Job ID = 2589629 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,315,009 reads read : 7,315,009 reads written : 7,315,009 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: 00:00:56 7315009 reads; of these: 7315009 (100.00%) were unpaired; of these: 4356280 (59.55%) aligned 0 times 2452046 (33.52%) aligned exactly 1 time 506683 (6.93%) aligned >1 times 40.45% overall alignment rate Time searching: 00:00:56 Overall time: 00:00:56 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 7 sequences. [bam_rmdupse_core] 180025 / 2958729 = 0.0608 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 @ Mon, 12 Aug 2019 18:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 18:09:30: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:09:30: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:09:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 18:09:31: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:09:31: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:09:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.bam'] # control file = None # effective genome size = 9.00e+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 @ Mon, 12 Aug 2019 18:09:32: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:09:32: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:09:38: 1000000 INFO @ Mon, 12 Aug 2019 18:09:39: 1000000 INFO @ Mon, 12 Aug 2019 18:09:40: 1000000 INFO @ Mon, 12 Aug 2019 18:09:46: 2000000 INFO @ Mon, 12 Aug 2019 18:09:47: 2000000 INFO @ Mon, 12 Aug 2019 18:09:49: 2000000 INFO @ Mon, 12 Aug 2019 18:09:53: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:09:53: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:09:53: #1 total tags in treatment: 2778704 INFO @ Mon, 12 Aug 2019 18:09:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:09:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:09:53: #1 tags after filtering in treatment: 2778704 INFO @ Mon, 12 Aug 2019 18:09:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:09:53: #1 finished! INFO @ Mon, 12 Aug 2019 18:09:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:09:53: #2 number of paired peaks: 993 WARNING @ Mon, 12 Aug 2019 18:09:53: Fewer paired peaks (993) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 993 pairs to build model! INFO @ Mon, 12 Aug 2019 18:09:53: start model_add_line... INFO @ Mon, 12 Aug 2019 18:09:53: start X-correlation... INFO @ Mon, 12 Aug 2019 18:09:53: end of X-cor INFO @ Mon, 12 Aug 2019 18:09:53: #2 finished! INFO @ Mon, 12 Aug 2019 18:09:53: #2 predicted fragment length is 118 bps INFO @ Mon, 12 Aug 2019 18:09:53: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 12 Aug 2019 18:09:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.05_model.r INFO @ Mon, 12 Aug 2019 18:09:53: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:09:53: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:09:53: #1 total tags in treatment: 2778704 INFO @ Mon, 12 Aug 2019 18:09:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:09:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:09:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:09:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:09:53: #1 tags after filtering in treatment: 2778704 INFO @ Mon, 12 Aug 2019 18:09:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:09:53: #1 finished! INFO @ Mon, 12 Aug 2019 18:09:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:09:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:09:54: #2 number of paired peaks: 993 WARNING @ Mon, 12 Aug 2019 18:09:54: Fewer paired peaks (993) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 993 pairs to build model! INFO @ Mon, 12 Aug 2019 18:09:54: start model_add_line... INFO @ Mon, 12 Aug 2019 18:09:54: start X-correlation... INFO @ Mon, 12 Aug 2019 18:09:54: end of X-cor INFO @ Mon, 12 Aug 2019 18:09:54: #2 finished! INFO @ Mon, 12 Aug 2019 18:09:54: #2 predicted fragment length is 118 bps INFO @ Mon, 12 Aug 2019 18:09:54: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 12 Aug 2019 18:09:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.10_model.r INFO @ Mon, 12 Aug 2019 18:09:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:09:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:09:55: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:09:55: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:09:55: #1 total tags in treatment: 2778704 INFO @ Mon, 12 Aug 2019 18:09:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:09:55: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 18:09:55: #1 tags after filtering in treatment: 2778704 INFO @ Mon, 12 Aug 2019 18:09:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:09:55: #1 finished! INFO @ Mon, 12 Aug 2019 18:09:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:09:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:09:55: #2 number of paired peaks: 993 WARNING @ Mon, 12 Aug 2019 18:09:55: Fewer paired peaks (993) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 993 pairs to build model! INFO @ Mon, 12 Aug 2019 18:09:55: start model_add_line... INFO @ Mon, 12 Aug 2019 18:09:55: start X-correlation... INFO @ Mon, 12 Aug 2019 18:09:55: end of X-cor INFO @ Mon, 12 Aug 2019 18:09:55: #2 finished! INFO @ Mon, 12 Aug 2019 18:09:55: #2 predicted fragment length is 118 bps INFO @ Mon, 12 Aug 2019 18:09:55: #2 alternative fragment length(s) may be 118 bps INFO @ Mon, 12 Aug 2019 18:09:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.20_model.r INFO @ Mon, 12 Aug 2019 18:09:55: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:09:55: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:10:02: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:10:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:10:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:10:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:10:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:10:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.05_summits.bed INFO @ Mon, 12 Aug 2019 18:10:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1064 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:10:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:10:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:10:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.10_summits.bed INFO @ Mon, 12 Aug 2019 18:10:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (601 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:10:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:10:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:10:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277068/SRX277068.20_summits.bed INFO @ Mon, 12 Aug 2019 18:10:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (286 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。