Job ID = 2009921 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 2,623,119 reads read : 5,246,238 reads written : 5,246,238 rm: cannot remove ‘[DSE]RR*’: No such file or directory 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: 00:01:49 2623119 reads; of these: 2623119 (100.00%) were paired; of these: 1517316 (57.84%) aligned concordantly 0 times 986131 (37.59%) aligned concordantly exactly 1 time 119672 (4.56%) aligned concordantly >1 times ---- 1517316 pairs aligned concordantly 0 times; of these: 33805 (2.23%) aligned discordantly 1 time ---- 1483511 pairs aligned 0 times concordantly or discordantly; of these: 2967022 mates make up the pairs; of these: 1961994 (66.13%) aligned 0 times 875950 (29.52%) aligned exactly 1 time 129078 (4.35%) aligned >1 times 62.60% overall alignment rate Time searching: 00:01:49 Overall time: 00:01:49 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_rmdup_core] processing reference chrI... [bam_rmdup_core] processing reference chrII... [bam_rmdup_core] processing reference chrIII... [bam_rmdup_core] processing reference chrIV... [bam_rmdup_core] processing reference chrIX... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrV... [bam_rmdup_core] processing reference chrVI... [bam_rmdup_core] processing reference chrVII... [bam_rmdup_core] processing reference chrVIII... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXI... [bam_rmdup_core] processing reference chrXII... [bam_rmdup_core] processing reference chrXIII... [bam_rmdup_core] processing reference chrXIV... [bam_rmdup_core] processing reference chrXV... [bam_rmdup_core] processing reference chrXVI... [bam_rmdup_core] 2186 / 1111365 = 0.0020 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, 05 Jul 2019 20:48:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.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, 05 Jul 2019 20:48:34: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:48:34: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:48:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.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, 05 Jul 2019 20:48:35: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:48:35: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:48:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.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, 05 Jul 2019 20:48:36: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:48:36: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:48:41: 1000000 INFO @ Fri, 05 Jul 2019 20:48:44: 1000000 INFO @ Fri, 05 Jul 2019 20:48:45: 1000000 INFO @ Fri, 05 Jul 2019 20:48:48: 2000000 INFO @ Fri, 05 Jul 2019 20:48:53: 2000000 INFO @ Fri, 05 Jul 2019 20:48:54: 2000000 INFO @ Fri, 05 Jul 2019 20:48:55: 3000000 INFO @ Fri, 05 Jul 2019 20:48:56: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:48:56: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:48:56: #1 total tags in treatment: 1103620 INFO @ Fri, 05 Jul 2019 20:48:56: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:48:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 20:48:57: #1 tags after filtering in treatment: 992466 INFO @ Fri, 05 Jul 2019 20:48:57: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 05 Jul 2019 20:48:57: #1 finished! INFO @ Fri, 05 Jul 2019 20:48:57: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:48:57: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:48:57: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 20:48:57: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 20:48:57: start model_add_line... INFO @ Fri, 05 Jul 2019 20:48:57: start X-correlation... INFO @ Fri, 05 Jul 2019 20:48:57: end of X-cor INFO @ Fri, 05 Jul 2019 20:48:57: #2 finished! INFO @ Fri, 05 Jul 2019 20:48:57: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 20:48:57: #2 alternative fragment length(s) may be 2,79,133,159,208,532,563,598 bps INFO @ Fri, 05 Jul 2019 20:48:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.05_model.r INFO @ Fri, 05 Jul 2019 20:48:57: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:48:57: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:49:00: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:49:01: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:49:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:49:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.05_summits.bed INFO @ Fri, 05 Jul 2019 20:49:01: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (19 records, 4 fields): 8 millis INFO @ Fri, 05 Jul 2019 20:49:03: 3000000 INFO @ Fri, 05 Jul 2019 20:49:03: 3000000 CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 20:49:05: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:49:05: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:49:05: #1 total tags in treatment: 1103620 INFO @ Fri, 05 Jul 2019 20:49:05: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:49:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 20:49:06: #1 tags after filtering in treatment: 992466 INFO @ Fri, 05 Jul 2019 20:49:06: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 05 Jul 2019 20:49:06: #1 finished! INFO @ Fri, 05 Jul 2019 20:49:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:49:06: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 20:49:06: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 20:49:06: start model_add_line... INFO @ Fri, 05 Jul 2019 20:49:06: start X-correlation... INFO @ Fri, 05 Jul 2019 20:49:06: end of X-cor INFO @ Fri, 05 Jul 2019 20:49:06: #2 finished! INFO @ Fri, 05 Jul 2019 20:49:06: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 20:49:06: #2 alternative fragment length(s) may be 2,79,133,159,208,532,563,598 bps INFO @ Fri, 05 Jul 2019 20:49:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.20_model.r INFO @ Fri, 05 Jul 2019 20:49:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:49:06: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 20:49:06: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 20:49:06: #1 total tags in treatment: 1103620 INFO @ Fri, 05 Jul 2019 20:49:06: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:49:06: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Fri, 05 Jul 2019 20:49:06: #1 tags after filtering in treatment: 992466 INFO @ Fri, 05 Jul 2019 20:49:06: #1 Redundant rate of treatment: 0.10 INFO @ Fri, 05 Jul 2019 20:49:06: #1 finished! INFO @ Fri, 05 Jul 2019 20:49:06: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:49:06: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:49:06: #2 number of paired peaks: 164 WARNING @ Fri, 05 Jul 2019 20:49:06: Fewer paired peaks (164) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 164 pairs to build model! INFO @ Fri, 05 Jul 2019 20:49:06: start model_add_line... INFO @ Fri, 05 Jul 2019 20:49:06: start X-correlation... INFO @ Fri, 05 Jul 2019 20:49:06: end of X-cor INFO @ Fri, 05 Jul 2019 20:49:06: #2 finished! INFO @ Fri, 05 Jul 2019 20:49:06: #2 predicted fragment length is 133 bps INFO @ Fri, 05 Jul 2019 20:49:06: #2 alternative fragment length(s) may be 2,79,133,159,208,532,563,598 bps INFO @ Fri, 05 Jul 2019 20:49:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.10_model.r INFO @ Fri, 05 Jul 2019 20:49:06: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:49:06: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:49:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:49:09: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:49:10: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:49:11: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:49:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:49:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.10_summits.bed INFO @ Fri, 05 Jul 2019 20:49:11: Done! pass1 - making usageList (2 chroms): 1 millis pass2 - checking and writing primary data (7 records, 4 fields): 1 millis INFO @ Fri, 05 Jul 2019 20:49:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:49:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX2339856/SRX2339856.20_summits.bed INFO @ Fri, 05 Jul 2019 20:49:11: Done! pass1 - making usageList (1 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。