Job ID = 4303119 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,854,365 reads read : 3,854,365 reads written : 3,854,365 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR1552264.sra.cache’: 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: 00:00:45 3854365 reads; of these: 3854365 (100.00%) were unpaired; of these: 394140 (10.23%) aligned 0 times 2760499 (71.62%) aligned exactly 1 time 699726 (18.15%) aligned >1 times 89.77% overall alignment rate Time searching: 00:00:45 Overall time: 00:00:45 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] 1545864 / 3460225 = 0.4468 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:46:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.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 @ Thu, 12 Dec 2019 00:46:09: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:46:09: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:46:13: 1000000 INFO @ Thu, 12 Dec 2019 00:46:17: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:46:17: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:46:17: #1 total tags in treatment: 1914361 INFO @ Thu, 12 Dec 2019 00:46:17: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:46:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:46:17: #1 tags after filtering in treatment: 1914361 INFO @ Thu, 12 Dec 2019 00:46:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:46:17: #1 finished! INFO @ Thu, 12 Dec 2019 00:46:17: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:46:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:46:18: #2 number of paired peaks: 710 WARNING @ Thu, 12 Dec 2019 00:46:18: Fewer paired peaks (710) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 710 pairs to build model! INFO @ Thu, 12 Dec 2019 00:46:18: start model_add_line... INFO @ Thu, 12 Dec 2019 00:46:18: start X-correlation... INFO @ Thu, 12 Dec 2019 00:46:18: end of X-cor INFO @ Thu, 12 Dec 2019 00:46:18: #2 finished! INFO @ Thu, 12 Dec 2019 00:46:18: #2 predicted fragment length is 82 bps INFO @ Thu, 12 Dec 2019 00:46:18: #2 alternative fragment length(s) may be 82 bps INFO @ Thu, 12 Dec 2019 00:46:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.05_model.r INFO @ Thu, 12 Dec 2019 00:46:18: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:46:18: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:46:21: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:46:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:46:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:46:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.05_summits.bed INFO @ Thu, 12 Dec 2019 00:46:22: Done! pass1 - making usageList (13 chroms): 0 millis pass2 - checking and writing primary data (1003 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:46:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.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 @ Thu, 12 Dec 2019 00:46:39: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:46:39: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:46:43: 1000000 INFO @ Thu, 12 Dec 2019 00:46:47: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:46:47: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:46:47: #1 total tags in treatment: 1914361 INFO @ Thu, 12 Dec 2019 00:46:47: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:46:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:46:47: #1 tags after filtering in treatment: 1914361 INFO @ Thu, 12 Dec 2019 00:46:47: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:46:47: #1 finished! INFO @ Thu, 12 Dec 2019 00:46:47: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:46:47: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:46:47: #2 number of paired peaks: 710 WARNING @ Thu, 12 Dec 2019 00:46:47: Fewer paired peaks (710) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 710 pairs to build model! INFO @ Thu, 12 Dec 2019 00:46:47: start model_add_line... INFO @ Thu, 12 Dec 2019 00:46:47: start X-correlation... INFO @ Thu, 12 Dec 2019 00:46:47: end of X-cor INFO @ Thu, 12 Dec 2019 00:46:47: #2 finished! INFO @ Thu, 12 Dec 2019 00:46:47: #2 predicted fragment length is 82 bps INFO @ Thu, 12 Dec 2019 00:46:47: #2 alternative fragment length(s) may be 82 bps INFO @ Thu, 12 Dec 2019 00:46:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.10_model.r INFO @ Thu, 12 Dec 2019 00:46:47: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:46:47: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:46:50: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:46:52: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:46:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:46:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.10_summits.bed INFO @ Thu, 12 Dec 2019 00:46:52: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (626 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:47:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.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 @ Thu, 12 Dec 2019 00:47:09: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:47:09: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:47:13: 1000000 INFO @ Thu, 12 Dec 2019 00:47:17: #1 tag size is determined as 36 bps INFO @ Thu, 12 Dec 2019 00:47:17: #1 tag size = 36 INFO @ Thu, 12 Dec 2019 00:47:17: #1 total tags in treatment: 1914361 INFO @ Thu, 12 Dec 2019 00:47:17: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:47:17: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:47:17: #1 tags after filtering in treatment: 1914361 INFO @ Thu, 12 Dec 2019 00:47:17: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:47:17: #1 finished! INFO @ Thu, 12 Dec 2019 00:47:17: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:47:17: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:47:17: #2 number of paired peaks: 710 WARNING @ Thu, 12 Dec 2019 00:47:17: Fewer paired peaks (710) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 710 pairs to build model! INFO @ Thu, 12 Dec 2019 00:47:17: start model_add_line... INFO @ Thu, 12 Dec 2019 00:47:17: start X-correlation... INFO @ Thu, 12 Dec 2019 00:47:17: end of X-cor INFO @ Thu, 12 Dec 2019 00:47:17: #2 finished! INFO @ Thu, 12 Dec 2019 00:47:17: #2 predicted fragment length is 82 bps INFO @ Thu, 12 Dec 2019 00:47:17: #2 alternative fragment length(s) may be 82 bps INFO @ Thu, 12 Dec 2019 00:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.20_model.r INFO @ Thu, 12 Dec 2019 00:47:17: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:47:20: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:47:22: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:47:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:47:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX681795/SRX681795.20_summits.bed INFO @ Thu, 12 Dec 2019 00:47:22: Done! pass1 - making usageList (12 chroms): 1 millis pass2 - checking and writing primary data (286 records, 4 fields): 70 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。