Job ID = 1293117 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 14,054,183 reads read : 14,054,183 reads written : 14,054,183 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: 00:03:26 14054183 reads; of these: 14054183 (100.00%) were unpaired; of these: 231957 (1.65%) aligned 0 times 11968847 (85.16%) aligned exactly 1 time 1853379 (13.19%) aligned >1 times 98.35% overall alignment rate Time searching: 00:03:26 Overall time: 00:03:26 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] 1519506 / 13822226 = 0.1099 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 22:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.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 22:03:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:03:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.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 22:03:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:03:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:03:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.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 22:03:53: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:03:53: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:04:02: 1000000 INFO @ Sun, 02 Jun 2019 22:04:03: 1000000 INFO @ Sun, 02 Jun 2019 22:04:03: 1000000 INFO @ Sun, 02 Jun 2019 22:04:11: 2000000 INFO @ Sun, 02 Jun 2019 22:04:11: 2000000 INFO @ Sun, 02 Jun 2019 22:04:12: 2000000 INFO @ Sun, 02 Jun 2019 22:04:20: 3000000 INFO @ Sun, 02 Jun 2019 22:04:20: 3000000 INFO @ Sun, 02 Jun 2019 22:04:21: 3000000 INFO @ Sun, 02 Jun 2019 22:04:28: 4000000 INFO @ Sun, 02 Jun 2019 22:04:30: 4000000 INFO @ Sun, 02 Jun 2019 22:04:31: 4000000 INFO @ Sun, 02 Jun 2019 22:04:36: 5000000 INFO @ Sun, 02 Jun 2019 22:04:39: 5000000 INFO @ Sun, 02 Jun 2019 22:04:40: 5000000 INFO @ Sun, 02 Jun 2019 22:04:46: 6000000 INFO @ Sun, 02 Jun 2019 22:04:47: 6000000 INFO @ Sun, 02 Jun 2019 22:04:50: 6000000 INFO @ Sun, 02 Jun 2019 22:04:56: 7000000 INFO @ Sun, 02 Jun 2019 22:04:56: 7000000 INFO @ Sun, 02 Jun 2019 22:05:00: 7000000 INFO @ Sun, 02 Jun 2019 22:05:05: 8000000 INFO @ Sun, 02 Jun 2019 22:05:05: 8000000 INFO @ Sun, 02 Jun 2019 22:05:09: 8000000 INFO @ Sun, 02 Jun 2019 22:05:14: 9000000 INFO @ Sun, 02 Jun 2019 22:05:14: 9000000 INFO @ Sun, 02 Jun 2019 22:05:19: 9000000 INFO @ Sun, 02 Jun 2019 22:05:22: 10000000 INFO @ Sun, 02 Jun 2019 22:05:24: 10000000 INFO @ Sun, 02 Jun 2019 22:05:28: 10000000 INFO @ Sun, 02 Jun 2019 22:05:31: 11000000 INFO @ Sun, 02 Jun 2019 22:05:33: 11000000 INFO @ Sun, 02 Jun 2019 22:05:38: 11000000 INFO @ Sun, 02 Jun 2019 22:05:40: 12000000 INFO @ Sun, 02 Jun 2019 22:05:42: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:05:42: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:05:42: #1 total tags in treatment: 12302720 INFO @ Sun, 02 Jun 2019 22:05:42: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:42: #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 22:05:42: #1 tags after filtering in treatment: 12302720 INFO @ Sun, 02 Jun 2019 22:05:42: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:42: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:42: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:42: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:43: 12000000 INFO @ Sun, 02 Jun 2019 22:05:44: #2 number of paired peaks: 127 WARNING @ Sun, 02 Jun 2019 22:05:44: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sun, 02 Jun 2019 22:05:44: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:44: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:44: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:44: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:44: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 22:05:44: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 22:05:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.20_model.r WARNING @ Sun, 02 Jun 2019 22:05:44: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:05:44: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 22:05:44: #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 22:05:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:46: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:05:46: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:05:46: #1 total tags in treatment: 12302720 INFO @ Sun, 02 Jun 2019 22:05:46: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:46: #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 22:05:46: #1 tags after filtering in treatment: 12302720 INFO @ Sun, 02 Jun 2019 22:05:46: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:46: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:46: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:46: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:47: 12000000 INFO @ Sun, 02 Jun 2019 22:05:47: #2 number of paired peaks: 127 WARNING @ Sun, 02 Jun 2019 22:05:47: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sun, 02 Jun 2019 22:05:47: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:47: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:47: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:47: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:47: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 22:05:47: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 22:05:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.10_model.r WARNING @ Sun, 02 Jun 2019 22:05:47: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:05:47: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 22:05:47: #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 22:05:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:50: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:05:50: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:05:50: #1 total tags in treatment: 12302720 INFO @ Sun, 02 Jun 2019 22:05:50: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:50: #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 22:05:50: #1 tags after filtering in treatment: 12302720 INFO @ Sun, 02 Jun 2019 22:05:50: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:50: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:50: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:50: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:51: #2 number of paired peaks: 127 WARNING @ Sun, 02 Jun 2019 22:05:51: Fewer paired peaks (127) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 127 pairs to build model! INFO @ Sun, 02 Jun 2019 22:05:51: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:51: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:51: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:51: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:51: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 22:05:51: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 22:05:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.05_model.r WARNING @ Sun, 02 Jun 2019 22:05:51: #2 Since the d (47) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:05:51: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 22:05:51: #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 22:05:51: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:51: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:06:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:06:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:06:23: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:06:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:06:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:06:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.20_summits.bed INFO @ Sun, 02 Jun 2019 22:06:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (102 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:06:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:06:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:06:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.10_summits.bed INFO @ Sun, 02 Jun 2019 22:06:34: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (248 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:06:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:06:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:06:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529228/SRX529228.05_summits.bed INFO @ Sun, 02 Jun 2019 22:06:38: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (445 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。