Job ID = 2589920 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,509,420 reads read : 3,509,420 reads written : 3,509,420 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947564.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: 00:00:43 3509420 reads; of these: 3509420 (100.00%) were unpaired; of these: 14784 (0.42%) aligned 0 times 2920915 (83.23%) aligned exactly 1 time 573721 (16.35%) aligned >1 times 99.58% overall alignment rate Time searching: 00:00:43 Overall time: 00:00:43 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] 188714 / 3494636 = 0.0540 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 18:46:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.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 18:46:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:46:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:51: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.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 18:46:51: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:46:51: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.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 18:46:52: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:46:52: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:46:58: 1000000 INFO @ Mon, 12 Aug 2019 18:46:59: 1000000 INFO @ Mon, 12 Aug 2019 18:47:00: 1000000 INFO @ Mon, 12 Aug 2019 18:47:06: 2000000 INFO @ Mon, 12 Aug 2019 18:47:07: 2000000 INFO @ Mon, 12 Aug 2019 18:47:08: 2000000 INFO @ Mon, 12 Aug 2019 18:47:14: 3000000 INFO @ Mon, 12 Aug 2019 18:47:15: 3000000 INFO @ Mon, 12 Aug 2019 18:47:16: 3000000 INFO @ Mon, 12 Aug 2019 18:47:16: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:47:16: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:47:16: #1 total tags in treatment: 3305922 INFO @ Mon, 12 Aug 2019 18:47:16: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:47:16: #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 18:47:16: #1 tags after filtering in treatment: 3305922 INFO @ Mon, 12 Aug 2019 18:47:16: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:47:16: #1 finished! INFO @ Mon, 12 Aug 2019 18:47:16: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:47:16: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:47:17: #2 number of paired peaks: 374 WARNING @ Mon, 12 Aug 2019 18:47:17: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 12 Aug 2019 18:47:17: start model_add_line... INFO @ Mon, 12 Aug 2019 18:47:17: start X-correlation... INFO @ Mon, 12 Aug 2019 18:47:17: end of X-cor INFO @ Mon, 12 Aug 2019 18:47:17: #2 finished! INFO @ Mon, 12 Aug 2019 18:47:17: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 18:47:17: #2 alternative fragment length(s) may be 4,33,87 bps INFO @ Mon, 12 Aug 2019 18:47:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.05_model.r WARNING @ Mon, 12 Aug 2019 18:47:17: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:47:17: #2 You may need to consider one of the other alternative d(s): 4,33,87 WARNING @ Mon, 12 Aug 2019 18:47:17: #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 18:47:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:47:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:47:18: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:47:18: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:47:18: #1 total tags in treatment: 3305922 INFO @ Mon, 12 Aug 2019 18:47:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:47:18: #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 18:47:18: #1 tags after filtering in treatment: 3305922 INFO @ Mon, 12 Aug 2019 18:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:47:18: #1 finished! INFO @ Mon, 12 Aug 2019 18:47:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:47:18: #2 number of paired peaks: 374 WARNING @ Mon, 12 Aug 2019 18:47:18: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 12 Aug 2019 18:47:18: start model_add_line... INFO @ Mon, 12 Aug 2019 18:47:18: start X-correlation... INFO @ Mon, 12 Aug 2019 18:47:18: end of X-cor INFO @ Mon, 12 Aug 2019 18:47:18: #2 finished! INFO @ Mon, 12 Aug 2019 18:47:18: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 18:47:18: #2 alternative fragment length(s) may be 4,33,87 bps INFO @ Mon, 12 Aug 2019 18:47:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.10_model.r WARNING @ Mon, 12 Aug 2019 18:47:18: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:47:18: #2 You may need to consider one of the other alternative d(s): 4,33,87 WARNING @ Mon, 12 Aug 2019 18:47:18: #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 18:47:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:47:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:47:18: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:47:18: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:47:18: #1 total tags in treatment: 3305922 INFO @ Mon, 12 Aug 2019 18:47:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:47:18: #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 18:47:18: #1 tags after filtering in treatment: 3305922 INFO @ Mon, 12 Aug 2019 18:47:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:47:18: #1 finished! INFO @ Mon, 12 Aug 2019 18:47:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:47:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:47:19: #2 number of paired peaks: 374 WARNING @ Mon, 12 Aug 2019 18:47:19: Fewer paired peaks (374) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 374 pairs to build model! INFO @ Mon, 12 Aug 2019 18:47:19: start model_add_line... INFO @ Mon, 12 Aug 2019 18:47:19: start X-correlation... INFO @ Mon, 12 Aug 2019 18:47:19: end of X-cor INFO @ Mon, 12 Aug 2019 18:47:19: #2 finished! INFO @ Mon, 12 Aug 2019 18:47:19: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 18:47:19: #2 alternative fragment length(s) may be 4,33,87 bps INFO @ Mon, 12 Aug 2019 18:47:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.20_model.r WARNING @ Mon, 12 Aug 2019 18:47:19: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:47:19: #2 You may need to consider one of the other alternative d(s): 4,33,87 WARNING @ Mon, 12 Aug 2019 18:47:19: #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 18:47:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:47:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:47:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:47:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:47:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.05_summits.bed INFO @ Mon, 12 Aug 2019 18:47:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (305 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:47:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.10_summits.bed INFO @ Mon, 12 Aug 2019 18:47:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (130 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:47:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:47:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:47:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331327/SRX331327.20_summits.bed INFO @ Mon, 12 Aug 2019 18:47:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (35 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。