Job ID = 1292346 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,755,494 reads read : 17,755,494 reads written : 17,755,494 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: 00:05:52 17755494 reads; of these: 17755494 (100.00%) were unpaired; of these: 1738628 (9.79%) aligned 0 times 14052698 (79.15%) aligned exactly 1 time 1964168 (11.06%) aligned >1 times 90.21% overall alignment rate Time searching: 00:05:52 Overall time: 00:05:52 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_sort_core] merging from 8 files... [bam_rmdupse_core] 7413756 / 16016866 = 0.4629 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 18:12:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.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 18:12:18: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:12:18: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.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 18:12:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:12:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:12:19: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.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 18:12:19: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:12:19: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:12:26: 1000000 INFO @ Sun, 02 Jun 2019 18:12:27: 1000000 INFO @ Sun, 02 Jun 2019 18:12:28: 1000000 INFO @ Sun, 02 Jun 2019 18:12:34: 2000000 INFO @ Sun, 02 Jun 2019 18:12:35: 2000000 INFO @ Sun, 02 Jun 2019 18:12:36: 2000000 INFO @ Sun, 02 Jun 2019 18:12:42: 3000000 INFO @ Sun, 02 Jun 2019 18:12:43: 3000000 INFO @ Sun, 02 Jun 2019 18:12:45: 3000000 INFO @ Sun, 02 Jun 2019 18:12:49: 4000000 INFO @ Sun, 02 Jun 2019 18:12:50: 4000000 INFO @ Sun, 02 Jun 2019 18:12:53: 4000000 INFO @ Sun, 02 Jun 2019 18:12:57: 5000000 INFO @ Sun, 02 Jun 2019 18:12:59: 5000000 INFO @ Sun, 02 Jun 2019 18:13:02: 5000000 INFO @ Sun, 02 Jun 2019 18:13:05: 6000000 INFO @ Sun, 02 Jun 2019 18:13:06: 6000000 INFO @ Sun, 02 Jun 2019 18:13:10: 6000000 INFO @ Sun, 02 Jun 2019 18:13:12: 7000000 INFO @ Sun, 02 Jun 2019 18:13:14: 7000000 INFO @ Sun, 02 Jun 2019 18:13:19: 7000000 INFO @ Sun, 02 Jun 2019 18:13:20: 8000000 INFO @ Sun, 02 Jun 2019 18:13:21: 8000000 INFO @ Sun, 02 Jun 2019 18:13:24: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:13:24: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:13:24: #1 total tags in treatment: 8603110 INFO @ Sun, 02 Jun 2019 18:13:24: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:13:24: #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 18:13:25: #1 tags after filtering in treatment: 8603110 INFO @ Sun, 02 Jun 2019 18:13:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:13:25: #1 finished! INFO @ Sun, 02 Jun 2019 18:13:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:13:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:13:25: #2 number of paired peaks: 381 WARNING @ Sun, 02 Jun 2019 18:13:25: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Sun, 02 Jun 2019 18:13:25: start model_add_line... INFO @ Sun, 02 Jun 2019 18:13:25: start X-correlation... INFO @ Sun, 02 Jun 2019 18:13:25: end of X-cor INFO @ Sun, 02 Jun 2019 18:13:25: #2 finished! INFO @ Sun, 02 Jun 2019 18:13:25: #2 predicted fragment length is 222 bps INFO @ Sun, 02 Jun 2019 18:13:25: #2 alternative fragment length(s) may be 3,193,206,222 bps INFO @ Sun, 02 Jun 2019 18:13:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.05_model.r INFO @ Sun, 02 Jun 2019 18:13:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:13:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:13:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:13:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:13:26: #1 total tags in treatment: 8603110 INFO @ Sun, 02 Jun 2019 18:13:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:13:26: #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 18:13:26: #1 tags after filtering in treatment: 8603110 INFO @ Sun, 02 Jun 2019 18:13:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:13:26: #1 finished! INFO @ Sun, 02 Jun 2019 18:13:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:13:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:13:27: #2 number of paired peaks: 381 WARNING @ Sun, 02 Jun 2019 18:13:27: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Sun, 02 Jun 2019 18:13:27: start model_add_line... INFO @ Sun, 02 Jun 2019 18:13:27: start X-correlation... INFO @ Sun, 02 Jun 2019 18:13:27: end of X-cor INFO @ Sun, 02 Jun 2019 18:13:27: #2 finished! INFO @ Sun, 02 Jun 2019 18:13:27: #2 predicted fragment length is 222 bps INFO @ Sun, 02 Jun 2019 18:13:27: #2 alternative fragment length(s) may be 3,193,206,222 bps INFO @ Sun, 02 Jun 2019 18:13:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.20_model.r INFO @ Sun, 02 Jun 2019 18:13:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:13:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:13:27: 8000000 INFO @ Sun, 02 Jun 2019 18:13:32: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:13:32: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:13:32: #1 total tags in treatment: 8603110 INFO @ Sun, 02 Jun 2019 18:13:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:13:32: #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 18:13:32: #1 tags after filtering in treatment: 8603110 INFO @ Sun, 02 Jun 2019 18:13:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:13:32: #1 finished! INFO @ Sun, 02 Jun 2019 18:13:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:13:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:13:33: #2 number of paired peaks: 381 WARNING @ Sun, 02 Jun 2019 18:13:33: Fewer paired peaks (381) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 381 pairs to build model! INFO @ Sun, 02 Jun 2019 18:13:33: start model_add_line... INFO @ Sun, 02 Jun 2019 18:13:33: start X-correlation... INFO @ Sun, 02 Jun 2019 18:13:33: end of X-cor INFO @ Sun, 02 Jun 2019 18:13:33: #2 finished! INFO @ Sun, 02 Jun 2019 18:13:33: #2 predicted fragment length is 222 bps INFO @ Sun, 02 Jun 2019 18:13:33: #2 alternative fragment length(s) may be 3,193,206,222 bps INFO @ Sun, 02 Jun 2019 18:13:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.10_model.r INFO @ Sun, 02 Jun 2019 18:13:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:13:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:13:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:13:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:14:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.05_summits.bed INFO @ Sun, 02 Jun 2019 18:14:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2093 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:14:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:14:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:14:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.20_summits.bed INFO @ Sun, 02 Jun 2019 18:14:07: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:14:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:14:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:14:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX341785/SRX341785.10_summits.bed INFO @ Sun, 02 Jun 2019 18:14:13: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (781 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。