Job ID = 2589642 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,104,389 reads read : 3,104,389 reads written : 3,104,389 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: 00:00:35 3104389 reads; of these: 3104389 (100.00%) were unpaired; of these: 114578 (3.69%) aligned 0 times 2554501 (82.29%) aligned exactly 1 time 435310 (14.02%) aligned >1 times 96.31% overall alignment rate Time searching: 00:00:35 Overall time: 00:00:35 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] 216100 / 2989811 = 0.0723 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 18:09:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.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 18:09:58: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:09:58: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:09:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.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 18:09:59: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:09:59: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:10:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.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 18:10:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:10:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:10:07: 1000000 INFO @ Mon, 12 Aug 2019 18:10:08: 1000000 INFO @ Mon, 12 Aug 2019 18:10:08: 1000000 INFO @ Mon, 12 Aug 2019 18:10:16: 2000000 INFO @ Mon, 12 Aug 2019 18:10:17: 2000000 INFO @ Mon, 12 Aug 2019 18:10:17: 2000000 INFO @ Mon, 12 Aug 2019 18:10:23: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:10:23: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:10:23: #1 total tags in treatment: 2773711 INFO @ Mon, 12 Aug 2019 18:10:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:10:23: #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 18:10:23: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:10:23: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:10:23: #1 total tags in treatment: 2773711 INFO @ Mon, 12 Aug 2019 18:10:23: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:10:23: #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 18:10:23: #1 tags after filtering in treatment: 2773711 INFO @ Mon, 12 Aug 2019 18:10:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:10:23: #1 finished! INFO @ Mon, 12 Aug 2019 18:10:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:10:23: #1 tags after filtering in treatment: 2773711 INFO @ Mon, 12 Aug 2019 18:10:23: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:10:23: #1 finished! INFO @ Mon, 12 Aug 2019 18:10:23: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:10:23: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:10:23: #2 number of paired peaks: 303 WARNING @ Mon, 12 Aug 2019 18:10:23: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Mon, 12 Aug 2019 18:10:23: start model_add_line... INFO @ Mon, 12 Aug 2019 18:10:23: #2 number of paired peaks: 303 WARNING @ Mon, 12 Aug 2019 18:10:23: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Mon, 12 Aug 2019 18:10:23: start model_add_line... INFO @ Mon, 12 Aug 2019 18:10:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:10:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:10:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:10:23: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 18:10:23: #2 alternative fragment length(s) may be 33,110,535,572 bps INFO @ Mon, 12 Aug 2019 18:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.10_model.r WARNING @ Mon, 12 Aug 2019 18:10:23: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:10:23: #2 You may need to consider one of the other alternative d(s): 33,110,535,572 WARNING @ Mon, 12 Aug 2019 18:10:23: #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 18:10:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:10:23: start X-correlation... INFO @ Mon, 12 Aug 2019 18:10:23: end of X-cor INFO @ Mon, 12 Aug 2019 18:10:23: #2 finished! INFO @ Mon, 12 Aug 2019 18:10:23: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 18:10:23: #2 alternative fragment length(s) may be 33,110,535,572 bps INFO @ Mon, 12 Aug 2019 18:10:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.20_model.r WARNING @ Mon, 12 Aug 2019 18:10:23: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:10:23: #2 You may need to consider one of the other alternative d(s): 33,110,535,572 WARNING @ Mon, 12 Aug 2019 18:10:23: #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 18:10:23: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:10:23: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:10:24: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:10:24: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:10:24: #1 total tags in treatment: 2773711 INFO @ Mon, 12 Aug 2019 18:10:24: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:10:24: #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 18:10:24: #1 tags after filtering in treatment: 2773711 INFO @ Mon, 12 Aug 2019 18:10:24: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:10:24: #1 finished! INFO @ Mon, 12 Aug 2019 18:10:24: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:10:24: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:10:24: #2 number of paired peaks: 303 WARNING @ Mon, 12 Aug 2019 18:10:24: Fewer paired peaks (303) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 303 pairs to build model! INFO @ Mon, 12 Aug 2019 18:10:24: start model_add_line... INFO @ Mon, 12 Aug 2019 18:10:24: start X-correlation... INFO @ Mon, 12 Aug 2019 18:10:24: end of X-cor INFO @ Mon, 12 Aug 2019 18:10:24: #2 finished! INFO @ Mon, 12 Aug 2019 18:10:24: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 18:10:24: #2 alternative fragment length(s) may be 33,110,535,572 bps INFO @ Mon, 12 Aug 2019 18:10:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.05_model.r WARNING @ Mon, 12 Aug 2019 18:10:24: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:10:24: #2 You may need to consider one of the other alternative d(s): 33,110,535,572 WARNING @ Mon, 12 Aug 2019 18:10:24: #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 18:10:24: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:10:24: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:10:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:10:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:10:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.20_summits.bed INFO @ Mon, 12 Aug 2019 18:10:36: Done! INFO @ Mon, 12 Aug 2019 18:10:36: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:10:36: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:10:36: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.10_summits.bed INFO @ Mon, 12 Aug 2019 18:10:36: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (38 records, 4 fields): 2 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (113 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:10:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:10:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:10:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX277086/SRX277086.05_summits.bed INFO @ Mon, 12 Aug 2019 18:10:37: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (256 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。