Job ID = 1292923 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,171,554 reads read : 7,171,554 reads written : 7,171,554 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: 00:01:45 7171554 reads; of these: 7171554 (100.00%) were unpaired; of these: 589996 (8.23%) aligned 0 times 5539258 (77.24%) aligned exactly 1 time 1042300 (14.53%) aligned >1 times 91.77% overall alignment rate Time searching: 00:01:45 Overall time: 00:01:45 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] 359174 / 6581558 = 0.0546 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 21:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.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 21:08:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:08:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.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 21:08:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:08:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:08:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.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 21:08:23: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:08:23: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:08:32: 1000000 INFO @ Sun, 02 Jun 2019 21:08:32: 1000000 INFO @ Sun, 02 Jun 2019 21:08:33: 1000000 INFO @ Sun, 02 Jun 2019 21:08:41: 2000000 INFO @ Sun, 02 Jun 2019 21:08:41: 2000000 INFO @ Sun, 02 Jun 2019 21:08:43: 2000000 INFO @ Sun, 02 Jun 2019 21:08:50: 3000000 INFO @ Sun, 02 Jun 2019 21:08:50: 3000000 INFO @ Sun, 02 Jun 2019 21:08:54: 3000000 INFO @ Sun, 02 Jun 2019 21:08:58: 4000000 INFO @ Sun, 02 Jun 2019 21:08:59: 4000000 INFO @ Sun, 02 Jun 2019 21:09:05: 4000000 INFO @ Sun, 02 Jun 2019 21:09:07: 5000000 INFO @ Sun, 02 Jun 2019 21:09:07: 5000000 INFO @ Sun, 02 Jun 2019 21:09:16: 6000000 INFO @ Sun, 02 Jun 2019 21:09:16: 6000000 INFO @ Sun, 02 Jun 2019 21:09:18: 5000000 INFO @ Sun, 02 Jun 2019 21:09:18: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:09:18: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:09:18: #1 total tags in treatment: 6222384 INFO @ Sun, 02 Jun 2019 21:09:18: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:09:18: #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 21:09:18: #1 tags after filtering in treatment: 6222384 INFO @ Sun, 02 Jun 2019 21:09:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:09:18: #1 finished! INFO @ Sun, 02 Jun 2019 21:09:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:09:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:09:19: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:09:19: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:09:19: #1 total tags in treatment: 6222384 INFO @ Sun, 02 Jun 2019 21:09:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:09:19: #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 21:09:19: #1 tags after filtering in treatment: 6222384 INFO @ Sun, 02 Jun 2019 21:09:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:09:19: #1 finished! INFO @ Sun, 02 Jun 2019 21:09:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:09:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:09:19: #2 number of paired peaks: 388 WARNING @ Sun, 02 Jun 2019 21:09:19: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Sun, 02 Jun 2019 21:09:19: start model_add_line... INFO @ Sun, 02 Jun 2019 21:09:19: start X-correlation... INFO @ Sun, 02 Jun 2019 21:09:19: end of X-cor INFO @ Sun, 02 Jun 2019 21:09:19: #2 finished! INFO @ Sun, 02 Jun 2019 21:09:19: #2 predicted fragment length is 63 bps INFO @ Sun, 02 Jun 2019 21:09:19: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 02 Jun 2019 21:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.10_model.r WARNING @ Sun, 02 Jun 2019 21:09:19: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:09:19: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 02 Jun 2019 21:09:19: #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 21:09:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:09:19: #2 number of paired peaks: 388 WARNING @ Sun, 02 Jun 2019 21:09:19: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Sun, 02 Jun 2019 21:09:19: start model_add_line... INFO @ Sun, 02 Jun 2019 21:09:19: start X-correlation... INFO @ Sun, 02 Jun 2019 21:09:19: end of X-cor INFO @ Sun, 02 Jun 2019 21:09:19: #2 finished! INFO @ Sun, 02 Jun 2019 21:09:19: #2 predicted fragment length is 63 bps INFO @ Sun, 02 Jun 2019 21:09:19: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 02 Jun 2019 21:09:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.05_model.r WARNING @ Sun, 02 Jun 2019 21:09:19: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:09:19: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 02 Jun 2019 21:09:19: #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 21:09:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:09:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:09:29: 6000000 INFO @ Sun, 02 Jun 2019 21:09:31: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:09:31: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:09:31: #1 total tags in treatment: 6222384 INFO @ Sun, 02 Jun 2019 21:09:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:09:31: #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 21:09:31: #1 tags after filtering in treatment: 6222384 INFO @ Sun, 02 Jun 2019 21:09:31: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:09:31: #1 finished! INFO @ Sun, 02 Jun 2019 21:09:31: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:09:31: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:09:32: #2 number of paired peaks: 388 WARNING @ Sun, 02 Jun 2019 21:09:32: Fewer paired peaks (388) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 388 pairs to build model! INFO @ Sun, 02 Jun 2019 21:09:32: start model_add_line... INFO @ Sun, 02 Jun 2019 21:09:32: start X-correlation... INFO @ Sun, 02 Jun 2019 21:09:32: end of X-cor INFO @ Sun, 02 Jun 2019 21:09:32: #2 finished! INFO @ Sun, 02 Jun 2019 21:09:32: #2 predicted fragment length is 63 bps INFO @ Sun, 02 Jun 2019 21:09:32: #2 alternative fragment length(s) may be 63 bps INFO @ Sun, 02 Jun 2019 21:09:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.20_model.r WARNING @ Sun, 02 Jun 2019 21:09:32: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:09:32: #2 You may need to consider one of the other alternative d(s): 63 WARNING @ Sun, 02 Jun 2019 21:09:32: #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 21:09:32: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:09:32: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:09:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:09:38: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:09:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:09:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:09:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.10_summits.bed INFO @ Sun, 02 Jun 2019 21:09:46: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (294 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:09:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:09:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:09:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.05_summits.bed INFO @ Sun, 02 Jun 2019 21:09:47: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (659 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:09:51: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:09:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:09:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:09:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020716/SRX5020716.20_summits.bed INFO @ Sun, 02 Jun 2019 21:09:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (119 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。