Job ID = 11171310 sra ファイルのダウンロード中... Completed: 218031K bytes transferred in 8 seconds (211442K 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 7618844 spots for /home/okishinya/chipatlas/results/dm3/SRX3032294/SRR5863984.sra Written 7618844 spots for /home/okishinya/chipatlas/results/dm3/SRX3032294/SRR5863984.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: 00:00:00 Time loading forward index: 00:00:00 Time loading mirror index: 00:00:00 Multiseed full-index search: 00:03:20 7618844 reads; of these: 7618844 (100.00%) were unpaired; of these: 1216171 (15.96%) aligned 0 times 5648875 (74.14%) aligned exactly 1 time 753798 (9.89%) aligned >1 times 84.04% overall alignment rate Time searching: 00:03:20 Overall time: 00:03:20 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 3368381 / 6402673 = 0.5261 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, 08 Sep 2018 13:41:27: # Command line: callpeak -t SRX3032294.bam -f BAM -g dm -n SRX3032294.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3032294.10 # format = BAM # ChIP-seq file = ['SRX3032294.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:41:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:41:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:41:27: # Command line: callpeak -t SRX3032294.bam -f BAM -g dm -n SRX3032294.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3032294.05 # format = BAM # ChIP-seq file = ['SRX3032294.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:41:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:41:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:41:27: # Command line: callpeak -t SRX3032294.bam -f BAM -g dm -n SRX3032294.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3032294.20 # format = BAM # ChIP-seq file = ['SRX3032294.bam'] # control file = None # effective genome size = 1.20e+08 # 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, 08 Sep 2018 13:41:27: #1 read tag files... INFO @ Sat, 08 Sep 2018 13:41:27: #1 read treatment tags... INFO @ Sat, 08 Sep 2018 13:41:33: 1000000 INFO @ Sat, 08 Sep 2018 13:41:33: 1000000 INFO @ Sat, 08 Sep 2018 13:41:33: 1000000 INFO @ Sat, 08 Sep 2018 13:41:40: 2000000 INFO @ Sat, 08 Sep 2018 13:41:40: 2000000 INFO @ Sat, 08 Sep 2018 13:41:40: 2000000 INFO @ Sat, 08 Sep 2018 13:41:47: 3000000 INFO @ Sat, 08 Sep 2018 13:41:47: #1 tag size is determined as 74 bps INFO @ Sat, 08 Sep 2018 13:41:47: #1 tag size = 74 INFO @ Sat, 08 Sep 2018 13:41:47: #1 total tags in treatment: 3034292 INFO @ Sat, 08 Sep 2018 13:41:47: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:41:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:41:47: #1 tags after filtering in treatment: 3034292 INFO @ Sat, 08 Sep 2018 13:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:41:47: #1 finished! INFO @ Sat, 08 Sep 2018 13:41:47: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:41:47: 3000000 INFO @ Sat, 08 Sep 2018 13:41:47: 3000000 INFO @ Sat, 08 Sep 2018 13:41:47: #1 tag size is determined as 74 bps INFO @ Sat, 08 Sep 2018 13:41:47: #1 tag size = 74 INFO @ Sat, 08 Sep 2018 13:41:47: #1 total tags in treatment: 3034292 INFO @ Sat, 08 Sep 2018 13:41:47: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:41:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:41:47: #1 tags after filtering in treatment: 3034292 INFO @ Sat, 08 Sep 2018 13:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:41:47: #1 finished! INFO @ Sat, 08 Sep 2018 13:41:47: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:41:47: #1 tag size is determined as 74 bps INFO @ Sat, 08 Sep 2018 13:41:47: #1 tag size = 74 INFO @ Sat, 08 Sep 2018 13:41:47: #1 total tags in treatment: 3034292 INFO @ Sat, 08 Sep 2018 13:41:47: #1 user defined the maximum tags... INFO @ Sat, 08 Sep 2018 13:41:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 