Job ID = 1292488 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,041,623 reads read : 10,041,623 reads written : 10,041,623 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: 00:02:16 10041623 reads; of these: 10041623 (100.00%) were unpaired; of these: 595778 (5.93%) aligned 0 times 8476833 (84.42%) aligned exactly 1 time 969012 (9.65%) aligned >1 times 94.07% overall alignment rate Time searching: 00:02:16 Overall time: 00:02:16 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_rmdupse_core] 2219564 / 9445845 = 0.2350 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 19:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.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 19:10:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:10:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.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 19:10:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:10:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:10:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.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 19:10:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:10:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:11:04: 1000000 INFO @ Sun, 02 Jun 2019 19:11:05: 1000000 INFO @ Sun, 02 Jun 2019 19:11:06: 1000000 INFO @ Sun, 02 Jun 2019 19:11:12: 2000000 INFO @ Sun, 02 Jun 2019 19:11:14: 2000000 INFO @ Sun, 02 Jun 2019 19:11:17: 2000000 INFO @ Sun, 02 Jun 2019 19:11:21: 3000000 INFO @ Sun, 02 Jun 2019 19:11:23: 3000000 INFO @ Sun, 02 Jun 2019 19:11:29: 3000000 INFO @ Sun, 02 Jun 2019 19:11:30: 4000000 INFO @ Sun, 02 Jun 2019 19:11:32: 4000000 INFO @ Sun, 02 Jun 2019 19:11:39: 5000000 INFO @ Sun, 02 Jun 2019 19:11:41: 5000000 INFO @ Sun, 02 Jun 2019 19:11:42: 4000000 INFO @ Sun, 02 Jun 2019 19:11:48: 6000000 INFO @ Sun, 02 Jun 2019 19:11:49: 6000000 INFO @ Sun, 02 Jun 2019 19:11:54: 5000000 INFO @ Sun, 02 Jun 2019 19:11:56: 7000000 INFO @ Sun, 02 Jun 2019 19:11:58: 7000000 INFO @ Sun, 02 Jun 2019 19:11:58: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:11:58: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:11:58: #1 total tags in treatment: 7226281 INFO @ Sun, 02 Jun 2019 19:11:58: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:11:58: #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 19:11:58: #1 tags after filtering in treatment: 7226281 INFO @ Sun, 02 Jun 2019 19:11:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:11:58: #1 finished! INFO @ Sun, 02 Jun 2019 19:11:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:11:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:11:59: #2 number of paired peaks: 591 WARNING @ Sun, 02 Jun 2019 19:11:59: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sun, 02 Jun 2019 19:11:59: start model_add_line... INFO @ Sun, 02 Jun 2019 19:11:59: start X-correlation... INFO @ Sun, 02 Jun 2019 19:11:59: end of X-cor INFO @ Sun, 02 Jun 2019 19:11:59: #2 finished! INFO @ Sun, 02 Jun 2019 19:11:59: #2 predicted fragment length is 85 bps INFO @ Sun, 02 Jun 2019 19:11:59: #2 alternative fragment length(s) may be 4,85,90 bps INFO @ Sun, 02 Jun 2019 19:11:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.10_model.r WARNING @ Sun, 02 Jun 2019 19:11:59: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:11:59: #2 You may need to consider one of the other alternative d(s): 4,85,90 WARNING @ Sun, 02 Jun 2019 19:11:59: #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 19:11:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:11:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:12:00: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:12:00: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:12:00: #1 total tags in treatment: 7226281 INFO @ Sun, 02 Jun 2019 19:12:00: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:12:00: #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 19:12:00: #1 tags after filtering in treatment: 7226281 INFO @ Sun, 02 Jun 2019 19:12:00: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:12:00: #1 finished! INFO @ Sun, 02 Jun 2019 19:12:00: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:12:00: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:12:00: #2 number of paired peaks: 591 WARNING @ Sun, 02 Jun 2019 19:12:00: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sun, 02 Jun 2019 19:12:00: start model_add_line... INFO @ Sun, 02 Jun 2019 19:12:01: start X-correlation... INFO @ Sun, 02 Jun 2019 19:12:01: end of X-cor INFO @ Sun, 02 Jun 2019 19:12:01: #2 finished! INFO @ Sun, 02 Jun 2019 19:12:01: #2 predicted fragment length is 85 bps INFO @ Sun, 02 Jun 2019 19:12:01: #2 alternative fragment length(s) may be 4,85,90 bps INFO @ Sun, 02 Jun 2019 19:12:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.20_model.r WARNING @ Sun, 02 Jun 2019 19:12:01: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:12:01: #2 You may need to consider one of the other alternative d(s): 4,85,90 WARNING @ Sun, 02 Jun 2019 19:12:01: #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 19:12:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:12:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:12:06: 6000000 INFO @ Sun, 02 Jun 2019 19:12:16: 7000000 INFO @ Sun, 02 Jun 2019 19:12:19: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 19:12:19: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 19:12:19: #1 total tags in treatment: 7226281 INFO @ Sun, 02 Jun 2019 19:12:19: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:12:19: #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 19:12:19: #1 tags after filtering in treatment: 7226281 INFO @ Sun, 02 Jun 2019 19:12:19: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:12:19: #1 finished! INFO @ Sun, 02 Jun 2019 19:12:19: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:12:19: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:12:19: #2 number of paired peaks: 591 WARNING @ Sun, 02 Jun 2019 19:12:19: Fewer paired peaks (591) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 591 pairs to build model! INFO @ Sun, 02 Jun 2019 19:12:19: start model_add_line... INFO @ Sun, 02 Jun 2019 19:12:19: start X-correlation... INFO @ Sun, 02 Jun 2019 19:12:20: end of X-cor INFO @ Sun, 02 Jun 2019 19:12:20: #2 finished! INFO @ Sun, 02 Jun 2019 19:12:20: #2 predicted fragment length is 85 bps INFO @ Sun, 02 Jun 2019 19:12:20: #2 alternative fragment length(s) may be 4,85,90 bps INFO @ Sun, 02 Jun 2019 19:12:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.05_model.r WARNING @ Sun, 02 Jun 2019 19:12:20: #2 Since the d (85) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 19:12:20: #2 You may need to consider one of the other alternative d(s): 4,85,90 WARNING @ Sun, 02 Jun 2019 19:12:20: #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 19:12:20: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:12:20: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:12:20: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:12:22: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:12:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.10_peaks.xls INFO @ Sun, 02 Jun 2019 19:12:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:12:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.10_summits.bed INFO @ Sun, 02 Jun 2019 19:12:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1273 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:12:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.20_peaks.xls INFO @ Sun, 02 Jun 2019 19:12:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:12:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.20_summits.bed INFO @ Sun, 02 Jun 2019 19:12:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (221 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 19:12:41: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 19:12:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.05_peaks.xls INFO @ Sun, 02 Jun 2019 19:12:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 19:12:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX466473/SRX466473.05_summits.bed INFO @ Sun, 02 Jun 2019 19:12:52: Done! pass1 - making usageList (6 chroms): 3 millis pass2 - checking and writing primary data (4812 records, 4 fields): 13 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。