Job ID = 1290605 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,448,041 reads read : 32,896,082 reads written : 16,448,041 reads 0-length : 16,448,041 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: 00:03:54 16448041 reads; of these: 16448041 (100.00%) were unpaired; of these: 2371929 (14.42%) aligned 0 times 11900697 (72.35%) aligned exactly 1 time 2175415 (13.23%) aligned >1 times 85.58% overall alignment rate Time searching: 00:03:54 Overall time: 00:03:54 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] 7534481 / 14076112 = 0.5353 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 21:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.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 21:52:46: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:52:46: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.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 21:52:46: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.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 21:52:46: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:52:46: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:52:46: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:52:46: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:52:54: 1000000 INFO @ Sat, 01 Jun 2019 21:52:54: 1000000 INFO @ Sat, 01 Jun 2019 21:52:54: 1000000 INFO @ Sat, 01 Jun 2019 21:53:01: 2000000 INFO @ Sat, 01 Jun 2019 21:53:02: 2000000 INFO @ Sat, 01 Jun 2019 21:53:02: 2000000 INFO @ Sat, 01 Jun 2019 21:53:08: 3000000 INFO @ Sat, 01 Jun 2019 21:53:10: 3000000 INFO @ Sat, 01 Jun 2019 21:53:10: 3000000 INFO @ Sat, 01 Jun 2019 21:53:15: 4000000 INFO @ Sat, 01 Jun 2019 21:53:18: 4000000 INFO @ Sat, 01 Jun 2019 21:53:18: 4000000 INFO @ Sat, 01 Jun 2019 21:53:21: 5000000 INFO @ Sat, 01 Jun 2019 21:53:25: 5000000 INFO @ Sat, 01 Jun 2019 21:53:25: 5000000 INFO @ Sat, 01 Jun 2019 21:53:28: 6000000 INFO @ Sat, 01 Jun 2019 21:53:32: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:53:32: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:53:32: #1 total tags in treatment: 6541631 INFO @ Sat, 01 Jun 2019 21:53:32: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:53:32: #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 21:53:32: #1 tags after filtering in treatment: 6541631 INFO @ Sat, 01 Jun 2019 21:53:32: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:53:32: #1 finished! INFO @ Sat, 01 Jun 2019 21:53:32: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:53:32: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:53:33: #2 number of paired peaks: 566 WARNING @ Sat, 01 Jun 2019 21:53:33: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Sat, 01 Jun 2019 21:53:33: start model_add_line... INFO @ Sat, 01 Jun 2019 21:53:33: start X-correlation... INFO @ Sat, 01 Jun 2019 21:53:33: end of X-cor INFO @ Sat, 01 Jun 2019 21:53:33: #2 finished! INFO @ Sat, 01 Jun 2019 21:53:33: #2 predicted fragment length is 57 bps INFO @ Sat, 01 Jun 2019 21:53:33: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 01 Jun 2019 21:53:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.20_model.r WARNING @ Sat, 01 Jun 2019 21:53:33: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:53:33: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 01 Jun 2019 21:53:33: #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 21:53:33: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:53:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:53:33: 6000000 INFO @ Sat, 01 Jun 2019 21:53:34: 6000000 INFO @ Sat, 01 Jun 2019 21:53:38: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:53:38: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:53:38: #1 total tags in treatment: 6541631 INFO @ Sat, 01 Jun 2019 21:53:38: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:53:38: #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 21:53:38: #1 tag size is determined as 50 bps INFO @ Sat, 01 Jun 2019 21:53:38: #1 tag size = 50 INFO @ Sat, 01 Jun 2019 21:53:38: #1 total tags in treatment: 6541631 INFO @ Sat, 01 Jun 2019 21:53:38: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:53:38: #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 21:53:38: #1 tags after filtering in treatment: 6541631 INFO @ Sat, 01 Jun 2019 21:53:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:53:38: #1 finished! INFO @ Sat, 01 Jun 2019 21:53:38: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:53:38: #1 tags after filtering in treatment: 6541631 INFO @ Sat, 01 Jun 2019 21:53:38: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:53:38: #1 finished! INFO @ Sat, 01 Jun 2019 21:53:38: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:53:38: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:53:38: #2 number of paired peaks: 566 WARNING @ Sat, 01 Jun 2019 21:53:38: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Sat, 01 Jun 2019 21:53:38: start model_add_line... INFO @ Sat, 01 Jun 2019 21:53:38: #2 number of paired peaks: 566 WARNING @ Sat, 01 Jun 2019 21:53:38: Fewer paired peaks (566) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 566 pairs to build model! INFO @ Sat, 01 Jun 2019 21:53:38: start model_add_line... INFO @ Sat, 01 Jun 2019 21:53:38: start X-correlation... INFO @ Sat, 01 Jun 2019 21:53:38: end of X-cor INFO @ Sat, 01 Jun 2019 21:53:38: #2 finished! INFO @ Sat, 01 Jun 2019 21:53:38: #2 predicted fragment length is 57 bps INFO @ Sat, 01 Jun 2019 21:53:38: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 01 Jun 2019 21:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.05_model.r INFO @ Sat, 01 Jun 2019 21:53:38: start X-correlation... WARNING @ Sat, 01 Jun 2019 21:53:38: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:53:38: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 01 Jun 2019 21:53:38: #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 21:53:38: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:53:38: end of X-cor INFO @ Sat, 01 Jun 2019 21:53:38: #2 finished! INFO @ Sat, 01 Jun 2019 21:53:38: #2 predicted fragment length is 57 bps INFO @ Sat, 01 Jun 2019 21:53:38: #2 alternative fragment length(s) may be 4,57 bps INFO @ Sat, 01 Jun 2019 21:53:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.10_model.r WARNING @ Sat, 01 Jun 2019 21:53:38: #2 Since the d (57) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sat, 01 Jun 2019 21:53:38: #2 You may need to consider one of the other alternative d(s): 4,57 WARNING @ Sat, 01 Jun 2019 21:53:38: #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 21:53:38: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:53:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:53:52: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:58: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:58: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:54:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:54:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:54:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.20_summits.bed INFO @ Sat, 01 Jun 2019 21:54:02: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (241 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:54:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:54:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:54:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.10_summits.bed INFO @ Sat, 01 Jun 2019 21:54:07: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (608 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:54:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:54:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:54:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4344417/SRX4344417.05_summits.bed INFO @ Sat, 01 Jun 2019 21:54:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1077 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。