08 Sep 2018 13:41:47: #1 tags after filtering in treatment: 3034292 INFO @ Sat, 08 Sep 2018 13:41:47: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 08 Sep 2018 13:41:47: #1 finished! INFO @ Sat, 08 Sep 2018 13:41:47: #2 Build Peak Model... INFO @ Sat, 08 Sep 2018 13:41:47: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 08 Sep 2018 13:41:47: #2 number of paired peaks: 7353 INFO @ Sat, 08 Sep 2018 13:41:47: start model_add_line... INFO @ Sat, 08 Sep 2018 13:41:47: start X-correlation... INFO @ Sat, 08 Sep 2018 13:41:47: end of X-cor INFO @ Sat, 08 Sep 2018 13:41:47: #2 finished! INFO @ Sat, 08 Sep 2018 13:41:47: #2 predicted fragment length is 154 bps INFO @ Sat, 08 Sep 2018 13:41:47: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 08 Sep 2018 13:41:47: #2.2 Generate R script for model : SRX3032294.10_model.r INFO @ Sat, 08 Sep 2018 13:41:47: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:41:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:41:48: #2 number of paired peaks: 7353 INFO @ Sat, 08 Sep 2018 13:41:48: start model_add_line... INFO @ Sat, 08 Sep 2018 13:41:48: start X-correlation... INFO @ Sat, 08 Sep 2018 13:41:48: end of X-cor INFO @ Sat, 08 Sep 2018 13:41:48: #2 finished! INFO @ Sat, 08 Sep 2018 13:41:48: #2 predicted fragment length is 154 bps INFO @ Sat, 08 Sep 2018 13:41:48: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 08 Sep 2018 13:41:48: #2.2 Generate R script for model : SRX3032294.05_model.r INFO @ Sat, 08 Sep 2018 13:41:48: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:41:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:41:48: #2 number of paired peaks: 7353 INFO @ Sat, 08 Sep 2018 13:41:48: start model_add_line... INFO @ Sat, 08 Sep 2018 13:41:48: start X-correlation... INFO @ Sat, 08 Sep 2018 13:41:48: end of X-cor INFO @ Sat, 08 Sep 2018 13:41:48: #2 finished! INFO @ Sat, 08 Sep 2018 13:41:48: #2 predicted fragment length is 154 bps INFO @ Sat, 08 Sep 2018 13:41:48: #2 alternative fragment length(s) may be 154 bps INFO @ Sat, 08 Sep 2018 13:41:48: #2.2 Generate R script for model : SRX3032294.20_model.r INFO @ Sat, 08 Sep 2018 13:41:48: #3 Call peaks... INFO @ Sat, 08 Sep 2018 13:41:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 08 Sep 2018 13:41:55: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:41:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:41:56: #3 Call peaks for each chromosome... INFO @ Sat, 08 Sep 2018 13:42:00: #4 Write output xls file... SRX3032294.10_peaks.xls INFO @ Sat, 08 Sep 2018 13:42:00: #4 Write peak in narrowPeak format file... SRX3032294.10_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:42:00: #4 Write summits bed file... SRX3032294.10_summits.bed INFO @ Sat, 08 Sep 2018 13:42:00: Done! pass1 - making usageList (13 chroms): 2 millis pass2 - checking and writing primary data (4728 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:42:00: #4 Write output xls file... SRX3032294.05_peaks.xls INFO @ Sat, 08 Sep 2018 13:42:00: #4 Write peak in narrowPeak format file... SRX3032294.05_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:42:00: #4 Write summits bed file... SRX3032294.05_summits.bed INFO @ Sat, 08 Sep 2018 13:42:00: Done! pass1 - making usageList (14 chroms): 3 millis pass2 - checking and writing primary data (6975 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sat, 08 Sep 2018 13:42:01: #4 Write output xls file... SRX3032294.20_peaks.xls INFO @ Sat, 08 Sep 2018 13:42:01: #4 Write peak in narrowPeak format file... SRX3032294.20_peaks.narrowPeak INFO @ Sat, 08 Sep 2018 13:42:01: #4 Write summits bed file... SRX3032294.20_summits.bed INFO @ Sat, 08 Sep 2018 13:42:01: Done! pass1 - making usageList (11 chroms): 8 millis pass2 - checking and writing primary data (2510 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。