Job ID = 2589559 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,231,623 reads read : 3,231,623 reads written : 3,231,623 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR707566.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: 00:00:36 3231623 reads; of these: 3231623 (100.00%) were unpaired; of these: 177041 (5.48%) aligned 0 times 2571323 (79.57%) aligned exactly 1 time 483259 (14.95%) aligned >1 times 94.52% overall alignment rate Time searching: 00:00:36 Overall time: 00:00:36 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] 131001 / 3054582 = 0.0429 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 17:57:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.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 17:57:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:57:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:57:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.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 17:57:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:57:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:57:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.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 17:57:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:57:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:58:02: 1000000 INFO @ Mon, 12 Aug 2019 17:58:03: 1000000 INFO @ Mon, 12 Aug 2019 17:58:04: 1000000 INFO @ Mon, 12 Aug 2019 17:58:10: 2000000 INFO @ Mon, 12 Aug 2019 17:58:11: 2000000 INFO @ Mon, 12 Aug 2019 17:58:13: 2000000 INFO @ Mon, 12 Aug 2019 17:58:17: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:58:17: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:58:17: #1 total tags in treatment: 2923581 INFO @ Mon, 12 Aug 2019 17:58:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:58:17: #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 17:58:17: #1 tags after filtering in treatment: 2923581 INFO @ Mon, 12 Aug 2019 17:58:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:58:17: #1 finished! INFO @ Mon, 12 Aug 2019 17:58:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:58:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:58:17: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 17:58:17: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 17:58:17: start model_add_line... INFO @ Mon, 12 Aug 2019 17:58:17: start X-correlation... INFO @ Mon, 12 Aug 2019 17:58:17: end of X-cor INFO @ Mon, 12 Aug 2019 17:58:17: #2 finished! INFO @ Mon, 12 Aug 2019 17:58:17: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 17:58:17: #2 alternative fragment length(s) may be 4,32,509,515,521,561,563 bps INFO @ Mon, 12 Aug 2019 17:58:17: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.05_model.r WARNING @ Mon, 12 Aug 2019 17:58:17: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:58:17: #2 You may need to consider one of the other alternative d(s): 4,32,509,515,521,561,563 WARNING @ Mon, 12 Aug 2019 17:58:17: #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 17:58:17: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:58:17: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:58:18: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:58:18: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:58:18: #1 total tags in treatment: 2923581 INFO @ Mon, 12 Aug 2019 17:58:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:58:18: #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 17:58:18: #1 tags after filtering in treatment: 2923581 INFO @ Mon, 12 Aug 2019 17:58:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:58:18: #1 finished! INFO @ Mon, 12 Aug 2019 17:58:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:58:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:58:19: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 17:58:19: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 17:58:19: start model_add_line... INFO @ Mon, 12 Aug 2019 17:58:19: start X-correlation... INFO @ Mon, 12 Aug 2019 17:58:19: end of X-cor INFO @ Mon, 12 Aug 2019 17:58:19: #2 finished! INFO @ Mon, 12 Aug 2019 17:58:19: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 17:58:19: #2 alternative fragment length(s) may be 4,32,509,515,521,561,563 bps INFO @ Mon, 12 Aug 2019 17:58:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.10_model.r WARNING @ Mon, 12 Aug 2019 17:58:19: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:58:19: #2 You may need to consider one of the other alternative d(s): 4,32,509,515,521,561,563 WARNING @ Mon, 12 Aug 2019 17:58:19: #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 17:58:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:58:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:58:21: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:58:21: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:58:21: #1 total tags in treatment: 2923581 INFO @ Mon, 12 Aug 2019 17:58:21: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:58:21: #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 17:58:21: #1 tags after filtering in treatment: 2923581 INFO @ Mon, 12 Aug 2019 17:58:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:58:21: #1 finished! INFO @ Mon, 12 Aug 2019 17:58:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:58:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:58:22: #2 number of paired peaks: 403 WARNING @ Mon, 12 Aug 2019 17:58:22: Fewer paired peaks (403) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 403 pairs to build model! INFO @ Mon, 12 Aug 2019 17:58:22: start model_add_line... INFO @ Mon, 12 Aug 2019 17:58:22: start X-correlation... INFO @ Mon, 12 Aug 2019 17:58:22: end of X-cor INFO @ Mon, 12 Aug 2019 17:58:22: #2 finished! INFO @ Mon, 12 Aug 2019 17:58:22: #2 predicted fragment length is 32 bps INFO @ Mon, 12 Aug 2019 17:58:22: #2 alternative fragment length(s) may be 4,32,509,515,521,561,563 bps INFO @ Mon, 12 Aug 2019 17:58:22: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.20_model.r WARNING @ Mon, 12 Aug 2019 17:58:22: #2 Since the d (32) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:58:22: #2 You may need to consider one of the other alternative d(s): 4,32,509,515,521,561,563 WARNING @ Mon, 12 Aug 2019 17:58:22: #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 17:58:22: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:58:22: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:58:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:58:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:58:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:58:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:58:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.05_summits.bed INFO @ Mon, 12 Aug 2019 17:58:30: Done! INFO @ Mon, 12 Aug 2019 17:58:30: #3 Call peaks for each chromosome... pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (364 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:58:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:58:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:58:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.10_summits.bed INFO @ Mon, 12 Aug 2019 17:58:32: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (162 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:58:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:58:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:58:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX234922/SRX234922.20_summits.bed INFO @ Mon, 12 Aug 2019 17:58:35: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (35 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。