Job ID = 2590000 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,144,049 reads read : 6,144,049 reads written : 6,144,049 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:08 6144049 reads; of these: 6144049 (100.00%) were unpaired; of these: 474957 (7.73%) aligned 0 times 4733634 (77.04%) aligned exactly 1 time 935458 (15.23%) aligned >1 times 92.27% overall alignment rate Time searching: 00:01:08 Overall time: 00:01:08 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] 337709 / 5669092 = 0.0596 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 @ Mon, 12 Aug 2019 19:01:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.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 @ Mon, 12 Aug 2019 19:01:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:01:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.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 @ Mon, 12 Aug 2019 19:01:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:01:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.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 @ Mon, 12 Aug 2019 19:01:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:01:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:01:07: 1000000 INFO @ Mon, 12 Aug 2019 19:01:08: 1000000 INFO @ Mon, 12 Aug 2019 19:01:11: 1000000 INFO @ Mon, 12 Aug 2019 19:01:14: 2000000 INFO @ Mon, 12 Aug 2019 19:01:17: 2000000 INFO @ Mon, 12 Aug 2019 19:01:20: 2000000 INFO @ Mon, 12 Aug 2019 19:01:21: 3000000 INFO @ Mon, 12 Aug 2019 19:01:26: 3000000 INFO @ Mon, 12 Aug 2019 19:01:27: 4000000 INFO @ Mon, 12 Aug 2019 19:01:30: 3000000 INFO @ Mon, 12 Aug 2019 19:01:33: 5000000 INFO @ Mon, 12 Aug 2019 19:01:35: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:01:35: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:01:35: #1 total tags in treatment: 5331383 INFO @ Mon, 12 Aug 2019 19:01:35: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:01:35: #1 tags after filtering in treatment: 5331383 INFO @ Mon, 12 Aug 2019 19:01:35: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:35: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:35: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:35: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:35: 4000000 INFO @ Mon, 12 Aug 2019 19:01:36: #2 number of paired peaks: 343 WARNING @ Mon, 12 Aug 2019 19:01:36: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:36: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:36: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:36: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:36: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:36: #2 predicted fragment length is 29 bps INFO @ Mon, 12 Aug 2019 19:01:36: #2 alternative fragment length(s) may be 4,29,524 bps INFO @ Mon, 12 Aug 2019 19:01:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.10_model.r WARNING @ Mon, 12 Aug 2019 19:01:36: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:01:36: #2 You may need to consider one of the other alternative d(s): 4,29,524 WARNING @ Mon, 12 Aug 2019 19:01:36: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:01:36: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:36: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:39: 4000000 INFO @ Mon, 12 Aug 2019 19:01:44: 5000000 INFO @ Mon, 12 Aug 2019 19:01:47: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:01:47: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:01:47: #1 total tags in treatment: 5331383 INFO @ Mon, 12 Aug 2019 19:01:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:47: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:01:47: #1 tags after filtering in treatment: 5331383 INFO @ Mon, 12 Aug 2019 19:01:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:47: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:47: #2 number of paired peaks: 343 WARNING @ Mon, 12 Aug 2019 19:01:47: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:47: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:47: 5000000 INFO @ Mon, 12 Aug 2019 19:01:47: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:47: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:47: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:47: #2 predicted fragment length is 29 bps INFO @ Mon, 12 Aug 2019 19:01:47: #2 alternative fragment length(s) may be 4,29,524 bps INFO @ Mon, 12 Aug 2019 19:01:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.05_model.r WARNING @ Mon, 12 Aug 2019 19:01:47: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:01:47: #2 You may need to consider one of the other alternative d(s): 4,29,524 WARNING @ Mon, 12 Aug 2019 19:01:47: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:01:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:50: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 19:01:50: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 19:01:50: #1 total tags in treatment: 5331383 INFO @ Mon, 12 Aug 2019 19:01:50: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:01:50: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:01:50: #1 tags after filtering in treatment: 5331383 INFO @ Mon, 12 Aug 2019 19:01:50: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:01:50: #1 finished! INFO @ Mon, 12 Aug 2019 19:01:50: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:01:50: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:01:50: #2 number of paired peaks: 343 WARNING @ Mon, 12 Aug 2019 19:01:50: Fewer paired peaks (343) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 343 pairs to build model! INFO @ Mon, 12 Aug 2019 19:01:50: start model_add_line... INFO @ Mon, 12 Aug 2019 19:01:50: start X-correlation... INFO @ Mon, 12 Aug 2019 19:01:50: end of X-cor INFO @ Mon, 12 Aug 2019 19:01:50: #2 finished! INFO @ Mon, 12 Aug 2019 19:01:50: #2 predicted fragment length is 29 bps INFO @ Mon, 12 Aug 2019 19:01:50: #2 alternative fragment length(s) may be 4,29,524 bps INFO @ Mon, 12 Aug 2019 19:01:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.20_model.r WARNING @ Mon, 12 Aug 2019 19:01:50: #2 Since the d (29) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:01:50: #2 You may need to consider one of the other alternative d(s): 4,29,524 WARNING @ Mon, 12 Aug 2019 19:01:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:01:50: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:01:50: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:01:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:01:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:01:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:01:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.10_summits.bed INFO @ Mon, 12 Aug 2019 19:01:59: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (205 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:02:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:02:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.05_summits.bed INFO @ Mon, 12 Aug 2019 19:02:11: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (429 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:02:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:02:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:02:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX467178/SRX467178.20_summits.bed INFO @ Mon, 12 Aug 2019 19:02:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (66 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。