Job ID = 1293136 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 33,352,250 reads read : 33,352,250 reads written : 33,352,250 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: 00:08:34 33352250 reads; of these: 33352250 (100.00%) were unpaired; of these: 4340507 (13.01%) aligned 0 times 24787414 (74.32%) aligned exactly 1 time 4224329 (12.67%) aligned >1 times 86.99% overall alignment rate Time searching: 00:08:34 Overall time: 00:08:34 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] 16144047 / 29011743 = 0.5565 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 22:30:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.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 22:30:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:30:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:30:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.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 22:30:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:30:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:30:04: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.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 22:30:04: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:30:04: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:30:12: 1000000 INFO @ Sun, 02 Jun 2019 22:30:16: 1000000 INFO @ Sun, 02 Jun 2019 22:30:16: 1000000 INFO @ Sun, 02 Jun 2019 22:30:20: 2000000 INFO @ Sun, 02 Jun 2019 22:30:27: 2000000 INFO @ Sun, 02 Jun 2019 22:30:27: 2000000 INFO @ Sun, 02 Jun 2019 22:30:28: 3000000 INFO @ Sun, 02 Jun 2019 22:30:35: 4000000 INFO @ Sun, 02 Jun 2019 22:30:38: 3000000 INFO @ Sun, 02 Jun 2019 22:30:38: 3000000 INFO @ Sun, 02 Jun 2019 22:30:43: 5000000 INFO @ Sun, 02 Jun 2019 22:30:49: 4000000 INFO @ Sun, 02 Jun 2019 22:30:49: 4000000 INFO @ Sun, 02 Jun 2019 22:30:51: 6000000 INFO @ Sun, 02 Jun 2019 22:30:59: 7000000 INFO @ Sun, 02 Jun 2019 22:31:00: 5000000 INFO @ Sun, 02 Jun 2019 22:31:00: 5000000 INFO @ Sun, 02 Jun 2019 22:31:06: 8000000 INFO @ Sun, 02 Jun 2019 22:31:11: 6000000 INFO @ Sun, 02 Jun 2019 22:31:11: 6000000 INFO @ Sun, 02 Jun 2019 22:31:14: 9000000 INFO @ Sun, 02 Jun 2019 22:31:22: 10000000 INFO @ Sun, 02 Jun 2019 22:31:22: 7000000 INFO @ Sun, 02 Jun 2019 22:31:22: 7000000 INFO @ Sun, 02 Jun 2019 22:31:30: 11000000 INFO @ Sun, 02 Jun 2019 22:31:33: 8000000 INFO @ Sun, 02 Jun 2019 22:31:33: 8000000 INFO @ Sun, 02 Jun 2019 22:31:37: 12000000 INFO @ Sun, 02 Jun 2019 22:31:44: 9000000 INFO @ Sun, 02 Jun 2019 22:31:44: 9000000 INFO @ Sun, 02 Jun 2019 22:31:44: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:31:44: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:31:44: #1 total tags in treatment: 12867696 INFO @ Sun, 02 Jun 2019 22:31:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:31:44: #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 22:31:44: #1 tags after filtering in treatment: 12867696 INFO @ Sun, 02 Jun 2019 22:31:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:31:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:31:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:31:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:31:45: #2 number of paired peaks: 367 WARNING @ Sun, 02 Jun 2019 22:31:45: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Sun, 02 Jun 2019 22:31:45: start model_add_line... INFO @ Sun, 02 Jun 2019 22:31:46: start X-correlation... INFO @ Sun, 02 Jun 2019 22:31:46: end of X-cor INFO @ Sun, 02 Jun 2019 22:31:46: #2 finished! INFO @ Sun, 02 Jun 2019 22:31:46: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 22:31:46: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 22:31:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.05_model.r WARNING @ Sun, 02 Jun 2019 22:31:46: #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 22:31:46: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 22:31:46: #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 22:31:46: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:31:46: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:31:55: 10000000 INFO @ Sun, 02 Jun 2019 22:31:55: 10000000 INFO @ Sun, 02 Jun 2019 22:32:06: 11000000 INFO @ Sun, 02 Jun 2019 22:32:06: 11000000 INFO @ Sun, 02 Jun 2019 22:32:17: 12000000 INFO @ Sun, 02 Jun 2019 22:32:17: 12000000 INFO @ Sun, 02 Jun 2019 22:32:19: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:32:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:32:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:32:26: #1 total tags in treatment: 12867696 INFO @ Sun, 02 Jun 2019 22:32:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:32:26: #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 22:32:26: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:32:26: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:32:26: #1 total tags in treatment: 12867696 INFO @ Sun, 02 Jun 2019 22:32:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:32:26: #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 22:32:26: #1 tags after filtering in treatment: 12867696 INFO @ Sun, 02 Jun 2019 22:32:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:32:26: #1 finished! INFO @ Sun, 02 Jun 2019 22:32:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:32:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:32:26: #1 tags after filtering in treatment: 12867696 INFO @ Sun, 02 Jun 2019 22:32:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:32:26: #1 finished! INFO @ Sun, 02 Jun 2019 22:32:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:32:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:32:28: #2 number of paired peaks: 367 WARNING @ Sun, 02 Jun 2019 22:32:28: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Sun, 02 Jun 2019 22:32:28: start model_add_line... INFO @ Sun, 02 Jun 2019 22:32:28: #2 number of paired peaks: 367 WARNING @ Sun, 02 Jun 2019 22:32:28: Fewer paired peaks (367) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 367 pairs to build model! INFO @ Sun, 02 Jun 2019 22:32:28: start model_add_line... INFO @ Sun, 02 Jun 2019 22:32:28: start X-correlation... INFO @ Sun, 02 Jun 2019 22:32:28: end of X-cor INFO @ Sun, 02 Jun 2019 22:32:28: #2 finished! INFO @ Sun, 02 Jun 2019 22:32:28: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 22:32:28: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 22:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.20_model.r WARNING @ Sun, 02 Jun 2019 22:32:28: #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 22:32:28: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 22:32:28: #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 22:32:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:32:28: start X-correlation... INFO @ Sun, 02 Jun 2019 22:32:28: end of X-cor INFO @ Sun, 02 Jun 2019 22:32:28: #2 finished! INFO @ Sun, 02 Jun 2019 22:32:28: #2 predicted fragment length is 47 bps INFO @ Sun, 02 Jun 2019 22:32:28: #2 alternative fragment length(s) may be 2,47 bps INFO @ Sun, 02 Jun 2019 22:32:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.10_model.r WARNING @ Sun, 02 Jun 2019 22:32:28: #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 22:32:28: #2 You may need to consider one of the other alternative d(s): 2,47 WARNING @ Sun, 02 Jun 2019 22:32:28: #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 22:32:28: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:32:28: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:32:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:32:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:32:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.05_summits.bed INFO @ Sun, 02 Jun 2019 22:32:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1801 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:33:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:33:01: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:33:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:33:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:33:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.10_summits.bed INFO @ Sun, 02 Jun 2019 22:33:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (471 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:33:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:33:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:33:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402708/SRX5402708.20_summits.bed INFO @ Sun, 02 Jun 2019 22:33:18: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (189 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。