFO @ Fri, 15 Feb 2019 06:40:37: 7000000 INFO @ Fri, 15 Feb 2019 06:40:39: 7000000 INFO @ Fri, 15 Feb 2019 06:40:41: 7000000 INFO @ Fri, 15 Feb 2019 06:40:43: 8000000 INFO @ Fri, 15 Feb 2019 06:40:45: 8000000 INFO @ Fri, 15 Feb 2019 06:40:48: 8000000 INFO @ Fri, 15 Feb 2019 06:40:50: 9000000 INFO @ Fri, 15 Feb 2019 06:40:52: 9000000 INFO @ Fri, 15 Feb 2019 06:40:56: 9000000 INFO @ Fri, 15 Feb 2019 06:40:57: 10000000 INFO @ Fri, 15 Feb 2019 06:40:57: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 06:40:57: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 06:40:57: #1 total tags in treatment: 10018100 INFO @ Fri, 15 Feb 2019 06:40:57: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:40:57: #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 06:40:57: #1 tags after filtering in treatment: 10017919 INFO @ Fri, 15 Feb 2019 06:40:57: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:40:57: #1 finished! INFO @ Fri, 15 Feb 2019 06:40:57: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:40:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:40:59: 10000000 INFO @ Fri, 15 Feb 2019 06:40:59: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 06:40:59: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 06:40:59: #1 total tags in treatment: 10018100 INFO @ Fri, 15 Feb 2019 06:40:59: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:40:59: #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 06:41:00: #1 tags after filtering in treatment: 10017919 INFO @ Fri, 15 Feb 2019 06:41:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:41:00: #1 finished! INFO @ Fri, 15 Feb 2019 06:41:00: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:41:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:41:01: #2 number of paired peaks: 60661 INFO @ Fri, 15 Feb 2019 06:41:01: start model_add_line... INFO @ Fri, 15 Feb 2019 06:41:01: start X-correlation... INFO @ Fri, 15 Feb 2019 06:41:01: end of X-cor INFO @ Fri, 15 Feb 2019 06:41:01: #2 finished! INFO @ Fri, 15 Feb 2019 06:41:01: #2 predicted fragment length is 137 bps INFO @ Fri, 15 Feb 2019 06:41:01: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 15 Feb 2019 06:41:01: #2.2 Generate R script for model : SRX3782461.20_model.r INFO @ Fri, 15 Feb 2019 06:41:01: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:41:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:41:03: 10000000 INFO @ Fri, 15 Feb 2019 06:41:03: #1 tag size is determined as 43 bps INFO @ Fri, 15 Feb 2019 06:41:03: #1 tag size = 43 INFO @ Fri, 15 Feb 2019 06:41:03: #1 total tags in treatment: 10018100 INFO @ Fri, 15 Feb 2019 06:41:03: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 06:41:03: #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 06:41:03: #2 number of paired peaks: 60661 INFO @ Fri, 15 Feb 2019 06:41:03: start model_add_line... INFO @ Fri, 15 Feb 2019 06:41:03: start X-correlation... INFO @ Fri, 15 Feb 2019 06:41:03: end of X-cor INFO @ Fri, 15 Feb 2019 06:41:03: #2 finished! INFO @ Fri, 15 Feb 2019 06:41:03: #2 predicted fragment length is 137 bps INFO @ Fri, 15 Feb 2019 06:41:03: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 15 Feb 2019 06:41:03: #2.2 Generate R script for model : SRX3782461.10_model.r INFO @ Fri, 15 Feb 2019 06:41:03: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:41:03: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:41:03: #1 tags after filtering in treatment: 10017919 INFO @ Fri, 15 Feb 2019 06:41:03: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 06:41:03: #1 finished! INFO @ Fri, 15 Feb 2019 06:41:03: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 06:41:03: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 06:41:07: #2 number of paired peaks: 60661 INFO @ Fri, 15 Feb 2019 06:41:07: start model_add_line... INFO @ Fri, 15 Feb 2019 06:41:07: start X-correlation... INFO @ Fri, 15 Feb 2019 06:41:07: end of X-cor INFO @ Fri, 15 Feb 2019 06:41:07: #2 finished! INFO @ Fri, 15 Feb 2019 06:41:07: #2 predicted fragment length is 137 bps INFO @ Fri, 15 Feb 2019 06:41:07: #2 alternative fragment length(s) may be 137 bps INFO @ Fri, 15 Feb 2019 06:41:07: #2.2 Generate R script for model : SRX3782461.05_model.r INFO @ Fri, 15 Feb 2019 06:41:07: #3 Call peaks... INFO @ Fri, 15 Feb 2019 06:41:07: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 06:41:26: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:41:28: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:41:32: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 06:41:39: #4 Write output xls file... SRX3782461.20_peaks.xls INFO @ Fri, 15 Feb 2019 06:41:39: #4 Write peak in narrowPeak format file... SRX3782461.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:41:39: #4 Write summits bed file... SRX3782461.20_summits.bed INFO @ Fri, 15 Feb 2019 06:41:39: Done! pass1 - making usageList (32 chroms): 10 millis pass2 - checking and writing primary data (348 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:41:42: #4 Write output xls file... SRX3782461.10_peaks.xls INFO @ Fri, 15 Feb 2019 06:41:42: #4 Write peak in narrowPeak format file... SRX3782461.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:41:42: #4 Write summits bed file... SRX3782461.10_summits.bed INFO @ Fri, 15 Feb 2019 06:41:42: Done! pass1 - making usageList (50 chroms): 9 millis pass2 - checking and writing primary data (1150 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 06:41:48: #4 Write output xls file... SRX3782461.05_peaks.xls INFO @ Fri, 15 Feb 2019 06:41:48: #4 Write peak in narrowPeak format file... SRX3782461.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 06:41:48: #4 Write summits bed file... SRX3782461.05_summits.bed INFO @ Fri, 15 Feb 2019 06:41:48: Done! pass1 - making usageList (99 chroms): 8 millis pass2 - checking and writing primary data (9541 records, 4 fields): 19 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。