Job ID = 2589883 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,672,660 reads read : 3,672,660 reads written : 3,672,660 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947518.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: 00:00:40 3672660 reads; of these: 3672660 (100.00%) were unpaired; of these: 73340 (2.00%) aligned 0 times 3053314 (83.14%) aligned exactly 1 time 546006 (14.87%) aligned >1 times 98.00% overall alignment rate Time searching: 00:00:40 Overall time: 00:00:40 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] 744579 / 3599320 = 0.2069 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 18:41:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.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 18:41:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:41:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:41:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.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 18:41:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:41:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:41:50: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.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 18:41:50: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:41:50: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:41:56: 1000000 INFO @ Mon, 12 Aug 2019 18:41:56: 1000000 INFO @ Mon, 12 Aug 2019 18:41:58: 1000000 INFO @ Mon, 12 Aug 2019 18:42:03: 2000000 INFO @ Mon, 12 Aug 2019 18:42:05: 2000000 INFO @ Mon, 12 Aug 2019 18:42:07: 2000000 INFO @ Mon, 12 Aug 2019 18:42:09: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:42:09: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:42:09: #1 total tags in treatment: 2854741 INFO @ Mon, 12 Aug 2019 18:42:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:42:09: #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 18:42:09: #1 tags after filtering in treatment: 2854741 INFO @ Mon, 12 Aug 2019 18:42:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:42:09: #1 finished! INFO @ Mon, 12 Aug 2019 18:42:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:42:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:42:09: #2 number of paired peaks: 241 WARNING @ Mon, 12 Aug 2019 18:42:09: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Mon, 12 Aug 2019 18:42:09: start model_add_line... INFO @ Mon, 12 Aug 2019 18:42:09: start X-correlation... INFO @ Mon, 12 Aug 2019 18:42:09: end of X-cor INFO @ Mon, 12 Aug 2019 18:42:09: #2 finished! INFO @ Mon, 12 Aug 2019 18:42:09: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 18:42:09: #2 alternative fragment length(s) may be 3,33,48,81,105,155,465,497,524,545,575,592 bps INFO @ Mon, 12 Aug 2019 18:42:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.10_model.r WARNING @ Mon, 12 Aug 2019 18:42:09: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:42:09: #2 You may need to consider one of the other alternative d(s): 3,33,48,81,105,155,465,497,524,545,575,592 WARNING @ Mon, 12 Aug 2019 18:42:09: #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 18:42:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:42:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:42:12: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:42:12: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:42:12: #1 total tags in treatment: 2854741 INFO @ Mon, 12 Aug 2019 18:42:12: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:42:12: #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 18:42:12: #1 tags after filtering in treatment: 2854741 INFO @ Mon, 12 Aug 2019 18:42:12: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:42:12: #1 finished! INFO @ Mon, 12 Aug 2019 18:42:12: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:42:12: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:42:13: #2 number of paired peaks: 241 WARNING @ Mon, 12 Aug 2019 18:42:13: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Mon, 12 Aug 2019 18:42:13: start model_add_line... INFO @ Mon, 12 Aug 2019 18:42:13: start X-correlation... INFO @ Mon, 12 Aug 2019 18:42:13: end of X-cor INFO @ Mon, 12 Aug 2019 18:42:13: #2 finished! INFO @ Mon, 12 Aug 2019 18:42:13: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 18:42:13: #2 alternative fragment length(s) may be 3,33,48,81,105,155,465,497,524,545,575,592 bps INFO @ Mon, 12 Aug 2019 18:42:13: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.05_model.r WARNING @ Mon, 12 Aug 2019 18:42:13: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:42:13: #2 You may need to consider one of the other alternative d(s): 3,33,48,81,105,155,465,497,524,545,575,592 WARNING @ Mon, 12 Aug 2019 18:42:13: #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 18:42:13: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:42:13: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:42:14: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:42:14: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:42:14: #1 total tags in treatment: 2854741 INFO @ Mon, 12 Aug 2019 18:42:14: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:42:14: #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 18:42:14: #1 tags after filtering in treatment: 2854741 INFO @ Mon, 12 Aug 2019 18:42:14: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:42:14: #1 finished! INFO @ Mon, 12 Aug 2019 18:42:14: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:42:14: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:42:15: #2 number of paired peaks: 241 WARNING @ Mon, 12 Aug 2019 18:42:15: Fewer paired peaks (241) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 241 pairs to build model! INFO @ Mon, 12 Aug 2019 18:42:15: start model_add_line... INFO @ Mon, 12 Aug 2019 18:42:15: start X-correlation... INFO @ Mon, 12 Aug 2019 18:42:15: end of X-cor INFO @ Mon, 12 Aug 2019 18:42:15: #2 finished! INFO @ Mon, 12 Aug 2019 18:42:15: #2 predicted fragment length is 33 bps INFO @ Mon, 12 Aug 2019 18:42:15: #2 alternative fragment length(s) may be 3,33,48,81,105,155,465,497,524,545,575,592 bps INFO @ Mon, 12 Aug 2019 18:42:15: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.20_model.r WARNING @ Mon, 12 Aug 2019 18:42:15: #2 Since the d (33) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:42:15: #2 You may need to consider one of the other alternative d(s): 3,33,48,81,105,155,465,497,524,545,575,592 WARNING @ Mon, 12 Aug 2019 18:42:15: #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 18:42:15: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:42:15: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:42:18: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:42:21: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:42:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:42:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:42:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.10_summits.bed INFO @ Mon, 12 Aug 2019 18:42:22: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (39 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:42:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:42:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:42:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:42:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.05_summits.bed INFO @ Mon, 12 Aug 2019 18:42:25: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (112 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:42:27: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:42:27: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:42:27: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331283/SRX331283.20_summits.bed INFO @ Mon, 12 Aug 2019 18:42:27: Done! pass1 - making usageList (3 chroms): 1 millis pass2 - checking and writing primary data (3 records, 4 fields): 1 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。