Job ID = 11192569 sra ファイルのダウンロード中... Completed: 1731978K bytes transferred in 16 seconds (854079K 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 53380909 spots for /home/okishinya/chipatlas/results/rn6/SRX2226581/SRR4374831.sra Written 53380909 spots for /home/okishinya/chipatlas/results/rn6/SRX2226581/SRR4374831.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: 00:31:35 53380909 reads; of these: 53380909 (100.00%) were unpaired; of these: 11368816 (21.30%) aligned 0 times 32138732 (60.21%) aligned exactly 1 time 9873361 (18.50%) aligned >1 times 78.70% overall alignment rate Time searching: 00:31:40 Overall time: 00:31:40 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 20 files... [bam_rmdupse_core] 31788692 / 42012093 = 0.7567 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 09:38:18: # Command line: callpeak -t SRX2226581.bam -f BAM -g 2.15e9 -n SRX2226581.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX2226581.20 # format = BAM # ChIP-seq file = ['SRX2226581.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 09:38:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:38:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:38:18: # Command line: callpeak -t SRX2226581.bam -f BAM -g 2.15e9 -n SRX2226581.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX2226581.10 # format = BAM # ChIP-seq file = ['SRX2226581.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 09:38:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:38:18: # Command line: callpeak -t SRX2226581.bam -f BAM -g 2.15e9 -n SRX2226581.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX2226581.05 # format = BAM # ChIP-seq file = ['SRX2226581.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 09:38:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:38:18: #1 read tag files... INFO @ Sat, 15 Sep 2018 09:38:18: #1 read treatment tags... INFO @ Sat, 15 Sep 2018 09:38:25: 1000000 INFO @ Sat, 15 Sep 2018 09:38:25: 1000000 INFO @ Sat, 15 Sep 2018 09:38:25: 1000000 INFO @ Sat, 15 Sep 2018 09:38:32: 2000000 INFO @ Sat, 15 Sep 2018 09:38:32: 2000000 INFO @ Sat, 15 Sep 2018 09:38:32: 2000000 INFO @ Sat, 15 Sep 2018 09:38:39: 3000000 INFO @ Sat, 15 Sep 2018 09:38:39: 3000000 INFO @ Sat, 15 Sep 2018 09:38:39: 3000000 INFO @ Sat, 15 Sep 2018 09:38:46: 4000000 INFO @ Sat, 15 Sep 2018 09:38:46: 4000000 INFO @ Sat, 15 Sep 2018 09:38:46: 4000000 INFO @ Sat, 15 Sep 2018 09:38:53: 5000000 INFO @ Sat, 15 Sep 2018 09:38:53: 5000000 INFO @ Sat, 15 Sep 2018 09:38:53: 5000000 INFO @ Sat, 15 Sep 2018 09:39:00: 6000000 INFO @ Sat, 15 Sep 2018 09:39:00: 6000000 INFO @ Sat, 15 Sep 2018 09:39:00: 6000000 INFO @ Sat, 15 Sep 2018 09:39:07: 7000000 INFO @ Sat, 15 Sep 2018 09:39:07: 7000000 INFO @ Sat, 15 Sep 2018 09:39:07: 7000000 INFO @ Sat, 15 Sep 2018 09:39:14: 8000000 INFO @ Sat, 15 Sep 2018 09:39:14: 8000000 INFO @ Sat, 15 Sep 2018 09:39:14: 8000000 INFO @ Sat, 15 Sep 2018 09:39:21: 9000000 INFO @ Sat, 15 Sep 2018 09:39:21: 9000000 INFO @ Sat, 15 Sep 2018 09:39:21: 9000000 INFO @ Sat, 15 Sep 2018 09:39:28: 10000000 INFO @ Sat, 15 Sep 2018 09:39:28: 10000000 INFO @ Sat, 15 Sep 2018 09:39:29: 10000000 INFO @ Sat, 15 Sep 2018 09:39:30: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:39:30: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:39:30: #1 total tags in treatment: 10223401 INFO @ Sat, 15 Sep 2018 09:39:30: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:39:30: #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 09:39:30: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:39:30: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:39:30: #1 total tags in treatment: 10223401 INFO @ Sat, 15 Sep 2018 09:39:30: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:39:30: #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 09:39:30: #1 tags after filtering in treatment: 10223236 INFO @ Sat, 15 Sep 2018 09:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:39:30: #1 finished! INFO @ Sat, 15 Sep 2018 09:39:30: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:39:30: #1 tags after filtering in treatment: 10223236 INFO @ Sat, 15 Sep 2018 09:39:30: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:39:30: #1 finished! INFO @ Sat, 15 Sep 