Job ID = 11296942 sra ファイルのダウンロード中... Completed: 17482K bytes transferred in 2 seconds (48521K 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 937598 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856356/SRR6908173.sra Written 937598 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3856356/SRR6908173.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: 00:00:15 937598 reads; of these: 937598 (100.00%) were unpaired; of these: 42075 (4.49%) aligned 0 times 579562 (61.81%) aligned exactly 1 time 315961 (33.70%) aligned >1 times 95.51% overall alignment rate Time searching: 00:00:15 Overall time: 00:00:15 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 17 sequences. [bam_rmdupse_core] 475284 / 895523 = 0.5307 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 @ Mon, 05 Nov 2018 17:58:34: # Command line: callpeak -t SRX3856356.bam -f BAM -g 12100000 -n SRX3856356.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3856356.05 # format = BAM # ChIP-seq file = ['SRX3856356.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Mon, 05 Nov 2018 17:58:34: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:58:34: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:58:34: # Command line: callpeak -t SRX3856356.bam -f BAM -g 12100000 -n SRX3856356.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3856356.20 # format = BAM # ChIP-seq file = ['SRX3856356.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Mon, 05 Nov 2018 17:58:34: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:58:34: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:58:34: # Command line: callpeak -t SRX3856356.bam -f BAM -g 12100000 -n SRX3856356.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3856356.10 # format = BAM # ChIP-seq file = ['SRX3856356.bam'] # control file = None # effective genome size = 1.21e+07 # 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 @ Mon, 05 Nov 2018 17:58:34: #1 read tag files... INFO @ Mon, 05 Nov 2018 17:58:34: #1 read treatment tags... INFO @ Mon, 05 Nov 2018 17:58:37: #1 tag size is determined as 58 bps INFO @ Mon, 05 Nov 2018 17:58:37: #1 tag size = 58 INFO @ Mon, 05 Nov 2018 17:58:37: #1 total tags in treatment: 420239 INFO @ Mon, 05 Nov 2018 17:58:37: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:58:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 17:58:37: #1 tags after filtering in treatment: 420239 INFO @ Mon, 05 Nov 2018 17:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:58:37: #1 finished! INFO @ Mon, 05 Nov 2018 17:58:37: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:58:37: #2 number of paired peaks: 382 WARNING @ Mon, 05 Nov 2018 17:58:37: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Mon, 05 Nov 2018 17:58:37: start model_add_line... INFO @ Mon, 05 Nov 2018 17:58:37: start X-correlation... INFO @ Mon, 05 Nov 2018 17:58:37: end of X-cor INFO @ Mon, 05 Nov 2018 17:58:37: #2 finished! INFO @ Mon, 05 Nov 2018 17:58:37: #2 predicted fragment length is 200 bps INFO @ Mon, 05 Nov 2018 17:58:37: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 05 Nov 2018 17:58:37: #2.2 Generate R script for model : SRX3856356.20_model.r INFO @ Mon, 05 Nov 2018 17:58:37: #3 Call peaks... INFO @ Mon, 05 Nov 2018 17:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Nov 2018 17:58:37: #1 tag size is determined as 58 bps INFO @ Mon, 05 Nov 2018 17:58:37: #1 tag size = 58 INFO @ Mon, 05 Nov 2018 17:58:37: #1 total tags in treatment: 420239 INFO @ Mon, 05 Nov 2018 17:58:37: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:58:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 17:58:37: #1 tags after filtering in treatment: 420239 INFO @ Mon, 05 Nov 