Job ID = 1293216 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 23,657,544 reads read : 47,315,088 reads written : 23,657,544 reads 0-length : 23,657,544 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: 00:05:59 23657544 reads; of these: 23657544 (100.00%) were unpaired; of these: 680896 (2.88%) aligned 0 times 19293018 (81.55%) aligned exactly 1 time 3683630 (15.57%) aligned >1 times 97.12% overall alignment rate Time searching: 00:05:59 Overall time: 00:05:59 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 12 files... [bam_rmdupse_core] 5907766 / 22976648 = 0.2571 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 22:35:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.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 22:35:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:35:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:35:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.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 22:35:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:35:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:35:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.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 22:35:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:35:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:35:52: 1000000 INFO @ Sun, 02 Jun 2019 22:35:52: 1000000 INFO @ Sun, 02 Jun 2019 22:35:54: 1000000 INFO @ Sun, 02 Jun 2019 22:36:01: 2000000 INFO @ Sun, 02 Jun 2019 22:36:01: 2000000 INFO @ Sun, 02 Jun 2019 22:36:04: 2000000 INFO @ Sun, 02 Jun 2019 22:36:10: 3000000 INFO @ Sun, 02 Jun 2019 22:36:10: 3000000 INFO @ Sun, 02 Jun 2019 22:36:15: 3000000 INFO @ Sun, 02 Jun 2019 22:36:19: 4000000 INFO @ Sun, 02 Jun 2019 22:36:19: 4000000 INFO @ Sun, 02 Jun 2019 22:36:25: 4000000 INFO @ Sun, 02 Jun 2019 22:36:27: 5000000 INFO @ Sun, 02 Jun 2019 22:36:27: 5000000 INFO @ Sun, 02 Jun 2019 22:36:35: 5000000 INFO @ Sun, 02 Jun 2019 22:36:36: 6000000 INFO @ Sun, 02 Jun 2019 22:36:36: 6000000 INFO @ Sun, 02 Jun 2019 22:36:45: 7000000 INFO @ Sun, 02 Jun 2019 22:36:45: 7000000 INFO @ Sun, 02 Jun 2019 22:36:46: 6000000 INFO @ Sun, 02 Jun 2019 22:36:54: 8000000 INFO @ Sun, 02 Jun 2019 22:36:54: 8000000 INFO @ Sun, 02 Jun 2019 22:36:56: 7000000 INFO @ Sun, 02 Jun 2019 22:37:02: 9000000 INFO @ Sun, 02 Jun 2019 22:37:02: 9000000 INFO @ Sun, 02 Jun 2019 22:37:06: 8000000 INFO @ Sun, 02 Jun 2019 22:37:11: 10000000 INFO @ Sun, 02 Jun 2019 22:37:11: 10000000 INFO @ Sun, 02 Jun 2019 22:37:16: 9000000 INFO @ Sun, 02 Jun 2019 22:37:19: 11000000 INFO @ Sun, 02 Jun 2019 22:37:19: 11000000 INFO @ Sun, 02 Jun 2019 22:37:26: 10000000 INFO @ Sun, 02 Jun 2019 22:37:27: 12000000 INFO @ Sun, 02 Jun 2019 22:37:28: 12000000 INFO @ Sun, 02 Jun 2019 22:37:35: 11000000 INFO @ Sun, 02 Jun 2019 22:37:36: 13000000 INFO @ Sun, 02 Jun 2019 22:37:36: 13000000 INFO @ Sun, 02 Jun 2019 22:37:44: 14000000 INFO @ Sun, 02 Jun 2019 22:37:44: 14000000 INFO @ Sun, 02 Jun 2019 22:37:45: 12000000 INFO @ Sun, 02 Jun 2019 22:37:53: 15000000 INFO @ Sun, 02 Jun 2019 22:37:53: 15000000 INFO @ Sun, 02 Jun 2019 22:37:54: 13000000 INFO @ Sun, 02 Jun 2019 22:38:01: 16000000 INFO @ Sun, 02 Jun 2019 22:38:02: 16000000 INFO @ Sun, 02 Jun 2019 22:38:03: 14000000 INFO @ Sun, 02 Jun 2019 22:38:10: 17000000 INFO @ Sun, 02 Jun 2019 22:38:10: 17000000 INFO @ Sun, 02 Jun 2019 22:38:11: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:38:11: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:38:11: #1 total tags in treatment: 17068882 INFO @ Sun, 02 Jun 2019 22:38:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:38:11: #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 22:38:11: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:38:11: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:38:11: #1 total tags in treatment: 17068882 INFO @ Sun, 02 Jun 2019 22:38:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:38:11: #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 22:38:11: #1 tags after filtering in treatment: 17068882 INFO @ Sun, 02 Jun 2019 22:38:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:38:11: #1 finished! INFO @ Sun, 02 Jun 2019 22:38:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:38:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:38:11: #1 tags after filtering in treatment: 17068882 INFO @ Sun, 02 Jun 2019 22:38:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:38:11: #1 finished! INFO @ Sun, 02 Jun 2019 22:38:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:38:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:38:13: #2 number of paired peaks: 229 WARNING @ Sun, 02 Jun 2019 