Job ID = 10937657 sra ファイルのダウンロード中... Completed: 100261K bytes transferred in 11 seconds (72870K 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 2992610 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3463305/SRR6367844.sra Written 2992610 spots for /home/okishinya/chipatlas/results/sacCer3/SRX3463305/SRR6367844.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: 00:00:25 2992610 reads; of these: 2992610 (100.00%) were unpaired; of these: 423985 (14.17%) aligned 0 times 2279832 (76.18%) aligned exactly 1 time 288793 (9.65%) aligned >1 times 85.83% overall alignment rate Time searching: 00:00:25 Overall time: 00:00:25 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] 842231 / 2568625 = 0.3279 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, 10 Aug 2018 02:46:44: # Command line: callpeak -t SRX3463305.bam -f BAM -g 12100000 -n SRX3463305.10 -q 1e-10 # ARGUMENTS LIST: # name = SRX3463305.10 # format = BAM # ChIP-seq file = ['SRX3463305.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 @ Fri, 10 Aug 2018 02:46:44: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:46:44: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:46:44: # Command line: callpeak -t SRX3463305.bam -f BAM -g 12100000 -n SRX3463305.20 -q 1e-20 # ARGUMENTS LIST: # name = SRX3463305.20 # format = BAM # ChIP-seq file = ['SRX3463305.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 @ Fri, 10 Aug 2018 02:46:44: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:46:44: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:46:44: # Command line: callpeak -t SRX3463305.bam -f BAM -g 12100000 -n SRX3463305.05 -q 1e-05 # ARGUMENTS LIST: # name = SRX3463305.05 # format = BAM # ChIP-seq file = ['SRX3463305.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 @ Fri, 10 Aug 2018 02:46:44: #1 read tag files... INFO @ Fri, 10 Aug 2018 02:46:44: #1 read treatment tags... INFO @ Fri, 10 Aug 2018 02:46:50: 1000000 INFO @ Fri, 10 Aug 2018 02:46:51: 1000000 INFO @ Fri, 10 Aug 2018 02:46:51: 1000000 INFO @ Fri, 10 Aug 2018 02:46:54: #1 tag size is determined as 45 bps INFO @ Fri, 10 Aug 2018 02:46:54: #1 tag size = 45 INFO @ Fri, 10 Aug 2018 02:46:54: #1 total tags in treatment: 1726394 INFO @ Fri, 10 Aug 2018 02:46:54: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:46:54: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:46:54: #1 tags after filtering in treatment: 1726394 INFO @ Fri, 10 Aug 2018 02:46:54: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 02:46:54: #1 finished! INFO @ Fri, 10 Aug 2018 02:46:54: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:46:54: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:46:54: #2 number of paired peaks: 177 WARNING @ Fri, 10 Aug 2018 02:46:54: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 10 Aug 2018 02:46:54: start model_add_line... INFO @ Fri, 10 Aug 2018 02:46:54: start X-correlation... INFO @ Fri, 10 Aug 2018 02:46:54: end of X-cor INFO @ Fri, 10 Aug 2018 02:46:54: #2 finished! INFO @ Fri, 10 Aug 2018 02:46:54: #2 predicted fragment length is 123 bps INFO @ Fri, 10 Aug 2018 02:46:54: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 10 Aug 2018 02:46:54: #2.2 Generate R script for model : SRX3463305.10_model.r INFO @ Fri, 10 Aug 2018 02:46:54: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:46:54: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:46:56: #1 tag size is determined as 45 bps INFO @ Fri, 10 Aug 2018 02:46:56: #1 tag size = 45 INFO @ Fri, 10 Aug 2018 02:46:56: #1 total tags in treatment: 1726394 INFO @ Fri, 10 Aug 2018 02:46:56: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:46:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:46:56: #1 tags after filtering in treatment: 1726394 INFO @ Fri, 10 Aug 2018 02:46:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 