Job ID = 2590055 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,727,987 reads read : 10,727,987 reads written : 10,727,987 rm: cannot remove ‘[DSE]RR*’: 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: 00:01:53 10727987 reads; of these: 10727987 (100.00%) were unpaired; of these: 2100076 (19.58%) aligned 0 times 7379845 (68.79%) aligned exactly 1 time 1248066 (11.63%) aligned >1 times 80.42% overall alignment rate Time searching: 00:01:53 Overall time: 00:01:53 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] 1364494 / 8627911 = 0.1581 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 @ Mon, 12 Aug 2019 19:26:42: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.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 @ Mon, 12 Aug 2019 19:26:42: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:26:42: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:26:43: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.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 @ Mon, 12 Aug 2019 19:26:43: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:26:43: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:26:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.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 @ Mon, 12 Aug 2019 19:26:44: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:26:44: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:26:51: 1000000 INFO @ Mon, 12 Aug 2019 19:26:52: 1000000 INFO @ Mon, 12 Aug 2019 19:26:52: 1000000 INFO @ Mon, 12 Aug 2019 19:26:58: 2000000 INFO @ Mon, 12 Aug 2019 19:26:59: 2000000 INFO @ Mon, 12 Aug 2019 19:27:00: 2000000 INFO @ Mon, 12 Aug 2019 19:27:05: 3000000 INFO @ Mon, 12 Aug 2019 19:27:06: 3000000 INFO @ Mon, 12 Aug 2019 19:27:09: 3000000 INFO @ Mon, 12 Aug 2019 19:27:12: 4000000 INFO @ Mon, 12 Aug 2019 19:27:14: 4000000 INFO @ Mon, 12 Aug 2019 19:27:17: 4000000 INFO @ Mon, 12 Aug 2019 19:27:20: 5000000 INFO @ Mon, 12 Aug 2019 19:27:21: 5000000 INFO @ Mon, 12 Aug 2019 19:27:26: 5000000 INFO @ Mon, 12 Aug 2019 19:27:27: 6000000 INFO @ Mon, 12 Aug 2019 19:27:28: 6000000 INFO @ Mon, 12 Aug 2019 19:27:34: 7000000 INFO @ Mon, 12 Aug 2019 19:27:35: 6000000 INFO @ Mon, 12 Aug 2019 19:27:36: 7000000 INFO @ Mon, 12 Aug 2019 19:27:36: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:27:36: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:27:36: #1 total tags in treatment: 7263417 INFO @ Mon, 12 Aug 2019 19:27:36: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:27:36: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:27:36: #1 tags after filtering in treatment: 7263417 INFO @ Mon, 12 Aug 2019 19:27:36: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:27:36: #1 finished! INFO @ Mon, 12 Aug 2019 19:27:36: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:27:36: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:27:37: #2 number of paired peaks: 289 WARNING @ Mon, 12 Aug 2019 19:27:37: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Mon, 12 Aug 2019 19:27:37: start model_add_line... INFO @ Mon, 12 Aug 2019 19:27:37: start X-correlation... INFO @ Mon, 12 Aug 2019 19:27:37: end of X-cor INFO @ Mon, 12 Aug 2019 19:27:37: #2 finished! INFO @ Mon, 12 Aug 2019 19:27:37: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 19:27:37: #2 alternative fragment length(s) may be 3,41,485,590,596 bps INFO @ Mon, 12 Aug 2019 19:27:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.10_model.r WARNING @ Mon, 12 Aug 2019 19:27:37: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:27:37: #2 You may need to consider one of the other alternative d(s): 3,41,485,590,596 WARNING @ Mon, 12 Aug 2019 19:27:37: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:27:37: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:27:37: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:27:38: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:27:38: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:27:38: #1 total tags in treatment: 7263417 INFO @ Mon, 12 Aug 2019 19:27:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:27:38: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:27:38: #1 tags after filtering in treatment: 7263417 INFO @ Mon, 12 Aug 2019 19:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:27:38: #1 finished! INFO @ Mon, 12 Aug 2019 19:27:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:27:39: #2 number of paired peaks: 289 WARNING @ Mon, 12 Aug 2019 19:27:39: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Mon, 12 Aug 2019 19:27:39: start model_add_line... INFO @ Mon, 12 Aug 2019 19:27:39: start X-correlation... INFO @ Mon, 12 Aug 2019 19:27:39: end of X-cor INFO @ Mon, 12 Aug 2019 19:27:39: #2 finished! INFO @ Mon, 12 Aug 2019 19:27:39: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 19:27:39: #2 alternative fragment length(s) may be 3,41,485,590,596 bps INFO @ Mon, 12 Aug 2019 19:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.20_model.r WARNING @ Mon, 12 Aug 2019 19:27:39: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:27:39: #2 You may need to consider one of the other alternative d(s): 3,41,485,590,596 WARNING @ Mon, 12 Aug 2019 19:27:39: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:27:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:27:43: 7000000 INFO @ Mon, 12 Aug 2019 19:27:45: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:27:45: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:27:45: #1 total tags in treatment: 7263417 INFO @ Mon, 12 Aug 2019 19:27:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:27:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:27:45: #1 tags after filtering in treatment: 7263417 INFO @ Mon, 12 Aug 2019 19:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:27:45: #1 finished! INFO @ Mon, 12 Aug 2019 19:27:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:27:46: #2 number of paired peaks: 289 WARNING @ Mon, 12 Aug 2019 19:27:46: Fewer paired peaks (289) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 289 pairs to build model! INFO @ Mon, 12 Aug 2019 19:27:46: start model_add_line... INFO @ Mon, 12 Aug 2019 19:27:46: start X-correlation... INFO @ Mon, 12 Aug 2019 19:27:46: end of X-cor INFO @ Mon, 12 Aug 2019 19:27:46: #2 finished! INFO @ Mon, 12 Aug 2019 19:27:46: #2 predicted fragment length is 41 bps INFO @ Mon, 12 Aug 2019 19:27:46: #2 alternative fragment length(s) may be 3,41,485,590,596 bps INFO @ Mon, 12 Aug 2019 19:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.05_model.r WARNING @ Mon, 12 Aug 2019 19:27:46: #2 Since the d (41) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 19:27:46: #2 You may need to consider one of the other alternative d(s): 3,41,485,590,596 WARNING @ Mon, 12 Aug 2019 19:27:46: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 19:27:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:27:57: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:27:59: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:28:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:28:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:28:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:28:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.10_summits.bed INFO @ Mon, 12 Aug 2019 19:28:07: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (265 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:28:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:28:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:28:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.20_summits.bed INFO @ Mon, 12 Aug 2019 19:28:08: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (85 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:28:16: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:28:16: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:28:16: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494899/SRX494899.05_summits.bed INFO @ Mon, 12 Aug 2019 19:28:16: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (481 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。