Job ID = 11632620 sra ファイルのダウンロード中... Completed: 376997K bytes transferred in 7 seconds (423198K 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 14840266 spots for /home/okishinya/chipatlas/results/rn6/ERX1844922/ERR1780368.sra Written 14840266 spots for /home/okishinya/chipatlas/results/rn6/ERX1844922/ERR1780368.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: 00:00:01 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:05:36 14840266 reads; of these: 14840266 (100.00%) were unpaired; of these: 4498279 (30.31%) aligned 0 times 7370522 (49.67%) aligned exactly 1 time 2971465 (20.02%) aligned >1 times 69.69% overall alignment rate Time searching: 00:05:38 Overall time: 00:05:38 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_rmdupse_core] 8670114 / 10341987 = 0.8383 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 05:38:44: # Command line: callpeak -t ERX1844922.bam -f BAM -g 2.15e9 -n ERX1844922.20 -q 1e-20 # ARGUMENTS LIST: # name = ERX1844922.20 # format = BAM # ChIP-seq file = ['ERX1844922.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 05:38:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:38:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:38:44: # Command line: callpeak -t ERX1844922.bam -f BAM -g 2.15e9 -n ERX1844922.10 -q 1e-10 # ARGUMENTS LIST: # name = ERX1844922.10 # format = BAM # ChIP-seq file = ['ERX1844922.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 05:38:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:38:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:38:44: # Command line: callpeak -t ERX1844922.bam -f BAM -g 2.15e9 -n ERX1844922.05 -q 1e-05 # ARGUMENTS LIST: # name = ERX1844922.05 # format = BAM # ChIP-seq file = ['ERX1844922.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 05:38:44: #1 read tag files... INFO @ Fri, 15 Feb 2019 05:38:44: #1 read treatment tags... INFO @ Fri, 15 Feb 2019 05:38:50: 1000000 INFO @ Fri, 15 Feb 2019 05:38:50: 1000000 INFO @ Fri, 15 Feb 2019 05:38:50: 1000000 INFO @ Fri, 15 Feb 2019 05:38:54: #1 tag size is determined as 36 bps INFO @ Fri, 15 Feb 2019 05:38:54: #1 tag size = 36 INFO @ Fri, 15 Feb 2019 05:38:54: #1 total tags in treatment: 1671873 INFO @ Fri, 15 Feb 2019 05:38:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:38:54: #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 05:38:54: #1 tags after filtering in treatment: 1671561 INFO @ Fri, 15 Feb 2019 05:38:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:38:54: #1 finished! INFO @ Fri, 15 Feb 2019 05:38:54: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:38:54: #1 tag size is determined as 36 bps INFO @ Fri, 15 Feb 2019 05:38:54: #1 tag size = 36 INFO @ Fri, 15 Feb 2019 05:38:54: #1 total tags in treatment: 1671873 INFO @ Fri, 15 Feb 2019 05:38:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:38:54: #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 05:38:54: #1 tag size is determined as 36 bps INFO @ Fri, 15 Feb 2019 05:38:54: #1 tag size = 36 INFO @ Fri, 15 Feb 2019 05:38:54: #1 total tags in treatment: 1671873 INFO @ Fri, 15 Feb 2019 05:38:54: #1 user defined the maximum tags... INFO @ Fri, 15 Feb 2019 05:38:54: #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 05:38:54: #1 tags after filtering in treatment: 1671561 INFO @ Fri, 15 Feb 2019 05:38:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:38:54: #1 finished! INFO @ Fri, 15 Feb 2019 05:38:54: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:38:54: #1 tags after filtering in treatment: 1671561 INFO @ Fri, 15 Feb 2019 05:38:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 15 Feb 2019 05:38:54: #1 finished! INFO @ Fri, 15 