Job ID = 1293075 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,311,814 reads read : 16,311,814 reads written : 16,311,814 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: 00:04:40 16311814 reads; of these: 16311814 (100.00%) were unpaired; of these: 562549 (3.45%) aligned 0 times 12340541 (75.65%) aligned exactly 1 time 3408724 (20.90%) aligned >1 times 96.55% overall alignment rate Time searching: 00:04:40 Overall time: 00:04:40 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] 2794695 / 15749265 = 0.1774 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 21:51:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.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 21:51:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:51:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:51:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.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 21:51:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:51:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:51:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.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 21:51:26: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:51:26: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:51:34: 1000000 INFO @ Sun, 02 Jun 2019 21:51:34: 1000000 INFO @ Sun, 02 Jun 2019 21:51:36: 1000000 INFO @ Sun, 02 Jun 2019 21:51:41: 2000000 INFO @ Sun, 02 Jun 2019 21:51:42: 2000000 INFO @ Sun, 02 Jun 2019 21:51:46: 2000000 INFO @ Sun, 02 Jun 2019 21:51:48: 3000000 INFO @ Sun, 02 Jun 2019 21:51:50: 3000000 INFO @ Sun, 02 Jun 2019 21:51:55: 3000000 INFO @ Sun, 02 Jun 2019 21:51:55: 4000000 INFO @ Sun, 02 Jun 2019 21:51:58: 4000000 INFO @ Sun, 02 Jun 2019 21:52:02: 5000000 INFO @ Sun, 02 Jun 2019 21:52:04: 4000000 INFO @ Sun, 02 Jun 2019 21:52:06: 5000000 INFO @ Sun, 02 Jun 2019 21:52:10: 6000000 INFO @ Sun, 02 Jun 2019 21:52:14: 6000000 INFO @ Sun, 02 Jun 2019 21:52:14: 5000000 INFO @ Sun, 02 Jun 2019 21:52:17: 7000000 INFO @ Sun, 02 Jun 2019 21:52:22: 7000000 INFO @ Sun, 02 Jun 2019 21:52:23: 6000000 INFO @ Sun, 02 Jun 2019 21:52:24: 8000000 INFO @ Sun, 02 Jun 2019 21:52:30: 8000000 INFO @ Sun, 02 Jun 2019 21:52:31: 9000000 INFO @ Sun, 02 Jun 2019 21:52:33: 7000000 INFO @ Sun, 02 Jun 2019 21:52:37: 9000000 INFO @ Sun, 02 Jun 2019 21:52:38: 10000000 INFO @ Sun, 02 Jun 2019 21:52:42: 8000000 INFO @ Sun, 02 Jun 2019 21:52:45: 10000000 INFO @ Sun, 02 Jun 2019 21:52:46: 11000000 INFO @ Sun, 02 Jun 2019 21:52:51: 9000000 INFO @ Sun, 02 Jun 2019 21:52:53: 12000000 INFO @ Sun, 02 Jun 2019 21:52:53: 11000000 INFO @ Sun, 02 Jun 2019 21:53:00: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:53:00: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:53:00: #1 total tags in treatment: 12954570 INFO @ Sun, 02 Jun 2019 21:53:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:53:00: #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 21:53:00: #1 tags after filtering in treatment: 12954570 INFO @ Sun, 02 Jun 2019 21:53:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:53:00: #1 finished! INFO @ Sun, 02 Jun 2019 21:53:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:53:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:53:01: 10000000 INFO @ Sun, 02 Jun 2019 21:53:01: 12000000 INFO @ Sun, 02 Jun 2019 21:53:01: #2 number of paired peaks: 495 WARNING @ Sun, 02 Jun 2019 21:53:01: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sun, 02 Jun 2019 21:53:01: start model_add_line... INFO @ Sun, 02 Jun 2019 21:53:01: start X-correlation... INFO @ Sun, 02 Jun 2019 21:53:01: end of X-cor INFO @ Sun, 02 Jun 2019 21:53:01: #2 finished! INFO @ Sun, 02 Jun 2019 21:53:01: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 21:53:01: #2 alternative fragment length(s) may be 2,42,571 bps INFO @ Sun, 02 Jun 2019 21:53:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.20_model.r WARNING @ Sun, 02 Jun 2019 21:53:01: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:53:01: #2 You may need to consider one of the other alternative d(s): 2,42,571 WARNING @ Sun, 02 Jun 2019 21:53:01: #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 21:53:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:53:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:53:08: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:53:08: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:53:08: #1 total tags in treatment: 12954570 INFO @ Sun, 02 Jun 2019 21:53:08: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:53:08: #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 21:53:08: #1 tags after filtering in treatment: 12954570 INFO @ Sun, 02 Jun 2019 21:53:08: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:53:08: #1 finished! INFO @ Sun, 02 Jun 2019 21:53:08: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:53:08: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:53:10: #2 number of paired peaks: 495 WARNING @ Sun, 02 Jun 2019 21:53:10: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sun, 02 Jun 2019 21:53:10: start model_add_line... INFO @ Sun, 02 Jun 2019 21:53:10: start X-correlation... INFO @ Sun, 02 Jun 2019 21:53:10: end of X-cor INFO @ Sun, 02 Jun 2019 21:53:10: #2 finished! INFO @ Sun, 02 Jun 2019 21:53:10: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 21:53:10: #2 alternative fragment length(s) may be 2,42,571 bps INFO @ Sun, 02 Jun 2019 21:53:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.10_model.r WARNING @ Sun, 02 Jun 2019 21:53:10: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:53:10: #2 You may need to consider one of the other alternative d(s): 2,42,571 WARNING @ Sun, 02 Jun 2019 21:53:10: #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 21:53:10: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:53:10: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:53:10: 11000000 INFO @ Sun, 02 Jun 2019 21:53:19: 12000000 INFO @ Sun, 02 Jun 2019 21:53:27: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:53:27: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:53:27: #1 total tags in treatment: 12954570 INFO @ Sun, 02 Jun 2019 21:53:27: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:53:27: #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 21:53:28: #1 tags after filtering in treatment: 12954570 INFO @ Sun, 02 Jun 2019 21:53:28: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:53:28: #1 finished! INFO @ Sun, 02 Jun 2019 21:53:28: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:53:28: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:53:29: #2 number of paired peaks: 495 WARNING @ Sun, 02 Jun 2019 21:53:29: Fewer paired peaks (495) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 495 pairs to build model! INFO @ Sun, 02 Jun 2019 21:53:29: start model_add_line... INFO @ Sun, 02 Jun 2019 21:53:29: start X-correlation... INFO @ Sun, 02 Jun 2019 21:53:29: end of X-cor INFO @ Sun, 02 Jun 2019 21:53:29: #2 finished! INFO @ Sun, 02 Jun 2019 21:53:29: #2 predicted fragment length is 2 bps INFO @ Sun, 02 Jun 2019 21:53:29: #2 alternative fragment length(s) may be 2,42,571 bps INFO @ Sun, 02 Jun 2019 21:53:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.05_model.r WARNING @ Sun, 02 Jun 2019 21:53:29: #2 Since the d (2) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:53:29: #2 You may need to consider one of the other alternative d(s): 2,42,571 WARNING @ Sun, 02 Jun 2019 21:53:29: #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 21:53:29: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:53:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:53:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:53:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:53:47: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:53:47: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:53:47: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.20_summits.bed INFO @ Sun, 02 Jun 2019 21:53:47: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:53:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:53:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:53:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.10_summits.bed INFO @ Sun, 02 Jun 2019 21:53:56: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:54:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:54:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:54:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:54:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020837/SRX5020837.05_summits.bed INFO @ Sun, 02 Jun 2019 21:54:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。