Job ID = 2589329 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,142,812 reads read : 6,142,812 reads written : 6,142,812 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217410.sra.cache’: 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: 00:00:55 6142812 reads; of these: 6142812 (100.00%) were unpaired; of these: 1694433 (27.58%) aligned 0 times 3733017 (60.77%) aligned exactly 1 time 715362 (11.65%) aligned >1 times 72.42% overall alignment rate Time searching: 00:00:55 Overall time: 00:00:55 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] 212339 / 4448379 = 0.0477 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 17:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.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 17:26:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:26:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:26:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.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 17:26:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:26:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:26:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.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 17:26:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:26:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:26:57: 1000000 INFO @ Mon, 12 Aug 2019 17:26:58: 1000000 INFO @ Mon, 12 Aug 2019 17:27:00: 1000000 INFO @ Mon, 12 Aug 2019 17:27:07: 2000000 INFO @ Mon, 12 Aug 2019 17:27:08: 2000000 INFO @ Mon, 12 Aug 2019 17:27:09: 2000000 INFO @ Mon, 12 Aug 2019 17:27:16: 3000000 INFO @ Mon, 12 Aug 2019 17:27:17: 3000000 INFO @ Mon, 12 Aug 2019 17:27:19: 3000000 INFO @ Mon, 12 Aug 2019 17:27:25: 4000000 INFO @ Mon, 12 Aug 2019 17:27:27: 4000000 INFO @ Mon, 12 Aug 2019 17:27:27: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:27:27: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:27:27: #1 total tags in treatment: 4236040 INFO @ Mon, 12 Aug 2019 17:27:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:27:27: #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 17:27:27: #1 tags after filtering in treatment: 4236040 INFO @ Mon, 12 Aug 2019 17:27:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:27:27: #1 finished! INFO @ Mon, 12 Aug 2019 17:27:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:27:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:27:28: 4000000 INFO @ Mon, 12 Aug 2019 17:27:28: #2 number of paired peaks: 386 WARNING @ Mon, 12 Aug 2019 17:27:28: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Mon, 12 Aug 2019 17:27:28: start model_add_line... INFO @ Mon, 12 Aug 2019 17:27:28: start X-correlation... INFO @ Mon, 12 Aug 2019 17:27:28: end of X-cor INFO @ Mon, 12 Aug 2019 17:27:28: #2 finished! INFO @ Mon, 12 Aug 2019 17:27:28: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 17:27:28: #2 alternative fragment length(s) may be 3,32,478,500,551,577 bps INFO @ Mon, 12 Aug 2019 17:27:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.05_model.r WARNING @ Mon, 12 Aug 2019 17:27:28: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:27:28: #2 You may need to consider one of the other alternative d(s): 3,32,478,500,551,577 WARNING @ Mon, 12 Aug 2019 17:27:28: #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 17:27:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:27:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:27:28: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:27:28: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:27:28: #1 total tags in treatment: 4236040 INFO @ Mon, 12 Aug 2019 17:27:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:27:28: #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 17:27:29: #1 tags after filtering in treatment: 4236040 INFO @ Mon, 12 Aug 2019 17:27:29: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:27:29: #1 finished! INFO @ Mon, 12 Aug 2019 17:27:29: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:27:29: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:27:29: #2 number of paired peaks: 386 WARNING @ Mon, 12 Aug 2019 17:27:29: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Mon, 12 Aug 2019 17:27:29: start model_add_line... INFO @ Mon, 12 Aug 2019 17:27:29: start X-correlation... INFO @ Mon, 12 Aug 2019 17:27:29: end of X-cor INFO @ Mon, 12 Aug 2019 17:27:29: #2 finished! INFO @ Mon, 12 Aug 2019 17:27:29: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 17:27:29: #2 alternative fragment length(s) may be 3,32,478,500,551,577 bps INFO @ Mon, 12 Aug 2019 17:27:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.10_model.r WARNING @ Mon, 12 Aug 2019 17:27:29: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:27:29: #2 You may need to consider one of the other alternative d(s): 3,32,478,500,551,577 WARNING @ Mon, 12 Aug 2019 17:27:29: #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 17:27:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:27:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:27:30: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:27:30: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:27:30: #1 total tags in treatment: 4236040 INFO @ Mon, 12 Aug 2019 17:27:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:27:30: #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 17:27:30: #1 tags after filtering in treatment: 4236040 INFO @ Mon, 12 Aug 2019 17:27:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:27:30: #1 finished! INFO @ Mon, 12 Aug 2019 17:27:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:27:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:27:30: #2 number of paired peaks: 386 WARNING @ Mon, 12 Aug 2019 17:27:30: Fewer paired peaks (386) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 386 pairs to build model! INFO @ Mon, 12 Aug 2019 17:27:30: start model_add_line... INFO @ Mon, 12 Aug 2019 17:27:30: start X-correlation... INFO @ Mon, 12 Aug 2019 17:27:30: end of X-cor INFO @ Mon, 12 Aug 2019 17:27:30: #2 finished! INFO @ Mon, 12 Aug 2019 17:27:30: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 17:27:30: #2 alternative fragment length(s) may be 3,32,478,500,551,577 bps INFO @ Mon, 12 Aug 2019 17:27:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.20_model.r WARNING @ Mon, 12 Aug 2019 17:27:30: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:27:30: #2 You may need to consider one of the other alternative d(s): 3,32,478,500,551,577 WARNING @ Mon, 12 Aug 2019 17:27:30: #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 17:27:30: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:27:30: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:27:40: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:27:42: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:27:43: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:27:46: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:27:46: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:27:46: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.05_summits.bed INFO @ Mon, 12 Aug 2019 17:27:46: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (381 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:27:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:27:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:27:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.10_summits.bed INFO @ Mon, 12 Aug 2019 17:27:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (185 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:27:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:27:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:27:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065704/SRX065704.20_summits.bed INFO @ Mon, 12 Aug 2019 17:27:49: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (34 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。