Job ID = 2589134 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 4,304,838 reads read : 4,304,838 reads written : 4,304,838 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107324.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: 00:00:49 4304838 reads; of these: 4304838 (100.00%) were unpaired; of these: 1154958 (26.83%) aligned 0 times 2681234 (62.28%) aligned exactly 1 time 468646 (10.89%) aligned >1 times 73.17% overall alignment rate Time searching: 00:00:49 Overall time: 00:00:49 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] 289393 / 3149880 = 0.0919 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 16:59:53: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.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 16:59:53: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:59:53: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:59:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.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 16:59:54: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:59:54: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 16:59:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.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 16:59:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 16:59:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:00:01: 1000000 INFO @ Mon, 12 Aug 2019 17:00:02: 1000000 INFO @ Mon, 12 Aug 2019 17:00:04: 1000000 INFO @ Mon, 12 Aug 2019 17:00:10: 2000000 INFO @ Mon, 12 Aug 2019 17:00:11: 2000000 INFO @ Mon, 12 Aug 2019 17:00:13: 2000000 INFO @ Mon, 12 Aug 2019 17:00:17: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:00:17: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:00:17: #1 total tags in treatment: 2860487 INFO @ Mon, 12 Aug 2019 17:00:17: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:00:17: #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 17:00:17: #1 tags after filtering in treatment: 2860487 INFO @ Mon, 12 Aug 2019 17:00:17: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:00:17: #1 finished! INFO @ Mon, 12 Aug 2019 17:00:17: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:00:17: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:00:18: #2 number of paired peaks: 296 WARNING @ Mon, 12 Aug 2019 17:00:18: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Mon, 12 Aug 2019 17:00:18: start model_add_line... INFO @ Mon, 12 Aug 2019 17:00:18: start X-correlation... INFO @ Mon, 12 Aug 2019 17:00:18: end of X-cor INFO @ Mon, 12 Aug 2019 17:00:18: #2 finished! INFO @ Mon, 12 Aug 2019 17:00:18: #2 predicted fragment length is 37 bps INFO @ Mon, 12 Aug 2019 17:00:18: #2 alternative fragment length(s) may be 2,37,73,527,562,582 bps INFO @ Mon, 12 Aug 2019 17:00:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.05_model.r WARNING @ Mon, 12 Aug 2019 17:00:18: #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 17:00:18: #2 You may need to consider one of the other alternative d(s): 2,37,73,527,562,582 WARNING @ Mon, 12 Aug 2019 17:00:18: #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 17:00:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:00:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:00:19: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:00:19: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:00:19: #1 total tags in treatment: 2860487 INFO @ Mon, 12 Aug 2019 17:00:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:00:19: #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 17:00:19: #1 tags after filtering in treatment: 2860487 INFO @ Mon, 12 Aug 2019 17:00:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:00:19: #1 finished! INFO @ Mon, 12 Aug 2019 17:00:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:00:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:00:19: #2 number of paired peaks: 296 WARNING @ Mon, 12 Aug 2019 17:00:19: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Mon, 12 Aug 2019 17:00:19: start model_add_line... INFO @ Mon, 12 Aug 2019 17:00:19: start X-correlation... INFO @ Mon, 12 Aug 2019 17:00:19: end of X-cor INFO @ Mon, 12 Aug 2019 17:00:19: #2 finished! INFO @ Mon, 12 Aug 2019 17:00:19: #2 predicted fragment length is 37 bps INFO @ Mon, 12 Aug 2019 17:00:19: #2 alternative fragment length(s) may be 2,37,73,527,562,582 bps INFO @ Mon, 12 Aug 2019 17:00:19: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.10_model.r WARNING @ Mon, 12 Aug 2019 17:00:19: #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 17:00:19: #2 You may need to consider one of the other alternative d(s): 2,37,73,527,562,582 WARNING @ Mon, 12 Aug 2019 17:00:19: #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 17:00:19: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:00:19: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:00:20: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:00:20: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:00:20: #1 total tags in treatment: 2860487 INFO @ Mon, 12 Aug 2019 17:00:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:00:20: #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 17:00:20: #1 tags after filtering in treatment: 2860487 INFO @ Mon, 12 Aug 2019 17:00:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:00:20: #1 finished! INFO @ Mon, 12 Aug 2019 17:00:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:00:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:00:21: #2 number of paired peaks: 296 WARNING @ Mon, 12 Aug 2019 17:00:21: Fewer paired peaks (296) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 296 pairs to build model! INFO @ Mon, 12 Aug 2019 17:00:21: start model_add_line... INFO @ Mon, 12 Aug 2019 17:00:21: start X-correlation... INFO @ Mon, 12 Aug 2019 17:00:21: end of X-cor INFO @ Mon, 12 Aug 2019 17:00:21: #2 finished! INFO @ Mon, 12 Aug 2019 17:00:21: #2 predicted fragment length is 37 bps INFO @ Mon, 12 Aug 2019 17:00:21: #2 alternative fragment length(s) may be 2,37,73,527,562,582 bps INFO @ Mon, 12 Aug 2019 17:00:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.20_model.r WARNING @ Mon, 12 Aug 2019 17:00:21: #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 17:00:21: #2 You may need to consider one of the other alternative d(s): 2,37,73,527,562,582 WARNING @ Mon, 12 Aug 2019 17:00:21: #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 17:00:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:00:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:00:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:00:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:00:29: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:00:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:00:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:00:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.05_summits.bed INFO @ Mon, 12 Aug 2019 17:00:30: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (231 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:00:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:00:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:00:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.10_summits.bed INFO @ Mon, 12 Aug 2019 17:00:32: 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 17:00:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:00:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:00:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043863/SRX043863.20_summits.bed INFO @ Mon, 12 Aug 2019 17:00:33: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (9 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。