Job ID = 2008392 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,268,236 reads read : 7,268,236 reads written : 7,268,236 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/ERR637542.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: 00:01:00 7268236 reads; of these: 7268236 (100.00%) were unpaired; of these: 3348520 (46.07%) aligned 0 times 3267089 (44.95%) aligned exactly 1 time 652627 (8.98%) aligned >1 times 53.93% overall alignment rate Time searching: 00:01:00 Overall time: 00:01:00 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] 1783017 / 3919716 = 0.4549 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 19:00:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.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 19:00:38: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:00:38: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.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 19:00:39: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:00:39: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:00:47: 1000000 INFO @ Fri, 05 Jul 2019 19:00:49: 1000000 INFO @ Fri, 05 Jul 2019 19:00:57: 2000000 INFO @ Fri, 05 Jul 2019 19:00:58: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:00:58: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:00:58: #1 total tags in treatment: 2136699 INFO @ Fri, 05 Jul 2019 19:00:58: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:00:58: #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 19:00:58: #1 tags after filtering in treatment: 2136699 INFO @ Fri, 05 Jul 2019 19:00:58: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:00:58: #1 finished! INFO @ Fri, 05 Jul 2019 19:00:58: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:00:58: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:00:58: #2 number of paired peaks: 379 WARNING @ Fri, 05 Jul 2019 19:00:58: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Fri, 05 Jul 2019 19:00:58: start model_add_line... INFO @ Fri, 05 Jul 2019 19:00:58: start X-correlation... INFO @ Fri, 05 Jul 2019 19:00:58: end of X-cor INFO @ Fri, 05 Jul 2019 19:00:58: #2 finished! INFO @ Fri, 05 Jul 2019 19:00:58: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 19:00:58: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 19:00:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.05_model.r INFO @ Fri, 05 Jul 2019 19:00:59: 2000000 INFO @ Fri, 05 Jul 2019 19:01:00: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:01:00: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:01:00: #1 total tags in treatment: 2136699 INFO @ Fri, 05 Jul 2019 19:01:00: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:01:00: #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 19:01:00: #1 tags after filtering in treatment: 2136699 INFO @ Fri, 05 Jul 2019 19:01:00: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:01:00: #1 finished! INFO @ Fri, 05 Jul 2019 19:01:00: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:01:00: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:01:00: #2 number of paired peaks: 379 WARNING @ Fri, 05 Jul 2019 19:01:00: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Fri, 05 Jul 2019 19:01:00: start model_add_line... INFO @ Fri, 05 Jul 2019 19:01:00: start X-correlation... INFO @ Fri, 05 Jul 2019 19:01:00: end of X-cor INFO @ Fri, 05 Jul 2019 19:01:00: #2 finished! INFO @ Fri, 05 Jul 2019 19:01:00: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 19:01:00: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 19:01:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.10_model.r INFO @ Fri, 05 Jul 2019 19:01:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:01:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:01:19: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:01:19: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:01:22: # Command line: callpeak -t /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.bam -f BAM -g 12100000 -n /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.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 19:01:22: #1 read tag files... INFO @ Fri, 05 Jul 2019 19:01:22: #1 read treatment tags... INFO @ Fri, 05 Jul 2019 19:01:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:01:27: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.05_peaks.xls INFO @ Fri, 05 Jul 2019 19:01:30: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.10_peaks.xls INFO @ Fri, 05 Jul 2019 19:01:31: 1000000 INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.10_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.05_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.10_summits.bed INFO @ Fri, 05 Jul 2019 19:01:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.05_summits.bed INFO @ Fri, 05 Jul 2019 19:01:35: Done! INFO @ Fri, 05 Jul 2019 19:01:35: Done! pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (2874 records, 4 fields): 10 millis pass1 - making usageList (16 chroms): 2 millis pass2 - checking and writing primary data (3507 records, 4 fields): 11 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Fri, 05 Jul 2019 19:01:40: 2000000 INFO @ Fri, 05 Jul 2019 19:01:41: #1 tag size is determined as 51 bps INFO @ Fri, 05 Jul 2019 19:01:41: #1 tag size = 51 INFO @ Fri, 05 Jul 2019 19:01:41: #1 total tags in treatment: 2136699 INFO @ Fri, 05 Jul 2019 19:01:41: #1 user defined the maximum tags... INFO @ Fri, 05 Jul 2019 19:01:41: #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 19:01:41: #1 tags after filtering in treatment: 2136699 INFO @ Fri, 05 Jul 2019 19:01:41: #1 Redundant rate of treatment: 0.00 INFO @ Fri, 05 Jul 2019 19:01:41: #1 finished! INFO @ Fri, 05 Jul 2019 19:01:41: #2 Build Peak Model... INFO @ Fri, 05 Jul 2019 19:01:41: #2 looking for paired plus/minus strand peaks... INFO @ Fri, 05 Jul 2019 19:01:42: #2 number of paired peaks: 379 WARNING @ Fri, 05 Jul 2019 19:01:42: Fewer paired peaks (379) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 379 pairs to build model! INFO @ Fri, 05 Jul 2019 19:01:42: start model_add_line... INFO @ Fri, 05 Jul 2019 19:01:42: start X-correlation... INFO @ Fri, 05 Jul 2019 19:01:42: end of X-cor INFO @ Fri, 05 Jul 2019 19:01:42: #2 finished! INFO @ Fri, 05 Jul 2019 19:01:42: #2 predicted fragment length is 155 bps INFO @ Fri, 05 Jul 2019 19:01:42: #2 alternative fragment length(s) may be 155 bps INFO @ Fri, 05 Jul 2019 19:01:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.20_model.r BedGraph に変換しました。 BigWig に変換中... INFO @ Fri, 05 Jul 2019 19:02:20: #3 Call peaks... INFO @ Fri, 05 Jul 2019 19:02:20: #3 Pre-compute pvalue-qvalue table... INFO @ Fri, 05 Jul 2019 19:02:28: #3 Call peaks for each chromosome... INFO @ Fri, 05 Jul 2019 19:02:31: #4 Write output xls file... /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.20_peaks.xls INFO @ Fri, 05 Jul 2019 19:02:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.20_peaks.narrowPeak INFO @ Fri, 05 Jul 2019 19:02:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/sacCer3/ERX594003/ERX594003.20_summits.bed INFO @ Fri, 05 Jul 2019 19:02:31: Done! pass1 - making usageList (16 chroms): 1 millis pass2 - checking and writing primary data (2097 records, 4 fields): 5 millis BigWig に変換しました。 CompletedMACS2peakCalling