Job ID = 1293046 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 19,040,438 reads read : 38,080,876 reads written : 19,040,438 reads 0-length : 19,040,438 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: 00:06:40 19040438 reads; of these: 19040438 (100.00%) were unpaired; of these: 1291243 (6.78%) aligned 0 times 14860181 (78.05%) aligned exactly 1 time 2889014 (15.17%) aligned >1 times 93.22% overall alignment rate Time searching: 00:06:40 Overall time: 00:06:40 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] 2118138 / 17749195 = 0.1193 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 21:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.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 21:50:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:50:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.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 21:50:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:50:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:50:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.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 21:50:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:50:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:50:20: 1000000 INFO @ Sun, 02 Jun 2019 21:50:22: 1000000 INFO @ Sun, 02 Jun 2019 21:50:22: 1000000 INFO @ Sun, 02 Jun 2019 21:50:29: 2000000 INFO @ Sun, 02 Jun 2019 21:50:32: 2000000 INFO @ Sun, 02 Jun 2019 21:50:35: 2000000 INFO @ Sun, 02 Jun 2019 21:50:39: 3000000 INFO @ Sun, 02 Jun 2019 21:50:43: 3000000 INFO @ Sun, 02 Jun 2019 21:50:47: 3000000 INFO @ Sun, 02 Jun 2019 21:50:48: 4000000 INFO @ Sun, 02 Jun 2019 21:50:54: 4000000 INFO @ Sun, 02 Jun 2019 21:50:59: 5000000 INFO @ Sun, 02 Jun 2019 21:50:59: 4000000 INFO @ Sun, 02 Jun 2019 21:51:04: 5000000 INFO @ Sun, 02 Jun 2019 21:51:09: 6000000 INFO @ Sun, 02 Jun 2019 21:51:11: 5000000 INFO @ Sun, 02 Jun 2019 21:51:15: 6000000 INFO @ Sun, 02 Jun 2019 21:51:19: 7000000 INFO @ Sun, 02 Jun 2019 21:51:24: 6000000 INFO @ Sun, 02 Jun 2019 21:51:25: 7000000 INFO @ Sun, 02 Jun 2019 21:51:29: 8000000 INFO @ Sun, 02 Jun 2019 21:51:36: 8000000 INFO @ Sun, 02 Jun 2019 21:51:36: 7000000 INFO @ Sun, 02 Jun 2019 21:51:39: 9000000 INFO @ Sun, 02 Jun 2019 21:51:46: 9000000 INFO @ Sun, 02 Jun 2019 21:51:48: 8000000 INFO @ Sun, 02 Jun 2019 21:51:49: 10000000 INFO @ Sun, 02 Jun 2019 21:51:56: 10000000 INFO @ Sun, 02 Jun 2019 21:52:00: 11000000 INFO @ Sun, 02 Jun 2019 21:52:00: 9000000 INFO @ Sun, 02 Jun 2019 21:52:07: 11000000 INFO @ Sun, 02 Jun 2019 21:52:10: 12000000 INFO @ Sun, 02 Jun 2019 21:52:13: 10000000 INFO @ Sun, 02 Jun 2019 21:52:17: 12000000 INFO @ Sun, 02 Jun 2019 21:52:20: 13000000 INFO @ Sun, 02 Jun 2019 21:52:25: 11000000 INFO @ Sun, 02 Jun 2019 21:52:27: 13000000 INFO @ Sun, 02 Jun 2019 21:52:30: 14000000 INFO @ Sun, 02 Jun 2019 21:52:37: 12000000 INFO @ Sun, 02 Jun 2019 21:52:38: 14000000 INFO @ Sun, 02 Jun 2019 21:52:40: 15000000 INFO @ Sun, 02 Jun 2019 21:52:46: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:52:46: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:52:46: #1 total tags in treatment: 15631057 INFO @ Sun, 02 Jun 2019 21:52:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:52:46: #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 21:52:47: #1 tags after filtering in treatment: 15631057 INFO @ Sun, 02 Jun 2019 21:52:47: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:52:47: #1 finished! INFO @ Sun, 02 Jun 2019 21:52:47: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:52:47: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:52:48: #2 number of paired peaks: 232 WARNING @ Sun, 02 Jun 2019 21:52:48: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sun, 02 Jun 2019 21:52:48: start model_add_line... INFO @ Sun, 02 Jun 2019 21:52:48: 15000000 INFO @ Sun, 02 Jun 2019 21:52:48: start X-correlation... INFO @ Sun, 02 Jun 2019 21:52:48: end of X-cor INFO @ Sun, 02 Jun 2019 21:52:48: #2 finished! INFO @ Sun, 02 Jun 2019 21:52:48: #2 predicted fragment length is 70 bps INFO @ Sun, 02 Jun 2019 21:52:48: #2 alternative fragment length(s) may be 3,70 bps INFO @ Sun, 02 Jun 2019 21:52:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.10_model.r WARNING @ Sun, 02 Jun 2019 21:52:48: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:52:48: #2 You may need to consider one of the other alternative d(s): 3,70 WARNING @ Sun, 02 Jun 2019 21:52:48: #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 21:52:48: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:52:48: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:52:49: 