Job ID = 1293225 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,152,034 reads read : 48,304,068 reads written : 24,152,034 reads 0-length : 24,152,034 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: 00:04:12 24152034 reads; of these: 24152034 (100.00%) were unpaired; of these: 10425106 (43.16%) aligned 0 times 11416999 (47.27%) aligned exactly 1 time 2309929 (9.56%) aligned >1 times 56.84% overall alignment rate Time searching: 00:04:12 Overall time: 00:04:12 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] 4125862 / 13726928 = 0.3006 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 22:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.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 22:36:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:36:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.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 22:36:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:36:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:36:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.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 22:36:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:36:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:36:27: 1000000 INFO @ Sun, 02 Jun 2019 22:36:27: 1000000 INFO @ Sun, 02 Jun 2019 22:36:27: 1000000 INFO @ Sun, 02 Jun 2019 22:36:34: 2000000 INFO @ Sun, 02 Jun 2019 22:36:36: 2000000 INFO @ Sun, 02 Jun 2019 22:36:36: 2000000 INFO @ Sun, 02 Jun 2019 22:36:42: 3000000 INFO @ Sun, 02 Jun 2019 22:36:44: 3000000 INFO @ Sun, 02 Jun 2019 22:36:45: 3000000 INFO @ Sun, 02 Jun 2019 22:36:49: 4000000 INFO @ Sun, 02 Jun 2019 22:36:53: 4000000 INFO @ Sun, 02 Jun 2019 22:36:54: 4000000 INFO @ Sun, 02 Jun 2019 22:36:57: 5000000 INFO @ Sun, 02 Jun 2019 22:37:01: 5000000 INFO @ Sun, 02 Jun 2019 22:37:02: 5000000 INFO @ Sun, 02 Jun 2019 22:37:04: 6000000 INFO @ Sun, 02 Jun 2019 22:37:09: 6000000 INFO @ Sun, 02 Jun 2019 22:37:11: 6000000 INFO @ Sun, 02 Jun 2019 22:37:12: 7000000 INFO @ Sun, 02 Jun 2019 22:37:18: 7000000 INFO @ Sun, 02 Jun 2019 22:37:19: 7000000 INFO @ Sun, 02 Jun 2019 22:37:19: 8000000 INFO @ Sun, 02 Jun 2019 22:37:26: 8000000 INFO @ Sun, 02 Jun 2019 22:37:27: 9000000 INFO @ Sun, 02 Jun 2019 22:37:28: 8000000 INFO @ Sun, 02 Jun 2019 22:37:32: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:37:32: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:37:32: #1 total tags in treatment: 9601066 INFO @ Sun, 02 Jun 2019 22:37:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:37:32: #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 22:37:32: #1 tags after filtering in treatment: 9601066 INFO @ Sun, 02 Jun 2019 22:37:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:37:32: #1 finished! INFO @ Sun, 02 Jun 2019 22:37:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:37:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:37:33: #2 number of paired peaks: 328 WARNING @ Sun, 02 Jun 2019 22:37:33: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sun, 02 Jun 2019 22:37:33: start model_add_line... INFO @ Sun, 02 Jun 2019 22:37:33: start X-correlation... INFO @ Sun, 02 Jun 2019 22:37:33: end of X-cor INFO @ Sun, 02 Jun 2019 22:37:33: #2 finished! INFO @ Sun, 02 Jun 2019 22:37:33: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 22:37:33: #2 alternative fragment length(s) may be 2,50,543 bps INFO @ Sun, 02 Jun 2019 22:37:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.10_model.r WARNING @ Sun, 02 Jun 2019 22:37:33: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:37:33: #2 You may need to consider one of the other alternative d(s): 2,50,543 WARNING @ Sun, 02 Jun 2019 22:37:33: #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 22:37:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:37:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:37:36: 9000000 INFO @ Sun, 02 Jun 2019 22:37:37: 9000000 INFO @ Sun, 02 Jun 2019 22:37:41: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:37:41: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:37:41: #1 total tags in treatment: 9601066 INFO @ Sun, 02 Jun 2019 22:37:41: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:37:41: #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 22:37:41: #1 tags after filtering in treatment: 9601066 INFO @ Sun, 02 Jun 2019 22:37:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:37:41: #1 finished! INFO @ Sun, 02 Jun 2019 22:37:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:37:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:37:42: #2 number of paired peaks: 328 WARNING @ Sun, 02 Jun 2019 22:37:42: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sun, 02 Jun 2019 22:37:42: start model_add_line... INFO @ Sun, 02 Jun 2019 22:37:42: start X-correlation... INFO @ Sun, 02 Jun 2019 22:37:42: end of X-cor INFO @ Sun, 02 Jun 2019 22:37:42: #2 finished! INFO @ Sun, 02 Jun 2019 22:37:42: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 22:37:42: #2 alternative fragment length(s) may be 2,50,543 bps INFO @ Sun, 02 Jun 2019 22:37:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.20_model.r WARNING @ Sun, 02 Jun 2019 22:37:42: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:37:42: #2 You may need to consider one of the other alternative d(s): 2,50,543 WARNING @ Sun, 02 Jun 2019 22:37:42: #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 22:37:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:37:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:37:42: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:37:42: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:37:42: #1 total tags in treatment: 9601066 INFO @ Sun, 02 Jun 2019 22:37:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:37:42: #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 22:37:42: #1 tags after filtering in treatment: 9601066 INFO @ Sun, 02 Jun 2019 22:37:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:37:42: #1 finished! INFO @ Sun, 02 Jun 2019 22:37:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:37:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:37:43: #2 number of paired peaks: 328 WARNING @ Sun, 02 Jun 2019 22:37:43: Fewer paired peaks (328) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 328 pairs to build model! INFO @ Sun, 02 Jun 2019 22:37:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:37:43: start X-correlation... INFO @ Sun, 02 Jun 2019 22:37:43: end of X-cor INFO @ Sun, 02 Jun 2019 22:37:43: #2 finished! INFO @ Sun, 02 Jun 2019 22:37:43: #2 predicted fragment length is 50 bps INFO @ Sun, 02 Jun 2019 22:37:43: #2 alternative fragment length(s) may be 2,50,543 bps INFO @ Sun, 02 Jun 2019 22:37:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.05_model.r WARNING @ Sun, 02 Jun 2019 22:37:43: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:37:43: #2 You may need to consider one of the other alternative d(s): 2,50,543 WARNING @ Sun, 02 Jun 2019 22:37:43: #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 22:37:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:37:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:37:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:38:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:38:09: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:38:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:38:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:38:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.10_summits.bed INFO @ Sun, 02 Jun 2019 22:38:11: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (396 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:38:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:38:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:38:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.20_summits.bed INFO @ Sun, 02 Jun 2019 22:38:20: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (180 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:38:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:38:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:38:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402774/SRX5402774.05_summits.bed INFO @ Sun, 02 Jun 2019 22:38:22: Done! pass1 - making usageList (7 chroms): 0 millis pass2 - checking and writing primary data (701 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。