2018 09:39:30: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:39:30: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:39:30: #1 tag size is determined as 50 bps INFO @ Sat, 15 Sep 2018 09:39:30: #1 tag size = 50 INFO @ Sat, 15 Sep 2018 09:39:30: #1 total tags in treatment: 10223401 INFO @ Sat, 15 Sep 2018 09:39:30: #1 user defined the maximum tags... INFO @ Sat, 15 Sep 2018 09:39:30: #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 09:39:31: #1 tags after filtering in treatment: 10223236 INFO @ Sat, 15 Sep 2018 09:39:31: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 15 Sep 2018 09:39:31: #1 finished! INFO @ Sat, 15 Sep 2018 09:39:31: #2 Build Peak Model... INFO @ Sat, 15 Sep 2018 09:39:31: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 15 Sep 2018 09:39:33: #2 number of paired peaks: 52495 INFO @ Sat, 15 Sep 2018 09:39:33: start model_add_line... INFO @ Sat, 15 Sep 2018 09:39:33: #2 number of paired peaks: 52495 INFO @ Sat, 15 Sep 2018 09:39:33: start model_add_line... INFO @ Sat, 15 Sep 2018 09:39:33: start X-correlation... INFO @ Sat, 15 Sep 2018 09:39:33: end of X-cor INFO @ Sat, 15 Sep 2018 09:39:33: #2 finished! INFO @ Sat, 15 Sep 2018 09:39:33: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Sep 2018 09:39:33: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 15 Sep 2018 09:39:33: #2.2 Generate R script for model : SRX2226581.20_model.r INFO @ Sat, 15 Sep 2018 09:39:33: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:39:33: start X-correlation... INFO @ Sat, 15 Sep 2018 09:39:33: end of X-cor INFO @ Sat, 15 Sep 2018 09:39:33: #2 finished! INFO @ Sat, 15 Sep 2018 09:39:33: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Sep 2018 09:39:33: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 15 Sep 2018 09:39:33: #2.2 Generate R script for model : SRX2226581.05_model.r INFO @ Sat, 15 Sep 2018 09:39:33: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:39:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:39:34: #2 number of paired peaks: 52495 INFO @ Sat, 15 Sep 2018 09:39:34: start model_add_line... INFO @ Sat, 15 Sep 2018 09:39:34: start X-correlation... INFO @ Sat, 15 Sep 2018 09:39:34: end of X-cor INFO @ Sat, 15 Sep 2018 09:39:34: #2 finished! INFO @ Sat, 15 Sep 2018 09:39:34: #2 predicted fragment length is 242 bps INFO @ Sat, 15 Sep 2018 09:39:34: #2 alternative fragment length(s) may be 242 bps INFO @ Sat, 15 Sep 2018 09:39:34: #2.2 Generate R script for model : SRX2226581.10_model.r INFO @ Sat, 15 Sep 2018 09:39:34: #3 Call peaks... INFO @ Sat, 15 Sep 2018 09:39:34: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 15 Sep 2018 09:39:59: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:40:00: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:40:01: #3 Call peaks for each chromosome... INFO @ Sat, 15 Sep 2018 09:40:15: #4 Write output xls file... SRX2226581.20_peaks.xls INFO @ Sat, 15 Sep 2018 09:40:15: #4 Write peak in narrowPeak format file... SRX2226581.20_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:40:15: #4 Write summits bed file... SRX2226581.20_summits.bed INFO @ Sat, 15 Sep 2018 09:40:15: Done! pass1 - making usageList (36 chroms): 1 millis pass2 - checking and writing primary data (332 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:40:16: #4 Write output xls file... SRX2226581.10_peaks.xls INFO @ Sat, 15 Sep 2018 09:40:16: #4 Write peak in narrowPeak format file... SRX2226581.10_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:40:16: #4 Write summits bed file... SRX2226581.10_summits.bed INFO @ Sat, 15 Sep 2018 09:40:16: Done! pass1 - making usageList (53 chroms): 1 millis pass2 - checking and writing primary data (915 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 15 Sep 2018 09:40:16: #4 Write output xls file... SRX2226581.05_peaks.xls INFO @ Sat, 15 Sep 2018 09:40:16: #4 Write peak in narrowPeak format file... SRX2226581.05_peaks.narrowPeak INFO @ Sat, 15 Sep 2018 09:40:16: #4 Write summits bed file... SRX2226581.05_summits.bed INFO @ Sat, 15 Sep 2018 09:40:16: Done! pass1 - making usageList (77 chroms): 3 millis pass2 - checking and writing primary data (3342 records, 4 fields): 15 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。