Job ID = 2590113 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,015,794 reads read : 10,015,794 reads written : 10,015,794 rm: cannot remove ‘[DSE]RR*’: 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: 00:02:30 10015794 reads; of these: 10015794 (100.00%) were unpaired; of these: 134290 (1.34%) aligned 0 times 7608272 (75.96%) aligned exactly 1 time 2273232 (22.70%) aligned >1 times 98.66% overall alignment rate Time searching: 00:02:30 Overall time: 00:02:30 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] 2069028 / 9881504 = 0.2094 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 19:46:05: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.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 19:46:05: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:46:05: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:46:06: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.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 19:46:06: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:46:06: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:46:07: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.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 19:46:07: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:46:07: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:46:13: 1000000 INFO @ Mon, 12 Aug 2019 19:46:13: 1000000 INFO @ Mon, 12 Aug 2019 19:46:14: 1000000 INFO @ Mon, 12 Aug 2019 19:46:20: 2000000 INFO @ Mon, 12 Aug 2019 19:46:20: 2000000 INFO @ Mon, 12 Aug 2019 19:46:21: 2000000 INFO @ Mon, 12 Aug 2019 19:46:27: 3000000 INFO @ Mon, 12 Aug 2019 19:46:27: 3000000 INFO @ Mon, 12 Aug 2019 19:46:27: 3000000 INFO @ Mon, 12 Aug 2019 19:46:33: 4000000 INFO @ Mon, 12 Aug 2019 19:46:34: 4000000 INFO @ Mon, 12 Aug 2019 19:46:34: 4000000 INFO @ Mon, 12 Aug 2019 19:46:40: 5000000 INFO @ Mon, 12 Aug 2019 19:46:41: 5000000 INFO @ Mon, 12 Aug 2019 19:46:41: 5000000 INFO @ Mon, 12 Aug 2019 19:46:47: 6000000 INFO @ Mon, 12 Aug 2019 19:46:47: 6000000 INFO @ Mon, 12 Aug 2019 19:46:48: 6000000 INFO @ Mon, 12 Aug 2019 19:46:53: 7000000 INFO @ Mon, 12 Aug 2019 19:46:54: 7000000 INFO @ Mon, 12 Aug 2019 19:46:55: 7000000 INFO @ Mon, 12 Aug 2019 19:46:58: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:46:58: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:46:58: #1 total tags in treatment: 7812476 INFO @ Mon, 12 Aug 2019 19:46:58: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:46:58: #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 19:46:58: #1 tags after filtering in treatment: 7812476 INFO @ Mon, 12 Aug 2019 19:46:58: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:46:58: #1 finished! INFO @ Mon, 12 Aug 2019 19:46:58: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:46:58: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:46:59: #2 number of paired peaks: 822 WARNING @ Mon, 12 Aug 2019 19:46:59: Fewer paired peaks (822) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 822 pairs to build model! INFO @ Mon, 12 Aug 2019 19:46:59: start model_add_line... INFO @ Mon, 12 Aug 2019 19:46:59: start X-correlation... INFO @ Mon, 12 Aug 2019 19:46:59: end of X-cor INFO @ Mon, 12 Aug 2019 19:46:59: #2 finished! INFO @ Mon, 12 Aug 2019 19:46:59: #2 predicted fragment length is 147 bps INFO @ Mon, 12 Aug 2019 19:46:59: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 12 Aug 2019 19:46:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.10_model.r INFO @ Mon, 12 Aug 2019 19:46:59: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:46:59: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:47:00: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:47:00: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:47:00: #1 total tags in treatment: 7812476 INFO @ Mon, 12 Aug 2019 19:47:00: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:47:00: #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 19:47:00: #1 tags after filtering in treatment: 7812476 INFO @ Mon, 12 Aug 2019 19:47:00: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:47:00: #1 finished! INFO @ Mon, 12 Aug 2019 19:47:00: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:47:00: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:47:01: #2 number of paired peaks: 822 WARNING @ Mon, 12 Aug 2019 19:47:01: Fewer paired peaks (822) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 822 pairs to build model! INFO @ Mon, 12 Aug 2019 19:47:01: start model_add_line... INFO @ Mon, 12 Aug 2019 19:47:01: start X-correlation... INFO @ Mon, 12 Aug 2019 19:47:01: end of X-cor INFO @ Mon, 12 Aug 2019 19:47:01: #2 finished! INFO @ Mon, 12 Aug 2019 19:47:01: #2 predicted fragment length is 147 bps INFO @ Mon, 12 Aug 2019 19:47:01: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 12 Aug 2019 19:47:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.20_model.r INFO @ Mon, 12 Aug 2019 19:47:01: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:47:01: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:47:01: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:47:01: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:47:01: #1 total tags in treatment: 7812476 INFO @ Mon, 12 Aug 2019 19:47:01: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:47:01: #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 19:47:01: #1 tags after filtering in treatment: 7812476 INFO @ Mon, 12 Aug 2019 19:47:01: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:47:01: #1 finished! INFO @ Mon, 12 Aug 2019 19:47:01: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:47:01: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:47:02: #2 number of paired peaks: 822 WARNING @ Mon, 12 Aug 2019 19:47:02: Fewer paired peaks (822) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 822 pairs to build model! INFO @ Mon, 12 Aug 2019 19:47:02: start model_add_line... INFO @ Mon, 12 Aug 2019 19:47:02: start X-correlation... INFO @ Mon, 12 Aug 2019 19:47:02: end of X-cor INFO @ Mon, 12 Aug 2019 19:47:02: #2 finished! INFO @ Mon, 12 Aug 2019 19:47:02: #2 predicted fragment length is 147 bps INFO @ Mon, 12 Aug 2019 19:47:02: #2 alternative fragment length(s) may be 147 bps INFO @ Mon, 12 Aug 2019 19:47:02: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.05_model.r INFO @ Mon, 12 Aug 2019 19:47:02: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:47:02: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:47:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:47:26: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:47:27: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:47:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:47:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:47:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.10_summits.bed INFO @ Mon, 12 Aug 2019 19:47:35: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3304 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:47:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:47:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:47:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.20_summits.bed INFO @ Mon, 12 Aug 2019 19:47:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1058 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:47:40: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:47:40: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:47:40: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494984/SRX494984.05_summits.bed INFO @ Mon, 12 Aug 2019 19:47:40: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (8501 records, 4 fields): 12 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。