Job ID = 2589874 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,701,813 reads read : 6,701,813 reads written : 6,701,813 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR947510.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: 00:01:09 6701813 reads; of these: 6701813 (100.00%) were unpaired; of these: 271490 (4.05%) aligned 0 times 5498543 (82.05%) aligned exactly 1 time 931780 (13.90%) aligned >1 times 95.95% overall alignment rate Time searching: 00:01:09 Overall time: 00:01:09 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] 880906 / 6430323 = 0.1370 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 18:42:00: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.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 18:42:00: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:42:00: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:42:01: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.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 18:42:01: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:42:01: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:42:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.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 18:42:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 18:42:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 18:42:09: 1000000 INFO @ Mon, 12 Aug 2019 18:42:10: 1000000 INFO @ Mon, 12 Aug 2019 18:42:11: 1000000 INFO @ Mon, 12 Aug 2019 18:42:16: 2000000 INFO @ Mon, 12 Aug 2019 18:42:19: 2000000 INFO @ Mon, 12 Aug 2019 18:42:21: 2000000 INFO @ Mon, 12 Aug 2019 18:42:23: 3000000 INFO @ Mon, 12 Aug 2019 18:42:29: 3000000 INFO @ Mon, 12 Aug 2019 18:42:30: 3000000 INFO @ Mon, 12 Aug 2019 18:42:30: 4000000 INFO @ Mon, 12 Aug 2019 18:42:37: 5000000 INFO @ Mon, 12 Aug 2019 18:42:38: 4000000 INFO @ Mon, 12 Aug 2019 18:42:40: 4000000 INFO @ Mon, 12 Aug 2019 18:42:41: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:42:41: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:42:41: #1 total tags in treatment: 5549417 INFO @ Mon, 12 Aug 2019 18:42:41: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:42:41: #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 18:42:41: #1 tags after filtering in treatment: 5549417 INFO @ Mon, 12 Aug 2019 18:42:41: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:42:41: #1 finished! INFO @ Mon, 12 Aug 2019 18:42:41: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:42:41: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:42:42: #2 number of paired peaks: 390 WARNING @ Mon, 12 Aug 2019 18:42:42: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Mon, 12 Aug 2019 18:42:42: start model_add_line... INFO @ Mon, 12 Aug 2019 18:42:42: start X-correlation... INFO @ Mon, 12 Aug 2019 18:42:42: end of X-cor INFO @ Mon, 12 Aug 2019 18:42:42: #2 finished! INFO @ Mon, 12 Aug 2019 18:42:42: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 18:42:42: #2 alternative fragment length(s) may be 3,34,436,497,556,571,594 bps INFO @ Mon, 12 Aug 2019 18:42:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.20_model.r WARNING @ Mon, 12 Aug 2019 18:42:42: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:42:42: #2 You may need to consider one of the other alternative d(s): 3,34,436,497,556,571,594 WARNING @ Mon, 12 Aug 2019 18:42:42: #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 18:42:42: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:42:42: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:42:48: 5000000 INFO @ Mon, 12 Aug 2019 18:42:49: 5000000 INFO @ Mon, 12 Aug 2019 18:42:53: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:42:53: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:42:53: #1 total tags in treatment: 5549417 INFO @ Mon, 12 Aug 2019 18:42:53: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:42:53: #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 18:42:53: #1 tags after filtering in treatment: 5549417 INFO @ Mon, 12 Aug 2019 18:42:53: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:42:53: #1 finished! INFO @ Mon, 12 Aug 2019 18:42:53: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:42:53: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:42:53: #2 number of paired peaks: 390 WARNING @ Mon, 12 Aug 2019 18:42:53: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Mon, 12 Aug 2019 18:42:53: start model_add_line... INFO @ Mon, 12 Aug 2019 18:42:53: start X-correlation... INFO @ Mon, 12 Aug 2019 18:42:53: end of X-cor INFO @ Mon, 12 Aug 2019 18:42:53: #2 finished! INFO @ Mon, 12 Aug 2019 18:42:53: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 18:42:53: #2 alternative fragment length(s) may be 3,34,436,497,556,571,594 bps INFO @ Mon, 12 Aug 2019 18:42:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.05_model.r WARNING @ Mon, 12 Aug 2019 18:42:53: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:42:53: #2 You may need to consider one of the other alternative d(s): 3,34,436,497,556,571,594 WARNING @ Mon, 12 Aug 2019 18:42:53: #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 18:42:53: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:42:53: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:42:54: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 18:42:54: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 18:42:54: #1 total tags in treatment: 5549417 INFO @ Mon, 12 Aug 2019 18:42:54: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 18:42:54: #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 18:42:54: #1 tags after filtering in treatment: 5549417 INFO @ Mon, 12 Aug 2019 18:42:54: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 18:42:54: #1 finished! INFO @ Mon, 12 Aug 2019 18:42:54: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 18:42:54: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 18:42:54: #2 number of paired peaks: 390 WARNING @ Mon, 12 Aug 2019 18:42:54: Fewer paired peaks (390) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 390 pairs to build model! INFO @ Mon, 12 Aug 2019 18:42:54: start model_add_line... INFO @ Mon, 12 Aug 2019 18:42:54: start X-correlation... INFO @ Mon, 12 Aug 2019 18:42:54: end of X-cor INFO @ Mon, 12 Aug 2019 18:42:54: #2 finished! INFO @ Mon, 12 Aug 2019 18:42:54: #2 predicted fragment length is 34 bps INFO @ Mon, 12 Aug 2019 18:42:54: #2 alternative fragment length(s) may be 3,34,436,497,556,571,594 bps INFO @ Mon, 12 Aug 2019 18:42:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.10_model.r WARNING @ Mon, 12 Aug 2019 18:42:54: #2 Since the d (34) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 18:42:54: #2 You may need to consider one of the other alternative d(s): 3,34,436,497,556,571,594 WARNING @ Mon, 12 Aug 2019 18:42:54: #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 18:42:54: #3 Call peaks... INFO @ Mon, 12 Aug 2019 18:42:54: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 18:42:58: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:43:05: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.20_peaks.xls INFO @ Mon, 12 Aug 2019 18:43:05: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:43:05: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.20_summits.bed INFO @ Mon, 12 Aug 2019 18:43:05: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (63 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:43:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:43:10: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 18:43:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.05_peaks.xls INFO @ Mon, 12 Aug 2019 18:43:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:43:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.05_summits.bed INFO @ Mon, 12 Aug 2019 18:43:17: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (458 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 18:43:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.10_peaks.xls INFO @ Mon, 12 Aug 2019 18:43:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 18:43:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331275/SRX331275.10_summits.bed INFO @ Mon, 12 Aug 2019 18:43:18: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (225 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。