Job ID = 1292921 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,412,425 reads read : 10,412,425 reads written : 10,412,425 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: 00:02:35 10412425 reads; of these: 10412425 (100.00%) were unpaired; of these: 184107 (1.77%) aligned 0 times 8344132 (80.14%) aligned exactly 1 time 1884186 (18.10%) aligned >1 times 98.23% overall alignment rate Time searching: 00:02:35 Overall time: 00:02:35 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] 686567 / 10228318 = 0.0671 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 21:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.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 21:09:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.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 21:09:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.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 21:09:28: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:28: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:36: 1000000 INFO @ Sun, 02 Jun 2019 21:09:37: 1000000 INFO @ Sun, 02 Jun 2019 21:09:37: 1000000 INFO @ Sun, 02 Jun 2019 21:09:43: 2000000 INFO @ Sun, 02 Jun 2019 21:09:45: 2000000 INFO @ Sun, 02 Jun 2019 21:09:45: 2000000 INFO @ Sun, 02 Jun 2019 21:09:50: 3000000 INFO @ Sun, 02 Jun 2019 21:09:53: 3000000 INFO @ Sun, 02 Jun 2019 21:09:53: 3000000 INFO @ Sun, 02 Jun 2019 21:09:57: 4000000 INFO @ Sun, 02 Jun 2019 21:10:01: 4000000 INFO @ Sun, 02 Jun 2019 21:10:01: 4000000 INFO @ Sun, 02 Jun 2019 21:10:04: 5000000 INFO @ Sun, 02 Jun 2019 21:10:09: 5000000 INFO @ Sun, 02 Jun 2019 21:10:09: 5000000 INFO @ Sun, 02 Jun 2019 21:10:12: 6000000 INFO @ Sun, 02 Jun 2019 21:10:17: 6000000 INFO @ Sun, 02 Jun 2019 21:10:17: 6000000 INFO @ Sun, 02 Jun 2019 21:10:19: 7000000 INFO @ Sun, 02 Jun 2019 21:10:25: 7000000 INFO @ Sun, 02 Jun 2019 21:10:25: 7000000 INFO @ Sun, 02 Jun 2019 21:10:26: 8000000 INFO @ Sun, 02 Jun 2019 21:10:33: 8000000 INFO @ Sun, 02 Jun 2019 21:10:33: 9000000 INFO @ Sun, 02 Jun 2019 21:10:33: 8000000 INFO @ Sun, 02 Jun 2019 21:10:37: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:37: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:37: #1 total tags in treatment: 9541751 INFO @ Sun, 02 Jun 2019 21:10:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:37: #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 21:10:37: #1 tags after filtering in treatment: 9541751 INFO @ Sun, 02 Jun 2019 21:10:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:37: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:38: #2 number of paired peaks: 335 WARNING @ Sun, 02 Jun 2019 21:10:38: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:38: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:38: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:38: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:38: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:38: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:10:38: #2 alternative fragment length(s) may be 3,49,557,598 bps INFO @ Sun, 02 Jun 2019 21:10:38: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.20_model.r WARNING @ Sun, 02 Jun 2019 21:10:38: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:10:38: #2 You may need to consider one of the other alternative d(s): 3,49,557,598 WARNING @ Sun, 02 Jun 2019 21:10:38: #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 21:10:38: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:38: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:41: 9000000 INFO @ Sun, 02 Jun 2019 21:10:41: 9000000 INFO @ Sun, 02 Jun 2019 21:10:45: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:45: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:45: #1 total tags in treatment: 9541751 INFO @ Sun, 02 Jun 2019 21:10:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:45: #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 21:10:45: #1 tags after filtering in treatment: 9541751 INFO @ Sun, 02 Jun 2019 21:10:45: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:45: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:45: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:45: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:45: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:45: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:45: #1 total tags in treatment: 9541751 INFO @ Sun, 02 Jun 2019 21:10:45: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:45: #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 21:10:46: #1 tags after filtering in treatment: 9541751 INFO @ Sun, 02 Jun 2019 21:10:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:46: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:46: #2 number of paired peaks: 335 WARNING @ Sun, 02 Jun 2019 21:10:46: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:46: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:46: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:46: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:46: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:46: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:10:46: #2 alternative fragment length(s) may be 3,49,557,598 bps INFO @ Sun, 02 Jun 2019 21:10:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.10_model.r WARNING @ Sun, 02 Jun 2019 21:10:46: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:10:46: #2 You may need to consider one of the other alternative d(s): 3,49,557,598 WARNING @ Sun, 02 Jun 2019 21:10:46: #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 21:10:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:46: #2 number of paired peaks: 335 WARNING @ Sun, 02 Jun 2019 21:10:46: Fewer paired peaks (335) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 335 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:46: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:47: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:47: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:47: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:47: #2 predicted fragment length is 49 bps INFO @ Sun, 02 Jun 2019 21:10:47: #2 alternative fragment length(s) may be 3,49,557,598 bps INFO @ Sun, 02 Jun 2019 21:10:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.05_model.r WARNING @ Sun, 02 Jun 2019 21:10:47: #2 Since the d (49) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:10:47: #2 You may need to consider one of the other alternative d(s): 3,49,557,598 WARNING @ Sun, 02 Jun 2019 21:10:47: #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 21:10:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:11:04: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:11:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:11:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:11:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:11:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:11:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.20_summits.bed INFO @ Sun, 02 Jun 2019 21:11:16: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (204 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:11:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:11:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.10_summits.bed INFO @ Sun, 02 Jun 2019 21:11:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (432 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:11:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:11:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:11:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020714/SRX5020714.05_summits.bed INFO @ Sun, 02 Jun 2019 21:11:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (689 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。