Job ID = 2589383 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,222,788 reads read : 7,222,788 reads written : 7,222,788 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: 00:01:16 7222788 reads; of these: 7222788 (100.00%) were unpaired; of these: 210393 (2.91%) aligned 0 times 5941519 (82.26%) aligned exactly 1 time 1070876 (14.83%) aligned >1 times 97.09% overall alignment rate Time searching: 00:01:16 Overall time: 00:01:16 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] 621674 / 7012395 = 0.0887 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 17:37:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.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 17:37:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:37:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:37:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.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 17:37:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:37:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:37:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.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 17:37:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:37:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:37:13: 1000000 INFO @ Mon, 12 Aug 2019 17:37:14: 1000000 INFO @ Mon, 12 Aug 2019 17:37:15: 1000000 INFO @ Mon, 12 Aug 2019 17:37:21: 2000000 INFO @ Mon, 12 Aug 2019 17:37:21: 2000000 INFO @ Mon, 12 Aug 2019 17:37:22: 2000000 INFO @ Mon, 12 Aug 2019 17:37:28: 3000000 INFO @ Mon, 12 Aug 2019 17:37:29: 3000000 INFO @ Mon, 12 Aug 2019 17:37:29: 3000000 INFO @ Mon, 12 Aug 2019 17:37:35: 4000000 INFO @ Mon, 12 Aug 2019 17:37:36: 4000000 INFO @ Mon, 12 Aug 2019 17:37:37: 4000000 INFO @ Mon, 12 Aug 2019 17:37:42: 5000000 INFO @ Mon, 12 Aug 2019 17:37:43: 5000000 INFO @ Mon, 12 Aug 2019 17:37:45: 5000000 INFO @ Mon, 12 Aug 2019 17:37:49: 6000000 INFO @ Mon, 12 Aug 2019 17:37:50: 6000000 INFO @ Mon, 12 Aug 2019 17:37:52: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:37:52: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:37:52: #1 total tags in treatment: 6390721 INFO @ Mon, 12 Aug 2019 17:37:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:37:52: #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 17:37:52: #1 tags after filtering in treatment: 6390721 INFO @ Mon, 12 Aug 2019 17:37:52: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:37:52: #1 finished! INFO @ Mon, 12 Aug 2019 17:37:52: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:37:52: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:37:52: 6000000 INFO @ Mon, 12 Aug 2019 17:37:52: #2 number of paired peaks: 293 WARNING @ Mon, 12 Aug 2019 17:37:52: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 12 Aug 2019 17:37:52: start model_add_line... INFO @ Mon, 12 Aug 2019 17:37:52: start X-correlation... INFO @ Mon, 12 Aug 2019 17:37:52: end of X-cor INFO @ Mon, 12 Aug 2019 17:37:52: #2 finished! INFO @ Mon, 12 Aug 2019 17:37:52: #2 predicted fragment length is 39 bps INFO @ Mon, 12 Aug 2019 17:37:52: #2 alternative fragment length(s) may be 3,39,568 bps INFO @ Mon, 12 Aug 2019 17:37:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.10_model.r WARNING @ Mon, 12 Aug 2019 17:37:52: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:37:52: #2 You may need to consider one of the other alternative d(s): 3,39,568 WARNING @ Mon, 12 Aug 2019 17:37:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:37:52: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:37:52: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:37:52: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:37:52: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:37:52: #1 total tags in treatment: 6390721 INFO @ Mon, 12 Aug 2019 17:37:52: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:37:52: #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 17:37:53: #1 tags after filtering in treatment: 6390721 INFO @ Mon, 12 Aug 2019 17:37:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:37:53: #1 finished! INFO @ Mon, 12 Aug 2019 17:37:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:37:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:37:53: #2 number of paired peaks: 293 WARNING @ Mon, 12 Aug 2019 17:37:53: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 12 Aug 2019 17:37:53: start model_add_line... INFO @ Mon, 12 Aug 2019 17:37:53: start X-correlation... INFO @ Mon, 12 Aug 2019 17:37:53: end of X-cor INFO @ Mon, 12 Aug 2019 17:37:53: #2 finished! INFO @ Mon, 12 Aug 2019 17:37:53: #2 predicted fragment length is 39 bps INFO @ Mon, 12 Aug 2019 17:37:53: #2 alternative fragment length(s) may be 3,39,568 bps INFO @ Mon, 12 Aug 2019 17:37:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.20_model.r WARNING @ Mon, 12 Aug 2019 17:37:53: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:37:53: #2 You may need to consider one of the other alternative d(s): 3,39,568 WARNING @ Mon, 12 Aug 2019 17:37:53: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:37:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:37:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:37:55: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:37:55: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:37:55: #1 total tags in treatment: 6390721 INFO @ Mon, 12 Aug 2019 17:37:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:37:55: #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 17:37:55: #1 tags after filtering in treatment: 6390721 INFO @ Mon, 12 Aug 2019 17:37:55: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:37:55: #1 finished! INFO @ Mon, 12 Aug 2019 17:37:55: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:37:55: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:37:56: #2 number of paired peaks: 293 WARNING @ Mon, 12 Aug 2019 17:37:56: Fewer paired peaks (293) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 293 pairs to build model! INFO @ Mon, 12 Aug 2019 17:37:56: start model_add_line... INFO @ Mon, 12 Aug 2019 17:37:56: start X-correlation... INFO @ Mon, 12 Aug 2019 17:37:56: end of X-cor INFO @ Mon, 12 Aug 2019 17:37:56: #2 finished! INFO @ Mon, 12 Aug 2019 17:37:56: #2 predicted fragment length is 39 bps INFO @ Mon, 12 Aug 2019 17:37:56: #2 alternative fragment length(s) may be 3,39,568 bps INFO @ Mon, 12 Aug 2019 17:37:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.05_model.r WARNING @ Mon, 12 Aug 2019 17:37:56: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:37:56: #2 You may need to consider one of the other alternative d(s): 3,39,568 WARNING @ Mon, 12 Aug 2019 17:37:56: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 17:37:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:37:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:38:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:38:11: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:38:14: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.10_summits.bed INFO @ Mon, 12 Aug 2019 17:38:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (178 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.20_summits.bed INFO @ Mon, 12 Aug 2019 17:38:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (52 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:38:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:38:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:38:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX118220/SRX118220.05_summits.bed INFO @ Mon, 12 Aug 2019 17:38:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (404 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。