Job ID = 2010018 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 130,832 reads read : 130,832 reads written : 130,832 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: 00:00:01 Multiseed full-index search: 00:00:01 130832 reads; of these: 130832 (100.00%) were unpaired; of these: 29212 (22.33%) aligned 0 times 86127 (65.83%) aligned exactly 1 time 15493 (11.84%) aligned >1 times 77.67% overall alignment rate Time searching: 00:00:02 Overall time: 00:00:02 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] 83330 / 101620 = 0.8200 in library ' ' BAM に変換しました。 Bed ファイルを作成中... BedGraph に変換中... BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。 INFO @ Fri, 05 Jul 2019 20:52:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.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 20:52:25: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:52:25: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:52:25: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 20:52:25: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 20:52:25: #1 total tags in treatment: 18290 INFO @ Fri, 05 Jul 2019 20:52:25: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:52:25: #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 20:52:25: #1 tags after filtering in treatment: 18290 INFO @ Fri, 05 Jul 2019 20:52:25: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:52:25: #1 finished! INFO @ Fri, 05 Jul 2019 20:52:25: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:52:25: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:52:25: #2 number of paired peaks: 399 WARNING @ Fri, 05 Jul 2019 20:52:25: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Fri, 05 Jul 2019 20:52:25: start model_add_line... INFO @ Fri, 05 Jul 2019 20:52:25: start X-correlation... INFO @ Fri, 05 Jul 2019 20:52:26: end of X-cor INFO @ Fri, 05 Jul 2019 20:52:26: #2 finished! INFO @ Fri, 05 Jul 2019 20:52:26: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 20:52:26: #2 alternative fragment length(s) may be 51,74,128,164,229,257,278,456,477,586 bps INFO @ Fri, 05 Jul 2019 20:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.05_model.r INFO @ Fri, 05 Jul 2019 20:52:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.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 20:52:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:52:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:52:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:52:26: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 20:52:26: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 20:52:26: #1 total tags in treatment: 18290 INFO @ Fri, 05 Jul 2019 20:52:26: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:52:26: #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 20:52:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:52:26: #1 tags after filtering in treatment: 18290 INFO @ Fri, 05 Jul 2019 20:52:26: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:52:26: #1 finished! INFO @ Fri, 05 Jul 2019 20:52:26: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:52:26: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:52:26: #2 number of paired peaks: 399 WARNING @ Fri, 05 Jul 2019 20:52:26: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Fri, 05 Jul 2019 20:52:26: start model_add_line... INFO @ Fri, 05 Jul 2019 20:52:26: start X-correlation... INFO @ Fri, 05 Jul 2019 20:52:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.05_peaks.xls INFO @ Fri, 05 Jul 2019 20:52:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:52:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.05_summits.bed INFO @ Fri, 05 Jul 2019 20:52:26: Done! INFO @ Fri, 05 Jul 2019 20:52:26: end of X-cor INFO @ Fri, 05 Jul 2019 20:52:26: #2 finished! INFO @ Fri, 05 Jul 2019 20:52:26: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 20:52:26: #2 alternative fragment length(s) may be 51,74,128,164,229,257,278,456,477,586 bps INFO @ Fri, 05 Jul 2019 20:52:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.10_model.r INFO @ Fri, 05 Jul 2019 20:52:26: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:52:26: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:52:26: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:52:26: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.10_peaks.xls INFO @ Fri, 05 Jul 2019 20:52:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:52:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.10_summits.bed INFO @ Fri, 05 Jul 2019 20:52:26: Done! pass1 - making usageList (6 chroms): 1 millis pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) pass2 - checking and writing primary data (6 records, 4 fields): 24 millis INFO @ Fri, 05 Jul 2019 20:52:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.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 20:52:26: #1 read tag files... INFO @ Fri, 05 Jul 2019 20:52:26: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 20:52:27: #1 tag size is determined as 40 bps INFO @ Fri, 05 Jul 2019 20:52:27: #1 tag size = 40 INFO @ Fri, 05 Jul 2019 20:52:27: #1 total tags in treatment: 18290 INFO @ Fri, 05 Jul 2019 20:52:27: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 20:52:27: #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 20:52:27: #1 tags after filtering in treatment: 18290 INFO @ Fri, 05 Jul 2019 20:52:27: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 20:52:27: #1 finished! INFO @ Fri, 05 Jul 2019 20:52:27: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 20:52:27: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 20:52:27: #2 number of paired peaks: 399 WARNING @ Fri, 05 Jul 2019 20:52:27: Fewer paired peaks (399) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 399 pairs to build model! INFO @ Fri, 05 Jul 2019 20:52:27: start model_add_line... INFO @ Fri, 05 Jul 2019 20:52:27: start X-correlation... INFO @ Fri, 05 Jul 2019 20:52:27: end of X-cor INFO @ Fri, 05 Jul 2019 20:52:27: #2 finished! INFO @ Fri, 05 Jul 2019 20:52:27: #2 predicted fragment length is 128 bps INFO @ Fri, 05 Jul 2019 20:52:27: #2 alternative fragment length(s) may be 51,74,128,164,229,257,278,456,477,586 bps INFO @ Fri, 05 Jul 2019 20:52:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.20_model.r INFO @ Fri, 05 Jul 2019 20:52:27: #3 Call peaks... INFO @ Fri, 05 Jul 2019 20:52:27: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 20:52:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 20:52:27: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.20_peaks.xls INFO @ Fri, 05 Jul 2019 20:52:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 20:52:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/SRX237127/SRX237127.20_summits.bed INFO @ Fri, 05 Jul 2019 20:52:27: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling CompletedMACS2peakCalling CompletedMACS2peakCalling