Job ID = 1292942 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,616,058 reads read : 7,616,058 reads written : 7,616,058 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: 00:01:47 7616058 reads; of these: 7616058 (100.00%) were unpaired; of these: 676770 (8.89%) aligned 0 times 5839080 (76.67%) aligned exactly 1 time 1100208 (14.45%) aligned >1 times 91.11% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 348154 / 6939288 = 0.0502 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 21:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.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 21:11:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:11:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.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 21:11:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:11:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:11:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.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 21:11:06: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:11:06: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:11:13: 1000000 INFO @ Sun, 02 Jun 2019 21:11:14: 1000000 INFO @ Sun, 02 Jun 2019 21:11:14: 1000000 INFO @ Sun, 02 Jun 2019 21:11:19: 2000000 INFO @ Sun, 02 Jun 2019 21:11:21: 2000000 INFO @ Sun, 02 Jun 2019 21:11:21: 2000000 INFO @ Sun, 02 Jun 2019 21:11:26: 3000000 INFO @ Sun, 02 Jun 2019 21:11:28: 3000000 INFO @ Sun, 02 Jun 2019 21:11:29: 3000000 INFO @ Sun, 02 Jun 2019 21:11:32: 4000000 INFO @ Sun, 02 Jun 2019 21:11:35: 4000000 INFO @ Sun, 02 Jun 2019 21:11:36: 4000000 INFO @ Sun, 02 Jun 2019 21:11:38: 5000000 INFO @ Sun, 02 Jun 2019 21:11:42: 5000000 INFO @ Sun, 02 Jun 2019 21:11:43: 5000000 INFO @ Sun, 02 Jun 2019 21:11:45: 6000000 INFO @ Sun, 02 Jun 2019 21:11:49: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:11:49: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:11:49: #1 total tags in treatment: 6591134 INFO @ Sun, 02 Jun 2019 21:11:49: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:11:49: #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 21:11:49: #1 tags after filtering in treatment: 6591134 INFO @ Sun, 02 Jun 2019 21:11:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:11:49: #1 finished! INFO @ Sun, 02 Jun 2019 21:11:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:11:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:11:49: 6000000 INFO @ Sun, 02 Jun 2019 21:11:49: #2 number of paired peaks: 324 WARNING @ Sun, 02 Jun 2019 21:11:49: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sun, 02 Jun 2019 21:11:49: start model_add_line... INFO @ Sun, 02 Jun 2019 21:11:49: start X-correlation... INFO @ Sun, 02 Jun 2019 21:11:50: end of X-cor INFO @ Sun, 02 Jun 2019 21:11:50: #2 finished! INFO @ Sun, 02 Jun 2019 21:11:50: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 21:11:50: #2 alternative fragment length(s) may be 4,51,501 bps INFO @ Sun, 02 Jun 2019 21:11:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.20_model.r WARNING @ Sun, 02 Jun 2019 21:11:50: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:11:50: #2 You may need to consider one of the other alternative d(s): 4,51,501 WARNING @ Sun, 02 Jun 2019 21:11:50: #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 21:11:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:11:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:11:50: 6000000 INFO @ Sun, 02 Jun 2019 21:11:53: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:11:53: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:11:53: #1 total tags in treatment: 6591134 INFO @ Sun, 02 Jun 2019 21:11:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:11:53: #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 21:11:53: #1 tags after filtering in treatment: 6591134 INFO @ Sun, 02 Jun 2019 21:11:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:11:53: #1 finished! INFO @ Sun, 02 Jun 2019 21:11:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:11:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:11:54: #2 number of paired peaks: 324 WARNING @ Sun, 02 Jun 2019 21:11:54: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sun, 02 Jun 2019 21:11:54: start model_add_line... INFO @ Sun, 02 Jun 2019 21:11:54: start X-correlation... INFO @ Sun, 02 Jun 2019 21:11:54: end of X-cor INFO @ Sun, 02 Jun 2019 21:11:54: #2 finished! INFO @ Sun, 02 Jun 2019 21:11:54: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 21:11:54: #2 alternative fragment length(s) may be 4,51,501 bps INFO @ Sun, 02 Jun 2019 21:11:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.05_model.r WARNING @ Sun, 02 Jun 2019 21:11:54: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:11:54: #2 You may need to consider one of the other alternative d(s): 4,51,501 WARNING @ Sun, 02 Jun 2019 21:11:54: #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 21:11:54: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:11:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:11:54: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:11:54: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:11:54: #1 total tags in treatment: 6591134 INFO @ Sun, 02 Jun 2019 21:11:54: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:11:54: #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 21:11:54: #1 tags after filtering in treatment: 6591134 INFO @ Sun, 02 Jun 2019 21:11:54: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:11:54: #1 finished! INFO @ Sun, 02 Jun 2019 21:11:54: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:11:54: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:11:55: #2 number of paired peaks: 324 WARNING @ Sun, 02 Jun 2019 21:11:55: Fewer paired peaks (324) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 324 pairs to build model! INFO @ Sun, 02 Jun 2019 21:11:55: start model_add_line... INFO @ Sun, 02 Jun 2019 21:11:55: start X-correlation... INFO @ Sun, 02 Jun 2019 21:11:55: end of X-cor INFO @ Sun, 02 Jun 2019 21:11:55: #2 finished! INFO @ Sun, 02 Jun 2019 21:11:55: #2 predicted fragment length is 51 bps INFO @ Sun, 02 Jun 2019 21:11:55: #2 alternative fragment length(s) may be 4,51,501 bps INFO @ Sun, 02 Jun 2019 21:11:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.10_model.r WARNING @ Sun, 02 Jun 2019 21:11:55: #2 Since the d (51) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:11:55: #2 You may need to consider one of the other alternative d(s): 4,51,501 WARNING @ Sun, 02 Jun 2019 21:11:55: #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 21:11:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:11:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:12:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:12:13: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:12:14: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:12:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:12:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:12:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.20_summits.bed INFO @ Sun, 02 Jun 2019 21:12:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (122 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:12:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:12:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:12:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.05_summits.bed INFO @ Sun, 02 Jun 2019 21:12:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (503 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:12:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:12:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:12:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020729/SRX5020729.10_summits.bed INFO @ Sun, 02 Jun 2019 21:12:23: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (303 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。