Job ID = 1292323 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 21,734,629 reads read : 21,734,629 reads written : 21,734,629 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: 00:06:19 21734629 reads; of these: 21734629 (100.00%) were unpaired; of these: 994803 (4.58%) aligned 0 times 17814979 (81.97%) aligned exactly 1 time 2924847 (13.46%) aligned >1 times 95.42% overall alignment rate Time searching: 00:06:19 Overall time: 00:06:19 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] 11445919 / 20739826 = 0.5519 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 18:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.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 18:13:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:13:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.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 18:13:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:13:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:13:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.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 18:13:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:13:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:13:28: 1000000 INFO @ Sun, 02 Jun 2019 18:13:29: 1000000 INFO @ Sun, 02 Jun 2019 18:13:30: 1000000 INFO @ Sun, 02 Jun 2019 18:13:36: 2000000 INFO @ Sun, 02 Jun 2019 18:13:38: 2000000 INFO @ Sun, 02 Jun 2019 18:13:39: 2000000 INFO @ Sun, 02 Jun 2019 18:13:43: 3000000 INFO @ Sun, 02 Jun 2019 18:13:46: 3000000 INFO @ Sun, 02 Jun 2019 18:13:48: 3000000 INFO @ Sun, 02 Jun 2019 18:13:51: 4000000 INFO @ Sun, 02 Jun 2019 18:13:54: 4000000 INFO @ Sun, 02 Jun 2019 18:13:56: 4000000 INFO @ Sun, 02 Jun 2019 18:13:58: 5000000 INFO @ Sun, 02 Jun 2019 18:14:02: 5000000 INFO @ Sun, 02 Jun 2019 18:14:05: 5000000 INFO @ Sun, 02 Jun 2019 18:14:05: 6000000 INFO @ Sun, 02 Jun 2019 18:14:11: 6000000 INFO @ Sun, 02 Jun 2019 18:14:13: 7000000 INFO @ Sun, 02 Jun 2019 18:14:14: 6000000 INFO @ Sun, 02 Jun 2019 18:14:19: 7000000 INFO @ Sun, 02 Jun 2019 18:14:21: 8000000 INFO @ Sun, 02 Jun 2019 18:14:22: 7000000 INFO @ Sun, 02 Jun 2019 18:14:28: 8000000 INFO @ Sun, 02 Jun 2019 18:14:29: 9000000 INFO @ Sun, 02 Jun 2019 18:14:31: 8000000 INFO @ Sun, 02 Jun 2019 18:14:31: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:14:31: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:14:31: #1 total tags in treatment: 9293907 INFO @ Sun, 02 Jun 2019 18:14:31: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:14:31: #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 18:14:32: #1 tags after filtering in treatment: 9293907 INFO @ Sun, 02 Jun 2019 18:14:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:14:32: #1 finished! INFO @ Sun, 02 Jun 2019 18:14:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:14:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:14:33: #2 number of paired peaks: 387 WARNING @ Sun, 02 Jun 2019 18:14:33: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Sun, 02 Jun 2019 18:14:33: start model_add_line... INFO @ Sun, 02 Jun 2019 18:14:33: start X-correlation... INFO @ Sun, 02 Jun 2019 18:14:33: end of X-cor INFO @ Sun, 02 Jun 2019 18:14:33: #2 finished! INFO @ Sun, 02 Jun 2019 18:14:33: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 18:14:33: #2 alternative fragment length(s) may be 3,45,505,520,540,563 bps INFO @ Sun, 02 Jun 2019 18:14:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.05_model.r WARNING @ Sun, 02 Jun 2019 18:14:33: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:14:33: #2 You may need to consider one of the other alternative d(s): 3,45,505,520,540,563 WARNING @ Sun, 02 Jun 2019 18:14:33: #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 18:14:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:14:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:14:37: 9000000 INFO @ Sun, 02 Jun 2019 18:14:40: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:14:40: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:14:40: #1 total tags in treatment: 9293907 INFO @ Sun, 02 Jun 2019 18:14:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:14:40: #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 18:14:40: #1 tags after filtering in treatment: 9293907 INFO @ Sun, 02 Jun 2019 18:14:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:14:40: #1 finished! INFO @ Sun, 02 Jun 2019 18:14:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:14:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:14:40: 9000000 INFO @ Sun, 02 Jun 2019 18:14:41: #2 number of paired peaks: 387 WARNING @ Sun, 02 Jun 2019 18:14:41: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Sun, 02 Jun 2019 18:14:41: start model_add_line... INFO @ Sun, 02 Jun 2019 18:14:41: start X-correlation... INFO @ Sun, 02 Jun 2019 18:14:41: end of X-cor INFO @ Sun, 02 Jun 2019 18:14:41: #2 finished! INFO @ Sun, 02 Jun 2019 18:14:41: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 18:14:41: #2 alternative fragment length(s) may be 3,45,505,520,540,563 bps INFO @ Sun, 02 Jun 2019 18:14:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.10_model.r WARNING @ Sun, 02 Jun 2019 18:14:41: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:14:41: #2 You may need to consider one of the other alternative d(s): 3,45,505,520,540,563 WARNING @ Sun, 02 Jun 2019 18:14:41: #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 18:14:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:14:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:14:43: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 18:14:43: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 18:14:43: #1 total tags in treatment: 9293907 INFO @ Sun, 02 Jun 2019 18:14:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:14:43: #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 18:14:43: #1 tags after filtering in treatment: 9293907 INFO @ Sun, 02 Jun 2019 18:14:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:14:43: #1 finished! INFO @ Sun, 02 Jun 2019 18:14:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:14:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:14:44: #2 number of paired peaks: 387 WARNING @ Sun, 02 Jun 2019 18:14:44: Fewer paired peaks (387) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 387 pairs to build model! INFO @ Sun, 02 Jun 2019 18:14:44: start model_add_line... INFO @ Sun, 02 Jun 2019 18:14:44: start X-correlation... INFO @ Sun, 02 Jun 2019 18:14:44: end of X-cor INFO @ Sun, 02 Jun 2019 18:14:44: #2 finished! INFO @ Sun, 02 Jun 2019 18:14:44: #2 predicted fragment length is 45 bps INFO @ Sun, 02 Jun 2019 18:14:44: #2 alternative fragment length(s) may be 3,45,505,520,540,563 bps INFO @ Sun, 02 Jun 2019 18:14:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.20_model.r WARNING @ Sun, 02 Jun 2019 18:14:44: #2 Since the d (45) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 18:14:44: #2 You may need to consider one of the other alternative d(s): 3,45,505,520,540,563 WARNING @ Sun, 02 Jun 2019 18:14:44: #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 18:14:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:14:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:14:58: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:15:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:15:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:15:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:15:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:15:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.05_summits.bed INFO @ Sun, 02 Jun 2019 18:15:11: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1002 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:15:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:15:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:15:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.10_summits.bed INFO @ Sun, 02 Jun 2019 18:15:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (475 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:15:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:15:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:15:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331347/SRX331347.20_summits.bed INFO @ Sun, 02 Jun 2019 18:15:23: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (154 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。