Job ID = 1292455 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,017,364 reads read : 11,017,364 reads written : 11,017,364 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: 00:02:03 11017364 reads; of these: 11017364 (100.00%) were unpaired; of these: 1680417 (15.25%) aligned 0 times 7892656 (71.64%) aligned exactly 1 time 1444291 (13.11%) aligned >1 times 84.75% overall alignment rate Time searching: 00:02:03 Overall time: 00:02:03 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] 5918947 / 9336947 = 0.6339 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 19:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.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 19:00:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:00:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.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 19:00:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:00:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:00:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.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 19:00:00: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:00:00: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:00:08: 1000000 INFO @ Sun, 02 Jun 2019 19:00:09: 1000000 INFO @ Sun, 02 Jun 2019 19:00:10: 1000000 INFO @ Sun, 02 Jun 2019 19:00:16: 2000000 INFO @ Sun, 02 Jun 2019 19:00:17: 2000000 INFO @ Sun, 02 Jun 2019 19:00:19: 2000000 INFO @ Sun, 02 Jun 2019 19:00:24: 3000000 INFO @ Sun, 02 Jun 2019 19:00:25: 3000000 INFO @ Sun, 02 Jun 2019 19:00:27: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:00:27: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:00:27: #1 total tags in treatment: 3418000 INFO @ Sun, 02 Jun 2019 19:00:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:00:27: #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 19:00:27: #1 tags after filtering in treatment: 3418000 INFO @ Sun, 02 Jun 2019 19:00:27: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:00:27: #1 finished! INFO @ Sun, 02 Jun 2019 19:00:27: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:00:27: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:00:27: #2 number of paired peaks: 885 WARNING @ Sun, 02 Jun 2019 19:00:27: Fewer paired peaks (885) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 885 pairs to build model! INFO @ Sun, 02 Jun 2019 19:00:27: start model_add_line... INFO @ Sun, 02 Jun 2019 19:00:27: start X-correlation... INFO @ Sun, 02 Jun 2019 19:00:27: end of X-cor INFO @ Sun, 02 Jun 2019 19:00:27: #2 finished! INFO @ Sun, 02 Jun 2019 19:00:27: #2 predicted fragment length is 122 bps INFO @ Sun, 02 Jun 2019 19:00:27: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 02 Jun 2019 19:00:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.20_model.r INFO @ Sun, 02 Jun 2019 19:00:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:00:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:00:28: 3000000 INFO @ Sun, 02 Jun 2019 19:00:29: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:00:29: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:00:29: #1 total tags in treatment: 3418000 INFO @ Sun, 02 Jun 2019 19:00:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:00:29: #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 19:00:29: #1 tags after filtering in treatment: 3418000 INFO @ Sun, 02 Jun 2019 19:00:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:00:29: #1 finished! INFO @ Sun, 02 Jun 2019 19:00:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:00:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:00:29: #2 number of paired peaks: 885 WARNING @ Sun, 02 Jun 2019 19:00:29: Fewer paired peaks (885) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 885 pairs to build model! INFO @ Sun, 02 Jun 2019 19:00:29: start model_add_line... INFO @ Sun, 02 Jun 2019 19:00:29: start X-correlation... INFO @ Sun, 02 Jun 2019 19:00:29: end of X-cor INFO @ Sun, 02 Jun 2019 19:00:29: #2 finished! INFO @ Sun, 02 Jun 2019 19:00:29: #2 predicted fragment length is 122 bps INFO @ Sun, 02 Jun 2019 19:00:29: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 02 Jun 2019 19:00:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.05_model.r INFO @ Sun, 02 Jun 2019 19:00:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:00:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:00:32: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:00:32: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:00:32: #1 total tags in treatment: 3418000 INFO @ Sun, 02 Jun 2019 19:00:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:00:32: #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 19:00:32: #1 tags after filtering in treatment: 3418000 INFO @ Sun, 02 Jun 2019 19:00:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:00:32: #1 finished! INFO @ Sun, 02 Jun 2019 19:00:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:00:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:00:32: #2 number of paired peaks: 885 WARNING @ Sun, 02 Jun 2019 19:00:32: Fewer paired peaks (885) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 885 pairs to build model! INFO @ Sun, 02 Jun 2019 19:00:32: start model_add_line... INFO @ Sun, 02 Jun 2019 19:00:32: start X-correlation... INFO @ Sun, 02 Jun 2019 19:00:32: end of X-cor INFO @ Sun, 02 Jun 2019 19:00:32: #2 finished! INFO @ Sun, 02 Jun 2019 19:00:32: #2 predicted fragment length is 122 bps INFO @ Sun, 02 Jun 2019 19:00:32: #2 alternative fragment length(s) may be 122 bps INFO @ Sun, 02 Jun 2019 19:00:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.10_model.r INFO @ Sun, 02 Jun 2019 19:00:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:00:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:00:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:40: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:00:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.20_summits.bed INFO @ Sun, 02 Jun 2019 19:00:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (426 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:00:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.05_summits.bed INFO @ Sun, 02 Jun 2019 19:00:46: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1829 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:00:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:00:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:00:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626829/SRX4626829.10_summits.bed INFO @ Sun, 02 Jun 2019 19:00:49: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (989 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。