22:38:13: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sun, 02 Jun 2019 22:38:13: start model_add_line... INFO @ Sun, 02 Jun 2019 22:38:13: start X-correlation... INFO @ Sun, 02 Jun 2019 22:38:13: end of X-cor INFO @ Sun, 02 Jun 2019 22:38:13: #2 finished! INFO @ Sun, 02 Jun 2019 22:38:13: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:38:13: #2 alternative fragment length(s) may be 1,47,520 bps INFO @ Sun, 02 Jun 2019 22:38:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.05_model.r WARNING @ Sun, 02 Jun 2019 22:38:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:38:13: #2 You may need to consider one of the other alternative d(s): 1,47,520 WARNING @ Sun, 02 Jun 2019 22:38:13: #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 22:38:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:38:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:38:13: #2 number of paired peaks: 229 WARNING @ Sun, 02 Jun 2019 22:38:13: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sun, 02 Jun 2019 22:38:13: start model_add_line... INFO @ Sun, 02 Jun 2019 22:38:13: 15000000 INFO @ Sun, 02 Jun 2019 22:38:13: start X-correlation... INFO @ Sun, 02 Jun 2019 22:38:13: end of X-cor INFO @ Sun, 02 Jun 2019 22:38:13: #2 finished! INFO @ Sun, 02 Jun 2019 22:38:13: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:38:13: #2 alternative fragment length(s) may be 1,47,520 bps INFO @ Sun, 02 Jun 2019 22:38:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.10_model.r WARNING @ Sun, 02 Jun 2019 22:38:13: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:38:13: #2 You may need to consider one of the other alternative d(s): 1,47,520 WARNING @ Sun, 02 Jun 2019 22:38:13: #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 22:38:13: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:38:13: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:38:23: 16000000 INFO @ Sun, 02 Jun 2019 22:38:32: 17000000 INFO @ Sun, 02 Jun 2019 22:38:33: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:38:33: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:38:33: #1 total tags in treatment: 17068882 INFO @ Sun, 02 Jun 2019 22:38:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:38:33: #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 22:38:33: #1 tags after filtering in treatment: 17068882 INFO @ Sun, 02 Jun 2019 22:38:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:38:33: #1 finished! INFO @ Sun, 02 Jun 2019 22:38:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:38:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:38:35: #2 number of paired peaks: 229 WARNING @ Sun, 02 Jun 2019 22:38:35: Fewer paired peaks (229) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 229 pairs to build model! INFO @ Sun, 02 Jun 2019 22:38:35: start model_add_line... INFO @ Sun, 02 Jun 2019 22:38:35: start X-correlation... INFO @ Sun, 02 Jun 2019 22:38:35: end of X-cor INFO @ Sun, 02 Jun 2019 22:38:35: #2 finished! INFO @ Sun, 02 Jun 2019 22:38:35: #2 predicted fragment length is 1 bps INFO @ Sun, 02 Jun 2019 22:38:35: #2 alternative fragment length(s) may be 1,47,520 bps INFO @ Sun, 02 Jun 2019 22:38:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.20_model.r WARNING @ Sun, 02 Jun 2019 22:38:35: #2 Since the d (1) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:38:35: #2 You may need to consider one of the other alternative d(s): 1,47,520 WARNING @ Sun, 02 Jun 2019 22:38:35: #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 22:38:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:38:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:38:55: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:38:56: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.05_summits.bed INFO @ Sun, 02 Jun 2019 22:39:15: Done! pass1 - making usageList (0 chroms): 2 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:39:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:39:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:39:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.10_summits.bed INFO @ Sun, 02 Jun 2019 22:39:15: Done! pass1 - making usageList (0 chroms): 1 millis needLargeMem: trying to allocate 0 bytes (limit: 17179869184) CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:39:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:39:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:39:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:39:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402766/SRX5402766.20_summits.bed INFO @ Sun, 02 Jun 2019 22:39:34: Done! pass1 - making usageList (0 chroms): 2 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。