Job ID = 1290622 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,734,806 reads read : 4,734,806 reads written : 4,734,806 spots read : 7,817,443 reads read : 7,817,443 reads written : 7,817,443 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: 00:02:14 12552249 reads; of these: 12552249 (100.00%) were unpaired; of these: 219470 (1.75%) aligned 0 times 10106683 (80.52%) aligned exactly 1 time 2226096 (17.73%) aligned >1 times 98.25% overall alignment rate Time searching: 00:02:14 Overall time: 00:02:14 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] 1776187 / 12332779 = 0.1440 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 @ Sat, 01 Jun 2019 21:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.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 @ Sat, 01 Jun 2019 21:50:30: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:30: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.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 @ Sat, 01 Jun 2019 21:50:30: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:30: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.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 @ Sat, 01 Jun 2019 21:50:30: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:30: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:37: 1000000 INFO @ Sat, 01 Jun 2019 21:50:38: 1000000 INFO @ Sat, 01 Jun 2019 21:50:40: 1000000 INFO @ Sat, 01 Jun 2019 21:50:45: 2000000 INFO @ Sat, 01 Jun 2019 21:50:46: 2000000 INFO @ Sat, 01 Jun 2019 21:50:49: 2000000 INFO @ Sat, 01 Jun 2019 21:50:52: 3000000 INFO @ Sat, 01 Jun 2019 21:50:53: 3000000 INFO @ Sat, 01 Jun 2019 21:50:59: 3000000 INFO @ Sat, 01 Jun 2019 21:51:00: 4000000 INFO @ Sat, 01 Jun 2019 21:51:01: 4000000 INFO @ Sat, 01 Jun 2019 21:51:07: 5000000 INFO @ Sat, 01 Jun 2019 21:51:08: 4000000 INFO @ Sat, 01 Jun 2019 21:51:08: 5000000 INFO @ Sat, 01 Jun 2019 21:51:14: 6000000 INFO @ Sat, 01 Jun 2019 21:51:16: 6000000 INFO @ Sat, 01 Jun 2019 21:51:17: 5000000 INFO @ Sat, 01 Jun 2019 21:51:22: 7000000 INFO @ Sat, 01 Jun 2019 21:51:23: 7000000 INFO @ Sat, 01 Jun 2019 21:51:26: 6000000 INFO @ Sat, 01 Jun 2019 21:51:29: 8000000 INFO @ Sat, 01 Jun 2019 21:51:31: 8000000 INFO @ Sat, 01 Jun 2019 21:51:35: 7000000 INFO @ Sat, 01 Jun 2019 21:51:36: 9000000 INFO @ Sat, 01 Jun 2019 21:51:38: 9000000 INFO @ Sat, 01 Jun 2019 21:51:44: 10000000 INFO @ Sat, 01 Jun 2019 21:51:44: 8000000 INFO @ Sat, 01 Jun 2019 21:51:46: 10000000 INFO @ Sat, 01 Jun 2019 21:51:48: #1 tag size is determined as 32 bps INFO @ Sat, 01 Jun 2019 21:51:48: #1 tag size = 32 INFO @ Sat, 01 Jun 2019 21:51:48: #1 total tags in treatment: 10556592 INFO @ Sat, 01 Jun 2019 21:51:48: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:48: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:48: #1 tags after filtering in treatment: 10556592 INFO @ Sat, 01 Jun 2019 21:51:48: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:48: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:48: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:48: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:49: #2 number of paired peaks: 788 WARNING @ Sat, 01 Jun 2019 21:51:49: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sat, 01 Jun 2019 21:51:49: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:49: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:49: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:49: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:49: #2 predicted fragment length is 105 bps INFO @ Sat, 01 Jun 2019 21:51:49: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 01 Jun 2019 21:51:49: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.05_model.r INFO @ Sat, 01 Jun 2019 21:51:49: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:49: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:50: #1 tag size is determined as 32 bps INFO @ Sat, 01 Jun 2019 21:51:50: #1 tag size = 32 INFO @ Sat, 01 Jun 2019 21:51:50: #1 total tags in treatment: 10556592 INFO @ Sat, 01 Jun 2019 21:51:50: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:51:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:51:51: #1 tags after filtering in treatment: 10556592 INFO @ Sat, 01 Jun 2019 21:51:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:51: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:51: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:52: #2 number of paired peaks: 788 WARNING @ Sat, 01 Jun 2019 21:51:52: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sat, 01 Jun 2019 21:51:52: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:52: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:52: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:52: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:52: #2 predicted fragment length is 105 bps INFO @ Sat, 01 Jun 2019 21:51:52: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 01 Jun 2019 21:51:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.20_model.r INFO @ Sat, 01 Jun 2019 21:51:52: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:53: 9000000 INFO @ Sat, 01 Jun 2019 21:52:02: 10000000 INFO @ Sat, 01 Jun 2019 21:52:07: #1 tag size is determined as 32 bps INFO @ Sat, 01 Jun 2019 21:52:07: #1 tag size = 32 INFO @ Sat, 01 Jun 2019 21:52:07: #1 total tags in treatment: 10556592 INFO @ Sat, 01 Jun 2019 21:52:07: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:07: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:07: #1 tags after filtering in treatment: 10556592 INFO @ Sat, 01 Jun 2019 21:52:07: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:07: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:07: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:07: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:08: #2 number of paired peaks: 788 WARNING @ Sat, 01 Jun 2019 21:52:08: Fewer paired peaks (788) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 788 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:08: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:08: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:08: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:08: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:08: #2 predicted fragment length is 105 bps INFO @ Sat, 01 Jun 2019 21:52:08: #2 alternative fragment length(s) may be 105 bps INFO @ Sat, 01 Jun 2019 21:52:08: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.10_model.r INFO @ Sat, 01 Jun 2019 21:52:08: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:08: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:19: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:23: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.05_summits.bed INFO @ Sat, 01 Jun 2019 21:52:35: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (9594 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:52:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.20_summits.bed INFO @ Sat, 01 Jun 2019 21:52:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1806 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:52:39: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX212235/SRX212235.10_summits.bed INFO @ Sat, 01 Jun 2019 21:52:54: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4190 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。