2018 17:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:58:37: #1 finished! INFO @ Mon, 05 Nov 2018 17:58:37: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:58:37: #1 tag size is determined as 58 bps INFO @ Mon, 05 Nov 2018 17:58:37: #1 tag size = 58 INFO @ Mon, 05 Nov 2018 17:58:37: #1 total tags in treatment: 420239 INFO @ Mon, 05 Nov 2018 17:58:37: #1 user defined the maximum tags... INFO @ Mon, 05 Nov 2018 17:58:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 05 Nov 2018 17:58:37: #1 tags after filtering in treatment: 420239 INFO @ Mon, 05 Nov 2018 17:58:37: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 05 Nov 2018 17:58:37: #1 finished! INFO @ Mon, 05 Nov 2018 17:58:37: #2 Build Peak Model... INFO @ Mon, 05 Nov 2018 17:58:37: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 05 Nov 2018 17:58:37: #2 number of paired peaks: 382 WARNING @ Mon, 05 Nov 2018 17:58:37: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Mon, 05 Nov 2018 17:58:37: start model_add_line... INFO @ Mon, 05 Nov 2018 17:58:37: start X-correlation... INFO @ Mon, 05 Nov 2018 17:58:37: end of X-cor INFO @ Mon, 05 Nov 2018 17:58:37: #2 finished! INFO @ Mon, 05 Nov 2018 17:58:37: #2 predicted fragment length is 200 bps INFO @ Mon, 05 Nov 2018 17:58:37: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 05 Nov 2018 17:58:37: #2.2 Generate R script for model : SRX3856356.10_model.r INFO @ Mon, 05 Nov 2018 17:58:37: #2 number of paired peaks: 382 WARNING @ Mon, 05 Nov 2018 17:58:37: Fewer paired peaks (382) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 382 pairs to build model! INFO @ Mon, 05 Nov 2018 17:58:37: start model_add_line... INFO @ Mon, 05 Nov 2018 17:58:37: #3 Call peaks... INFO @ Mon, 05 Nov 2018 17:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Nov 2018 17:58:37: start X-correlation... INFO @ Mon, 05 Nov 2018 17:58:37: end of X-cor INFO @ Mon, 05 Nov 2018 17:58:37: #2 finished! INFO @ Mon, 05 Nov 2018 17:58:37: #2 predicted fragment length is 200 bps INFO @ Mon, 05 Nov 2018 17:58:37: #2 alternative fragment length(s) may be 200 bps INFO @ Mon, 05 Nov 2018 17:58:37: #2.2 Generate R script for model : SRX3856356.05_model.r INFO @ Mon, 05 Nov 2018 17:58:37: #3 Call peaks... INFO @ Mon, 05 Nov 2018 17:58:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 05 Nov 2018 17:58:40: #3 Call peaks for each chromosome... INFO @ Mon, 05 Nov 2018 17:58:40: #3 Call peaks for each chromosome... INFO @ Mon, 05 Nov 2018 17:58:40: #3 Call peaks for each chromosome... INFO @ Mon, 05 Nov 2018 17:58:40: #4 Write output xls file... SRX3856356.20_peaks.xls INFO @ Mon, 05 Nov 2018 17:58:40: #4 Write peak in narrowPeak format file... SRX3856356.20_peaks.narrowPeak INFO @ Mon, 05 Nov 2018 17:58:40: #4 Write summits bed file... SRX3856356.20_summits.bed INFO @ Mon, 05 Nov 2018 17:58:40: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (287 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 05 Nov 2018 17:58:40: #4 Write output xls file... SRX3856356.10_peaks.xls INFO @ Mon, 05 Nov 2018 17:58:40: #4 Write peak in narrowPeak format file... SRX3856356.10_peaks.narrowPeak INFO @ Mon, 05 Nov 2018 17:58:40: #4 Write summits bed file... SRX3856356.10_summits.bed INFO @ Mon, 05 Nov 2018 17:58:40: Done! INFO @ Mon, 05 Nov 2018 17:58:40: #4 Write output xls file... SRX3856356.05_peaks.xls INFO @ Mon, 05 Nov 2018 17:58:40: #4 Write peak in narrowPeak format file... SRX3856356.05_peaks.narrowPeak INFO @ Mon, 05 Nov 2018 17:58:40: #4 Write summits bed file... SRX3856356.05_summits.bed INFO @ Mon, 05 Nov 2018 17:58:40: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (323 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。