Job ID = 2589393 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,307,945 reads read : 6,307,945 reads written : 6,307,945 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR408772.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: 00:00:54 6307945 reads; of these: 6307945 (100.00%) were unpaired; of these: 1841305 (29.19%) aligned 0 times 3774896 (59.84%) aligned exactly 1 time 691744 (10.97%) aligned >1 times 70.81% overall alignment rate Time searching: 00:00:54 Overall time: 00:00:54 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] 338791 / 4466640 = 0.0758 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 17:35:34: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.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 17:35:34: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:35:34: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:35:35: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.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 17:35:35: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:35:35: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:35:36: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.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 17:35:36: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:35:36: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:35:41: 1000000 INFO @ Mon, 12 Aug 2019 17:35:43: 1000000 INFO @ Mon, 12 Aug 2019 17:35:44: 1000000 INFO @ Mon, 12 Aug 2019 17:35:48: 2000000 INFO @ Mon, 12 Aug 2019 17:35:52: 2000000 INFO @ Mon, 12 Aug 2019 17:35:53: 2000000 INFO @ Mon, 12 Aug 2019 17:35:55: 3000000 INFO @ Mon, 12 Aug 2019 17:36:00: 3000000 INFO @ Mon, 12 Aug 2019 17:36:01: 3000000 INFO @ Mon, 12 Aug 2019 17:36:01: 4000000 INFO @ Mon, 12 Aug 2019 17:36:02: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:36:02: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:36:02: #1 total tags in treatment: 4127849 INFO @ Mon, 12 Aug 2019 17:36:02: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:36:02: #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 17:36:02: #1 tags after filtering in treatment: 4127849 INFO @ Mon, 12 Aug 2019 17:36:02: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:36:02: #1 finished! INFO @ Mon, 12 Aug 2019 17:36:02: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:36:02: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:36:02: #2 number of paired peaks: 608 WARNING @ Mon, 12 Aug 2019 17:36:02: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Mon, 12 Aug 2019 17:36:02: start model_add_line... INFO @ Mon, 12 Aug 2019 17:36:02: start X-correlation... INFO @ Mon, 12 Aug 2019 17:36:02: end of X-cor INFO @ Mon, 12 Aug 2019 17:36:02: #2 finished! INFO @ Mon, 12 Aug 2019 17:36:02: #2 predicted fragment length is 124 bps INFO @ Mon, 12 Aug 2019 17:36:02: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 12 Aug 2019 17:36:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.05_model.r INFO @ Mon, 12 Aug 2019 17:36:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:36:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:36:08: 4000000 INFO @ Mon, 12 Aug 2019 17:36:09: 4000000 INFO @ Mon, 12 Aug 2019 17:36:09: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:36:09: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:36:09: #1 total tags in treatment: 4127849 INFO @ Mon, 12 Aug 2019 17:36:09: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:36:09: #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 17:36:09: #1 tags after filtering in treatment: 4127849 INFO @ Mon, 12 Aug 2019 17:36:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:36:09: #1 finished! INFO @ Mon, 12 Aug 2019 17:36:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:36:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:36:09: #2 number of paired peaks: 608 WARNING @ Mon, 12 Aug 2019 17:36:09: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Mon, 12 Aug 2019 17:36:09: start model_add_line... INFO @ Mon, 12 Aug 2019 17:36:09: start X-correlation... INFO @ Mon, 12 Aug 2019 17:36:09: end of X-cor INFO @ Mon, 12 Aug 2019 17:36:09: #2 finished! INFO @ Mon, 12 Aug 2019 17:36:09: #2 predicted fragment length is 124 bps INFO @ Mon, 12 Aug 2019 17:36:09: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 12 Aug 2019 17:36:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.10_model.r INFO @ Mon, 12 Aug 2019 17:36:09: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:36:09: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:36:10: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:36:10: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:36:10: #1 total tags in treatment: 4127849 INFO @ Mon, 12 Aug 2019 17:36:10: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:36:10: #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 17:36:10: #1 tags after filtering in treatment: 4127849 INFO @ Mon, 12 Aug 2019 17:36:10: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:36:10: #1 finished! INFO @ Mon, 12 Aug 2019 17:36:10: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:36:10: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:36:10: #2 number of paired peaks: 608 WARNING @ Mon, 12 Aug 2019 17:36:10: Fewer paired peaks (608) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 608 pairs to build model! INFO @ Mon, 12 Aug 2019 17:36:10: start model_add_line... INFO @ Mon, 12 Aug 2019 17:36:10: start X-correlation... INFO @ Mon, 12 Aug 2019 17:36:10: end of X-cor INFO @ Mon, 12 Aug 2019 17:36:10: #2 finished! INFO @ Mon, 12 Aug 2019 17:36:10: #2 predicted fragment length is 124 bps INFO @ Mon, 12 Aug 2019 17:36:10: #2 alternative fragment length(s) may be 124 bps INFO @ Mon, 12 Aug 2019 17:36:10: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.20_model.r INFO @ Mon, 12 Aug 2019 17:36:10: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:36:10: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:36:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:36:22: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:36:22: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:36:22: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.05_summits.bed INFO @ Mon, 12 Aug 2019 17:36:22: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1937 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:36:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:36:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.10_summits.bed INFO @ Mon, 12 Aug 2019 17:36:29: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (978 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:36:29: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:36:29: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:36:29: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX120286/SRX120286.20_summits.bed INFO @ Mon, 12 Aug 2019 17:36:30: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (350 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。