02:46:56: #1 finished! INFO @ Fri, 10 Aug 2018 02:46:56: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:46:56: #2 number of paired peaks: 177 WARNING @ Fri, 10 Aug 2018 02:46:56: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 10 Aug 2018 02:46:56: start model_add_line... INFO @ Fri, 10 Aug 2018 02:46:56: start X-correlation... INFO @ Fri, 10 Aug 2018 02:46:56: end of X-cor INFO @ Fri, 10 Aug 2018 02:46:56: #2 finished! INFO @ Fri, 10 Aug 2018 02:46:56: #2 predicted fragment length is 123 bps INFO @ Fri, 10 Aug 2018 02:46:56: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 10 Aug 2018 02:46:56: #2.2 Generate R script for model : SRX3463305.05_model.r INFO @ Fri, 10 Aug 2018 02:46:56: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:46:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:46:56: #1 tag size is determined as 45 bps INFO @ Fri, 10 Aug 2018 02:46:56: #1 tag size = 45 INFO @ Fri, 10 Aug 2018 02:46:56: #1 total tags in treatment: 1726394 INFO @ Fri, 10 Aug 2018 02:46:56: #1 user defined the maximum tags... INFO @ Fri, 10 Aug 2018 02:46:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 10 Aug 2018 02:46:56: #1 tags after filtering in treatment: 1726394 INFO @ Fri, 10 Aug 2018 02:46:56: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 10 Aug 2018 02:46:56: #1 finished! INFO @ Fri, 10 Aug 2018 02:46:56: #2 Build Peak Model... INFO @ Fri, 10 Aug 2018 02:46:56: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 10 Aug 2018 02:46:56: #2 number of paired peaks: 177 WARNING @ Fri, 10 Aug 2018 02:46:56: Fewer paired peaks (177) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 177 pairs to build model! INFO @ Fri, 10 Aug 2018 02:46:56: start model_add_line... INFO @ Fri, 10 Aug 2018 02:46:56: start X-correlation... INFO @ Fri, 10 Aug 2018 02:46:56: end of X-cor INFO @ Fri, 10 Aug 2018 02:46:56: #2 finished! INFO @ Fri, 10 Aug 2018 02:46:56: #2 predicted fragment length is 123 bps INFO @ Fri, 10 Aug 2018 02:46:56: #2 alternative fragment length(s) may be 123 bps INFO @ Fri, 10 Aug 2018 02:46:56: #2.2 Generate R script for model : SRX3463305.20_model.r INFO @ Fri, 10 Aug 2018 02:46:56: #3 Call peaks... INFO @ Fri, 10 Aug 2018 02:46:56: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 10 Aug 2018 02:46:59: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:47:01: #3 Call peaks for each chromosome... INFO @ Fri, 10 Aug 2018 02:47:01: #4 Write output xls file... SRX3463305.10_peaks.xls INFO @ Fri, 10 Aug 2018 02:47:01: #4 Write peak in narrowPeak format file... SRX3463305.10_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:47:01: #4 Write summits bed file... SRX3463305.10_summits.bed INFO @ Fri, 10 Aug 2018 02:47:01: Done! pass1 - making usageList (17 chroms): 1 millis INFO @ Fri, 10 Aug 2018 02:47:01: #3 Call peaks for each chromosome... pass2 - checking and writing primary data (861 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:47:03: #4 Write output xls file... SRX3463305.05_peaks.xls INFO @ Fri, 10 Aug 2018 02:47:03: #4 Write peak in narrowPeak format file... SRX3463305.05_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:47:03: #4 Write summits bed file... SRX3463305.05_summits.bed INFO @ Fri, 10 Aug 2018 02:47:03: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (1576 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Fri, 10 Aug 2018 02:47:03: #4 Write output xls file... SRX3463305.20_peaks.xls INFO @ Fri, 10 Aug 2018 02:47:03: #4 Write peak in narrowPeak format file... SRX3463305.20_peaks.narrowPeak INFO @ Fri, 10 Aug 2018 02:47:03: #4 Write summits bed file... SRX3463305.20_summits.bed INFO @ Fri, 10 Aug 2018 02:47:03: Done! pass1 - making usageList (17 chroms): 1 millis pass2 - checking and writing primary data (428 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。