13000000 INFO @ Sun, 02 Jun 2019 21:52:55: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:52:55: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:52:55: #1 total tags in treatment: 15631057 INFO @ Sun, 02 Jun 2019 21:52:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:52:55: #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 21:52:55: #1 tags after filtering in treatment: 15631057 INFO @ Sun, 02 Jun 2019 21:52:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:52:55: #1 finished! INFO @ Sun, 02 Jun 2019 21:52:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:52:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:52:56: #2 number of paired peaks: 232 WARNING @ Sun, 02 Jun 2019 21:52:56: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sun, 02 Jun 2019 21:52:56: start model_add_line... INFO @ Sun, 02 Jun 2019 21:52:56: start X-correlation... INFO @ Sun, 02 Jun 2019 21:52:56: end of X-cor INFO @ Sun, 02 Jun 2019 21:52:56: #2 finished! INFO @ Sun, 02 Jun 2019 21:52:56: #2 predicted fragment length is 70 bps INFO @ Sun, 02 Jun 2019 21:52:56: #2 alternative fragment length(s) may be 3,70 bps INFO @ Sun, 02 Jun 2019 21:52:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.20_model.r WARNING @ Sun, 02 Jun 2019 21:52:56: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:52:56: #2 You may need to consider one of the other alternative d(s): 3,70 WARNING @ Sun, 02 Jun 2019 21:52:56: #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 21:52:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:52:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:53:00: 14000000 INFO @ Sun, 02 Jun 2019 21:53:11: 15000000 INFO @ Sun, 02 Jun 2019 21:53:17: #1 tag size is determined as 76 bps INFO @ Sun, 02 Jun 2019 21:53:17: #1 tag size = 76 INFO @ Sun, 02 Jun 2019 21:53:17: #1 total tags in treatment: 15631057 INFO @ Sun, 02 Jun 2019 21:53:17: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:53:17: #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 21:53:18: #1 tags after filtering in treatment: 15631057 INFO @ Sun, 02 Jun 2019 21:53:18: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:53:18: #1 finished! INFO @ Sun, 02 Jun 2019 21:53:18: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:53:18: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:53:19: #2 number of paired peaks: 232 WARNING @ Sun, 02 Jun 2019 21:53:19: Fewer paired peaks (232) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 232 pairs to build model! INFO @ Sun, 02 Jun 2019 21:53:19: start model_add_line... INFO @ Sun, 02 Jun 2019 21:53:19: start X-correlation... INFO @ Sun, 02 Jun 2019 21:53:19: end of X-cor INFO @ Sun, 02 Jun 2019 21:53:19: #2 finished! INFO @ Sun, 02 Jun 2019 21:53:19: #2 predicted fragment length is 70 bps INFO @ Sun, 02 Jun 2019 21:53:19: #2 alternative fragment length(s) may be 3,70 bps INFO @ Sun, 02 Jun 2019 21:53:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.05_model.r WARNING @ Sun, 02 Jun 2019 21:53:19: #2 Since the d (70) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 21:53:19: #2 You may need to consider one of the other alternative d(s): 3,70 WARNING @ Sun, 02 Jun 2019 21:53:19: #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 21:53:19: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:53:19: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:53:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:53:35: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:53:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:53:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:53:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.10_summits.bed INFO @ Sun, 02 Jun 2019 21:53:45: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (416 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:53:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:53:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:53:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.20_summits.bed INFO @ Sun, 02 Jun 2019 21:53:53: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (211 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:53:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:54:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:54:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:54:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020810/SRX5020810.05_summits.bed INFO @ Sun, 02 Jun 2019 21:54:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (581 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。