Feb 2019 05:38:54: #2 Build Peak Model... INFO @ Fri, 15 Feb 2019 05:38:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 15 Feb 2019 05:39:00: #2 number of paired peaks: 175906 INFO @ Fri, 15 Feb 2019 05:39:00: start model_add_line... INFO @ Fri, 15 Feb 2019 05:39:00: start X-correlation... INFO @ Fri, 15 Feb 2019 05:39:00: end of X-cor INFO @ Fri, 15 Feb 2019 05:39:00: #2 finished! INFO @ Fri, 15 Feb 2019 05:39:00: #2 predicted fragment length is 83 bps INFO @ Fri, 15 Feb 2019 05:39:00: #2 alternative fragment length(s) may be 83,248,290 bps INFO @ Fri, 15 Feb 2019 05:39:00: #2.2 Generate R script for model : ERX1844922.20_model.r INFO @ Fri, 15 Feb 2019 05:39:00: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:39:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:39:00: #2 number of paired peaks: 175906 INFO @ Fri, 15 Feb 2019 05:39:00: start model_add_line... INFO @ Fri, 15 Feb 2019 05:39:00: #2 number of paired peaks: 175906 INFO @ Fri, 15 Feb 2019 05:39:00: start model_add_line... INFO @ Fri, 15 Feb 2019 05:39:00: start X-correlation... INFO @ Fri, 15 Feb 2019 05:39:00: end of X-cor INFO @ Fri, 15 Feb 2019 05:39:00: #2 finished! INFO @ Fri, 15 Feb 2019 05:39:00: #2 predicted fragment length is 83 bps INFO @ Fri, 15 Feb 2019 05:39:00: #2 alternative fragment length(s) may be 83,248,290 bps INFO @ Fri, 15 Feb 2019 05:39:00: #2.2 Generate R script for model : ERX1844922.10_model.r INFO @ Fri, 15 Feb 2019 05:39:00: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:39:00: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:39:01: start X-correlation... INFO @ Fri, 15 Feb 2019 05:39:01: end of X-cor INFO @ Fri, 15 Feb 2019 05:39:01: #2 finished! INFO @ Fri, 15 Feb 2019 05:39:01: #2 predicted fragment length is 83 bps INFO @ Fri, 15 Feb 2019 05:39:01: #2 alternative fragment length(s) may be 83,248,290 bps INFO @ Fri, 15 Feb 2019 05:39:01: #2.2 Generate R script for model : ERX1844922.05_model.r INFO @ Fri, 15 Feb 2019 05:39:01: #3 Call peaks... INFO @ Fri, 15 Feb 2019 05:39:01: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 15 Feb 2019 05:39:05: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:39:05: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:39:05: #3 Call peaks for each chromosome... INFO @ Fri, 15 Feb 2019 05:39:07: #4 Write output xls file... ERX1844922.20_peaks.xls INFO @ Fri, 15 Feb 2019 05:39:07: #4 Write peak in narrowPeak format file... ERX1844922.20_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:39:07: #4 Write summits bed file... ERX1844922.20_summits.bed INFO @ Fri, 15 Feb 2019 05:39:07: Done! pass1 - making usageList (25 chroms): 5 millis pass2 - checking and writing primary data (147 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 05:39:07: #4 Write output xls file... ERX1844922.10_peaks.xls INFO @ Fri, 15 Feb 2019 05:39:07: #4 Write peak in narrowPeak format file... ERX1844922.10_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:39:07: #4 Write summits bed file... ERX1844922.10_summits.bed INFO @ Fri, 15 Feb 2019 05:39:07: Done! pass1 - making usageList (32 chroms): 2 millis pass2 - checking and writing primary data (316 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 15 Feb 2019 05:39:07: #4 Write output xls file... ERX1844922.05_peaks.xls INFO @ Fri, 15 Feb 2019 05:39:07: #4 Write peak in narrowPeak format file... ERX1844922.05_peaks.narrowPeak INFO @ Fri, 15 Feb 2019 05:39:07: #4 Write summits bed file... ERX1844922.05_summits.bed INFO @ Fri, 15 Feb 2019 05:39:07: Done! pass1 - making usageList (49 chroms): 3 millis pass2 - checking and writing primary data (738 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。