Job ID = 1290639 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,386,177 reads read : 9,386,177 reads written : 9,386,177 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: 00:02:25 9386177 reads; of these: 9386177 (100.00%) were unpaired; of these: 222327 (2.37%) aligned 0 times 7811004 (83.22%) aligned exactly 1 time 1352846 (14.41%) aligned >1 times 97.63% overall alignment rate Time searching: 00:02:25 Overall time: 00:02:25 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] 614013 / 9163850 = 0.0670 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 21:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.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 21:50:29: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:29: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.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 21:50:29: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:29: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.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 21:50:29: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:50:29: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:50:39: 1000000 INFO @ Sat, 01 Jun 2019 21:50:40: 1000000 INFO @ Sat, 01 Jun 2019 21:50:42: 1000000 INFO @ Sat, 01 Jun 2019 21:50:49: 2000000 INFO @ Sat, 01 Jun 2019 21:50:50: 2000000 INFO @ Sat, 01 Jun 2019 21:50:54: 2000000 INFO @ Sat, 01 Jun 2019 21:50:59: 3000000 INFO @ Sat, 01 Jun 2019 21:51:00: 3000000 INFO @ Sat, 01 Jun 2019 21:51:06: 3000000 INFO @ Sat, 01 Jun 2019 21:51:08: 4000000 INFO @ Sat, 01 Jun 2019 21:51:10: 4000000 INFO @ Sat, 01 Jun 2019 21:51:17: 5000000 INFO @ Sat, 01 Jun 2019 21:51:17: 4000000 INFO @ Sat, 01 Jun 2019 21:51:18: 5000000 INFO @ Sat, 01 Jun 2019 21:51:25: 6000000 INFO @ Sat, 01 Jun 2019 21:51:27: 6000000 INFO @ Sat, 01 Jun 2019 21:51:28: 5000000 INFO @ Sat, 01 Jun 2019 21:51:34: 7000000 INFO @ Sat, 01 Jun 2019 21:51:36: 7000000 INFO @ Sat, 01 Jun 2019 21:51:39: 6000000 INFO @ Sat, 01 Jun 2019 21:51:44: 8000000 INFO @ Sat, 01 Jun 2019 21:51:45: 8000000 INFO @ Sat, 01 Jun 2019 21:51:50: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:51:50: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:51:50: #1 total tags in treatment: 8549837 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 21:51:50: #1 tags after filtering in treatment: 8549837 INFO @ Sat, 01 Jun 2019 21:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:50: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:50: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:50: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:51:50: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:51:50: #1 total tags in treatment: 8549837 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 21:51:50: #1 tags after filtering in treatment: 8549837 INFO @ Sat, 01 Jun 2019 21:51:50: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:51:50: #1 finished! INFO @ Sat, 01 Jun 2019 21:51:50: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:51:50: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:51:51: 7000000 INFO @ Sat, 01 Jun 2019 21:51:51: #2 number of paired peaks: 277 WARNING @ Sat, 01 Jun 2019 21:51:51: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 01 Jun 2019 21:51:51: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:51: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:51: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:51: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:51: #2 predicted fragment length is 50 bps INFO @ Sat, 01 Jun 2019 21:51:51: #2 alternative fragment length(s) may be 4,50,494,570,592,598 bps INFO @ Sat, 01 Jun 2019 21:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.05_model.r WARNING @ Sat, 01 Jun 2019 21:51:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:51:51: #2 You may need to consider one of the other alternative d(s): 4,50,494,570,592,598 WARNING @ Sat, 01 Jun 2019 21:51:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:51:51: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:51:51: #2 number of paired peaks: 277 WARNING @ Sat, 01 Jun 2019 21:51:51: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 01 Jun 2019 21:51:51: start model_add_line... INFO @ Sat, 01 Jun 2019 21:51:51: start X-correlation... INFO @ Sat, 01 Jun 2019 21:51:51: end of X-cor INFO @ Sat, 01 Jun 2019 21:51:51: #2 finished! INFO @ Sat, 01 Jun 2019 21:51:51: #2 predicted fragment length is 50 bps INFO @ Sat, 01 Jun 2019 21:51:51: #2 alternative fragment length(s) may be 4,50,494,570,592,598 bps INFO @ Sat, 01 Jun 2019 21:51:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.10_model.r WARNING @ Sat, 01 Jun 2019 21:51:51: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:51:51: #2 You may need to consider one of the other alternative d(s): 4,50,494,570,592,598 WARNING @ Sat, 01 Jun 2019 21:51:51: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:51:51: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:51:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:02: 8000000 INFO @ Sat, 01 Jun 2019 21:52:08: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:08: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:08: #1 total tags in treatment: 8549837 INFO @ Sat, 01 Jun 2019 21:52:08: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:08: #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 21:52:08: #1 tags after filtering in treatment: 8549837 INFO @ Sat, 01 Jun 2019 21:52:08: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:08: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:08: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:08: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:09: #2 number of paired peaks: 277 WARNING @ Sat, 01 Jun 2019 21:52:09: Fewer paired peaks (277) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 277 pairs to build model! INFO @ Sat, 01 Jun 2019 21:52:09: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:09: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:09: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:09: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:09: #2 predicted fragment length is 50 bps INFO @ Sat, 01 Jun 2019 21:52:09: #2 alternative fragment length(s) may be 4,50,494,570,592,598 bps INFO @ Sat, 01 Jun 2019 21:52:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.20_model.r WARNING @ Sat, 01 Jun 2019 21:52:09: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:52:09: #2 You may need to consider one of the other alternative d(s): 4,50,494,570,592,598 WARNING @ Sat, 01 Jun 2019 21:52:09: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sat, 01 Jun 2019 21:52:09: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:16: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:16: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.05_summits.bed INFO @ Sat, 01 Jun 2019 21:52:28: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (496 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:52:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.10_summits.bed INFO @ Sat, 01 Jun 2019 21:52:28: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (284 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:52:33: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:52:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:52:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:52:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX982094/SRX982094.20_summits.bed INFO @ Sat, 01 Jun 2019 21:52:44: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (109 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。