Job ID = 2589169 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,078,616 reads read : 4,078,616 reads written : 4,078,616 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107552.sra.cache’: 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: 00:00:46 4078616 reads; of these: 4078616 (100.00%) were unpaired; of these: 1054069 (25.84%) aligned 0 times 2609262 (63.97%) aligned exactly 1 time 415285 (10.18%) aligned >1 times 74.16% overall alignment rate Time searching: 00:00:46 Overall time: 00:00:46 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] 143751 / 3024547 = 0.0475 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 17:04:33: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.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 17:04:33: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:04:33: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:04:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.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 17:04:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:04:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:04:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.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 17:04:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:04:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:04:41: 1000000 INFO @ Mon, 12 Aug 2019 17:04:42: 1000000 INFO @ Mon, 12 Aug 2019 17:04:44: 1000000 INFO @ Mon, 12 Aug 2019 17:04:49: 2000000 INFO @ Mon, 12 Aug 2019 17:04:50: 2000000 INFO @ Mon, 12 Aug 2019 17:04:52: 2000000 INFO @ Mon, 12 Aug 2019 17:04:55: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:04:55: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:04:55: #1 total tags in treatment: 2880796 INFO @ Mon, 12 Aug 2019 17:04:55: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:04:55: #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 17:04:56: #1 tags after filtering in treatment: 2880796 INFO @ Mon, 12 Aug 2019 17:04:56: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:04:56: #1 finished! INFO @ Mon, 12 Aug 2019 17:04:56: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:04:56: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:04:56: #2 number of paired peaks: 279 WARNING @ Mon, 12 Aug 2019 17:04:56: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Mon, 12 Aug 2019 17:04:56: start model_add_line... INFO @ Mon, 12 Aug 2019 17:04:56: start X-correlation... INFO @ Mon, 12 Aug 2019 17:04:56: end of X-cor INFO @ Mon, 12 Aug 2019 17:04:56: #2 finished! INFO @ Mon, 12 Aug 2019 17:04:56: #2 predicted fragment length is 37 bps INFO @ Mon, 12 Aug 2019 17:04:56: #2 alternative fragment length(s) may be 4,37,493,532,598 bps INFO @ Mon, 12 Aug 2019 17:04:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.05_model.r WARNING @ Mon, 12 Aug 2019 17:04:56: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:04:56: #2 You may need to consider one of the other alternative d(s): 4,37,493,532,598 WARNING @ Mon, 12 Aug 2019 17:04:56: #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 17:04:56: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:04:56: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:04:56: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:04:56: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:04:56: #1 total tags in treatment: 2880796 INFO @ Mon, 12 Aug 2019 17:04:56: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:04:56: #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 17:04:57: #1 tags after filtering in treatment: 2880796 INFO @ Mon, 12 Aug 2019 17:04:57: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:04:57: #1 finished! INFO @ Mon, 12 Aug 2019 17:04:57: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:04:57: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:04:57: #2 number of paired peaks: 279 WARNING @ Mon, 12 Aug 2019 17:04:57: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Mon, 12 Aug 2019 17:04:57: start model_add_line... INFO @ Mon, 12 Aug 2019 17:04:57: start X-correlation... INFO @ Mon, 12 Aug 2019 17:04:57: end of X-cor INFO @ Mon, 12 Aug 2019 17:04:57: #2 finished! INFO @ Mon, 12 Aug 2019 17:04:57: #2 predicted fragment length is 37 bps INFO @ Mon, 12 Aug 2019 17:04:57: #2 alternative fragment length(s) may be 4,37,493,532,598 bps INFO @ Mon, 12 Aug 2019 17:04:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.10_model.r WARNING @ Mon, 12 Aug 2019 17:04:57: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:04:57: #2 You may need to consider one of the other alternative d(s): 4,37,493,532,598 WARNING @ Mon, 12 Aug 2019 17:04:57: #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 17:04:57: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:04:57: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:00: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:05:00: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:05:00: #1 total tags in treatment: 2880796 INFO @ Mon, 12 Aug 2019 17:05:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:05:00: #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 17:05:00: #1 tags after filtering in treatment: 2880796 INFO @ Mon, 12 Aug 2019 17:05:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:05:00: #1 finished! INFO @ Mon, 12 Aug 2019 17:05:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:05:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:05:00: #2 number of paired peaks: 279 WARNING @ Mon, 12 Aug 2019 17:05:00: Fewer paired peaks (279) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 279 pairs to build model! INFO @ Mon, 12 Aug 2019 17:05:00: start model_add_line... INFO @ Mon, 12 Aug 2019 17:05:00: start X-correlation... INFO @ Mon, 12 Aug 2019 17:05:00: end of X-cor INFO @ Mon, 12 Aug 2019 17:05:00: #2 finished! INFO @ Mon, 12 Aug 2019 17:05:00: #2 predicted fragment length is 37 bps INFO @ Mon, 12 Aug 2019 17:05:00: #2 alternative fragment length(s) may be 4,37,493,532,598 bps INFO @ Mon, 12 Aug 2019 17:05:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.20_model.r WARNING @ Mon, 12 Aug 2019 17:05:00: #2 Since the d (37) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:05:00: #2 You may need to consider one of the other alternative d(s): 4,37,493,532,598 WARNING @ Mon, 12 Aug 2019 17:05:00: #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 17:05:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:05:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:05:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:06: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.05_summits.bed INFO @ Mon, 12 Aug 2019 17:05:09: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (219 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:05:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:05:10: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:10: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.10_summits.bed INFO @ Mon, 12 Aug 2019 17:05:10: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (91 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:05:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:05:13: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:05:13: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043977/SRX043977.20_summits.bed INFO @ Mon, 12 Aug 2019 17:05:13: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (14 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。