Job ID = 1292464 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 12,020,472 reads read : 12,020,472 reads written : 12,020,472 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: 00:01:59 12020472 reads; of these: 12020472 (100.00%) were unpaired; of these: 4625935 (38.48%) aligned 0 times 6166413 (51.30%) aligned exactly 1 time 1228124 (10.22%) aligned >1 times 61.52% overall alignment rate Time searching: 00:01:59 Overall time: 00:01:59 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] 4925828 / 7394537 = 0.6661 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 19:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.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 19:03:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:03:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.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 19:03:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:03:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:03:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.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 19:03:25: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:03:25: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:03:33: 1000000 INFO @ Sun, 02 Jun 2019 19:03:34: 1000000 INFO @ Sun, 02 Jun 2019 19:03:36: 1000000 INFO @ Sun, 02 Jun 2019 19:03:41: 2000000 INFO @ Sun, 02 Jun 2019 19:03:44: 2000000 INFO @ Sun, 02 Jun 2019 19:03:45: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:03:45: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:03:45: #1 total tags in treatment: 2468709 INFO @ Sun, 02 Jun 2019 19:03:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:03:45: #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 19:03:45: #1 tags after filtering in treatment: 2468709 INFO @ Sun, 02 Jun 2019 19:03:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:03:45: #1 finished! INFO @ Sun, 02 Jun 2019 19:03:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:03:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:03:45: #2 number of paired peaks: 807 WARNING @ Sun, 02 Jun 2019 19:03:45: Fewer paired peaks (807) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 807 pairs to build model! INFO @ Sun, 02 Jun 2019 19:03:45: start model_add_line... INFO @ Sun, 02 Jun 2019 19:03:45: start X-correlation... INFO @ Sun, 02 Jun 2019 19:03:45: end of X-cor INFO @ Sun, 02 Jun 2019 19:03:45: #2 finished! INFO @ Sun, 02 Jun 2019 19:03:45: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 19:03:45: #2 alternative fragment length(s) may be 39,563,578 bps INFO @ Sun, 02 Jun 2019 19:03:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.05_model.r WARNING @ Sun, 02 Jun 2019 19:03:45: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:03:45: #2 You may need to consider one of the other alternative d(s): 39,563,578 WARNING @ Sun, 02 Jun 2019 19:03:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:03:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:03:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:03:47: 2000000 INFO @ Sun, 02 Jun 2019 19:03:48: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:03:48: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:03:48: #1 total tags in treatment: 2468709 INFO @ Sun, 02 Jun 2019 19:03:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:03:48: #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 19:03:48: #1 tags after filtering in treatment: 2468709 INFO @ Sun, 02 Jun 2019 19:03:48: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:03:48: #1 finished! INFO @ Sun, 02 Jun 2019 19:03:48: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:03:48: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:03:48: #2 number of paired peaks: 807 WARNING @ Sun, 02 Jun 2019 19:03:48: Fewer paired peaks (807) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 807 pairs to build model! INFO @ Sun, 02 Jun 2019 19:03:48: start model_add_line... INFO @ Sun, 02 Jun 2019 19:03:48: start X-correlation... INFO @ Sun, 02 Jun 2019 19:03:48: end of X-cor INFO @ Sun, 02 Jun 2019 19:03:48: #2 finished! INFO @ Sun, 02 Jun 2019 19:03:48: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 19:03:48: #2 alternative fragment length(s) may be 39,563,578 bps INFO @ Sun, 02 Jun 2019 19:03:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.10_model.r WARNING @ Sun, 02 Jun 2019 19:03:48: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:03:48: #2 You may need to consider one of the other alternative d(s): 39,563,578 WARNING @ Sun, 02 Jun 2019 19:03:48: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:03:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:03:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:03:52: #1 tag size is determined as 40 bps INFO @ Sun, 02 Jun 2019 19:03:52: #1 tag size = 40 INFO @ Sun, 02 Jun 2019 19:03:52: #1 total tags in treatment: 2468709 INFO @ Sun, 02 Jun 2019 19:03:52: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:03:52: #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 19:03:52: #1 tags after filtering in treatment: 2468709 INFO @ Sun, 02 Jun 2019 19:03:52: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:03:52: #1 finished! INFO @ Sun, 02 Jun 2019 19:03:52: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:03:52: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:03:52: #2 number of paired peaks: 807 WARNING @ Sun, 02 Jun 2019 19:03:52: Fewer paired peaks (807) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 807 pairs to build model! INFO @ Sun, 02 Jun 2019 19:03:52: start model_add_line... INFO @ Sun, 02 Jun 2019 19:03:52: start X-correlation... INFO @ Sun, 02 Jun 2019 19:03:52: end of X-cor INFO @ Sun, 02 Jun 2019 19:03:52: #2 finished! INFO @ Sun, 02 Jun 2019 19:03:52: #2 predicted fragment length is 39 bps INFO @ Sun, 02 Jun 2019 19:03:52: #2 alternative fragment length(s) may be 39,563,578 bps INFO @ Sun, 02 Jun 2019 19:03:52: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.20_model.r WARNING @ Sun, 02 Jun 2019 19:03:52: #2 Since the d (39) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:03:52: #2 You may need to consider one of the other alternative d(s): 39,563,578 WARNING @ Sun, 02 Jun 2019 19:03:52: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 19:03:52: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:03:52: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:03:53: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:03:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:03:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:03:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:03:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.05_summits.bed INFO @ Sun, 02 Jun 2019 19:03:57: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (665 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:04:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:04:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:04:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.10_summits.bed INFO @ Sun, 02 Jun 2019 19:04:00: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (366 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:04:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:04:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:04:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:04:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4626837/SRX4626837.20_summits.bed INFO @ Sun, 02 Jun 2019 19:04:04: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (93 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。