Job ID = 1292858 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,226,623 reads read : 13,226,623 reads written : 13,226,623 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:02:50 13226623 reads; of these: 13226623 (100.00%) were unpaired; of these: 2155449 (16.30%) aligned 0 times 9125764 (69.00%) aligned exactly 1 time 1945410 (14.71%) aligned >1 times 83.70% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 5526225 / 11071174 = 0.4992 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 @ Sun, 02 Jun 2019 20:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.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 @ Sun, 02 Jun 2019 20:57:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:57:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.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 @ Sun, 02 Jun 2019 20:57:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:57:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:57:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.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 @ Sun, 02 Jun 2019 20:57:50: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:57:50: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:58:00: 1000000 INFO @ Sun, 02 Jun 2019 20:58:00: 1000000 INFO @ Sun, 02 Jun 2019 20:58:00: 1000000 INFO @ Sun, 02 Jun 2019 20:58:10: 2000000 INFO @ Sun, 02 Jun 2019 20:58:10: 2000000 INFO @ Sun, 02 Jun 2019 20:58:12: 2000000 INFO @ Sun, 02 Jun 2019 20:58:19: 3000000 INFO @ Sun, 02 Jun 2019 20:58:19: 3000000 INFO @ Sun, 02 Jun 2019 20:58:24: 3000000 INFO @ Sun, 02 Jun 2019 20:58:28: 4000000 INFO @ Sun, 02 Jun 2019 20:58:29: 4000000 INFO @ Sun, 02 Jun 2019 20:58:35: 4000000 INFO @ Sun, 02 Jun 2019 20:58:38: 5000000 INFO @ Sun, 02 Jun 2019 20:58:38: 5000000 INFO @ Sun, 02 Jun 2019 20:58:43: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:58:43: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:58:43: #1 total tags in treatment: 5544949 INFO @ Sun, 02 Jun 2019 20:58:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:58:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:58:43: #1 tags after filtering in treatment: 5544949 INFO @ Sun, 02 Jun 2019 20:58:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:58:43: #1 finished! INFO @ Sun, 02 Jun 2019 20:58:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:58:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:58:43: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:58:43: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:58:43: #1 total tags in treatment: 5544949 INFO @ Sun, 02 Jun 2019 20:58:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:58:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:58:43: #2 number of paired peaks: 751 WARNING @ Sun, 02 Jun 2019 20:58:43: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Sun, 02 Jun 2019 20:58:43: start model_add_line... INFO @ Sun, 02 Jun 2019 20:58:44: #1 tags after filtering in treatment: 5544949 INFO @ Sun, 02 Jun 2019 20:58:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:58:44: #1 finished! INFO @ Sun, 02 Jun 2019 20:58:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:58:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:58:44: start X-correlation... INFO @ Sun, 02 Jun 2019 20:58:44: end of X-cor INFO @ Sun, 02 Jun 2019 20:58:44: #2 finished! INFO @ Sun, 02 Jun 2019 20:58:44: #2 predicted fragment length is 170 bps INFO @ Sun, 02 Jun 2019 20:58:44: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 02 Jun 2019 20:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.05_model.r INFO @ Sun, 02 Jun 2019 20:58:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:58:44: #2 number of paired peaks: 751 WARNING @ Sun, 02 Jun 2019 20:58:44: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Sun, 02 Jun 2019 20:58:44: start model_add_line... INFO @ Sun, 02 Jun 2019 20:58:44: start X-correlation... INFO @ Sun, 02 Jun 2019 20:58:44: end of X-cor INFO @ Sun, 02 Jun 2019 20:58:44: #2 finished! INFO @ Sun, 02 Jun 2019 20:58:44: #2 predicted fragment length is 170 bps INFO @ Sun, 02 Jun 2019 20:58:44: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 02 Jun 2019 20:58:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.10_model.r INFO @ Sun, 02 Jun 2019 20:58:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:58:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:58:47: 5000000 INFO @ Sun, 02 Jun 2019 20:58:53: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:58:53: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:58:53: #1 total tags in treatment: 5544949 INFO @ Sun, 02 Jun 2019 20:58:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:58:53: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:58:53: #1 tags after filtering in treatment: 5544949 INFO @ Sun, 02 Jun 2019 20:58:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:58:53: #1 finished! INFO @ Sun, 02 Jun 2019 20:58:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:58:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:58:54: #2 number of paired peaks: 751 WARNING @ Sun, 02 Jun 2019 20:58:54: Fewer paired peaks (751) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 751 pairs to build model! INFO @ Sun, 02 Jun 2019 20:58:54: start model_add_line... INFO @ Sun, 02 Jun 2019 20:58:54: start X-correlation... INFO @ Sun, 02 Jun 2019 20:58:54: end of X-cor INFO @ Sun, 02 Jun 2019 20:58:54: #2 finished! INFO @ Sun, 02 Jun 2019 20:58:54: #2 predicted fragment length is 170 bps INFO @ Sun, 02 Jun 2019 20:58:54: #2 alternative fragment length(s) may be 170 bps INFO @ Sun, 02 Jun 2019 20:58:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.20_model.r INFO @ Sun, 02 Jun 2019 20:58:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:58:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:59:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:59:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:59:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:59:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:59:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.05_summits.bed INFO @ Sun, 02 Jun 2019 20:59:11: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1799 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:59:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:59:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:59:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.10_summits.bed INFO @ Sun, 02 Jun 2019 20:59:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (954 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:59:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:59:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:59:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:59:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495084/SRX495084.20_summits.bed INFO @ Sun, 02 Jun 2019 20:59:22: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (492 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。