Job ID = 1292609 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,764,051 reads read : 15,764,051 reads written : 15,764,051 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:03:01 15764051 reads; of these: 15764051 (100.00%) were unpaired; of these: 524039 (3.32%) aligned 0 times 13470100 (85.45%) aligned exactly 1 time 1769912 (11.23%) aligned >1 times 96.68% overall alignment rate Time searching: 00:03:01 Overall time: 00:03:01 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] 4262641 / 15240012 = 0.2797 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 @ Sun, 02 Jun 2019 19:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.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 @ Sun, 02 Jun 2019 19:58:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:58:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.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 @ Sun, 02 Jun 2019 19:58:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:58:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:58:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.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 @ Sun, 02 Jun 2019 19:58:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 19:58:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 19:58:36: 1000000 INFO @ Sun, 02 Jun 2019 19:58:36: 1000000 INFO @ Sun, 02 Jun 2019 19:58:38: 1000000 INFO @ Sun, 02 Jun 2019 19:58:43: 2000000 INFO @ Sun, 02 Jun 2019 19:58:43: 2000000 INFO @ Sun, 02 Jun 2019 19:58:47: 2000000 INFO @ Sun, 02 Jun 2019 19:58:50: 3000000 INFO @ Sun, 02 Jun 2019 19:58:50: 3000000 INFO @ Sun, 02 Jun 2019 19:58:55: 3000000 INFO @ Sun, 02 Jun 2019 19:58:56: 4000000 INFO @ Sun, 02 Jun 2019 19:58:57: 4000000 INFO @ Sun, 02 Jun 2019 19:59:03: 5000000 INFO @ Sun, 02 Jun 2019 19:59:03: 5000000 INFO @ Sun, 02 Jun 2019 19:59:04: 4000000 INFO @ Sun, 02 Jun 2019 19:59:10: 6000000 INFO @ Sun, 02 Jun 2019 19:59:10: 6000000 INFO @ Sun, 02 Jun 2019 19:59:12: 5000000 INFO @ Sun, 02 Jun 2019 19:59:17: 7000000 INFO @ Sun, 02 Jun 2019 19:59:17: 7000000 INFO @ Sun, 02 Jun 2019 19:59:21: 6000000 INFO @ Sun, 02 Jun 2019 19:59:23: 8000000 INFO @ Sun, 02 Jun 2019 19:59:24: 8000000 INFO @ Sun, 02 Jun 2019 19:59:29: 7000000 INFO @ Sun, 02 Jun 2019 19:59:30: 9000000 INFO @ Sun, 02 Jun 2019 19:59:30: 9000000 INFO @ Sun, 02 Jun 2019 19:59:37: 10000000 INFO @ Sun, 02 Jun 2019 19:59:37: 10000000 INFO @ Sun, 02 Jun 2019 19:59:38: 8000000 INFO @ Sun, 02 Jun 2019 19:59:43: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:59:43: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:59:43: #1 total tags in treatment: 10977371 INFO @ Sun, 02 Jun 2019 19:59:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:59:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:59:44: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 19:59:44: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 19:59:44: #1 total tags in treatment: 10977371 INFO @ Sun, 02 Jun 2019 19:59:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 19:59:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 19:59:44: #1 tags after filtering in treatment: 10977371 INFO @ Sun, 02 Jun 2019 19:59:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:59:44: #1 finished! INFO @ Sun, 02 Jun 2019 19:59:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:59:44: #1 tags after filtering in treatment: 10977371 INFO @ Sun, 02 Jun 2019 19:59:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 19:59:44: #1 finished! INFO @ Sun, 02 Jun 2019 19:59:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 19:59:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 19:59:45: #2 number of paired peaks: 950 WARNING @ Sun, 02 Jun 2019 19:59:45: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Sun, 02 Jun 2019 19:59:45: start model_add_line... INFO @ Sun, 02 Jun 2019 19:59:45: start X-correlation... INFO @ Sun, 02 Jun 2019 19:59:45: end of X-cor INFO @ Sun, 02 Jun 2019 19:59:45: #2 finished! INFO @ Sun, 02 Jun 2019 19:59:45: #2 predicted fragment length is 197 bps INFO @ Sun, 02 Jun 2019 19:59:45: #2 alternative fragment length(s) may be 3,174,197 bps INFO @ Sun, 02 Jun 2019 19:59:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.05_model.r INFO @ Sun, 02 Jun 2019 19:59:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:59:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:59:45: #2 number of paired peaks: 950 WARNING @ Sun, 02 Jun 2019 19:59:45: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Sun, 02 Jun 2019 19:59:45: start model_add_line... INFO @ Sun, 02 Jun 2019 19:59:45: start X-correlation... INFO @ Sun, 02 Jun 2019 19:59:45: end of X-cor INFO @ Sun, 02 Jun 2019 19:59:45: #2 finished! INFO @ Sun, 02 Jun 2019 19:59:45: #2 predicted fragment length is 197 bps INFO @ Sun, 02 Jun 2019 19:59:45: #2 alternative fragment length(s) may be 3,174,197 bps INFO @ Sun, 02 Jun 2019 19:59:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.20_model.r INFO @ Sun, 02 Jun 2019 19:59:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 19:59:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 19:59:46: 9000000 INFO @ Sun, 02 Jun 2019 19:59:54: 10000000 INFO @ Sun, 02 Jun 2019 20:00:02: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:00:02: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:00:02: #1 total tags in treatment: 10977371 INFO @ Sun, 02 Jun 2019 20:00:02: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:00:02: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 20:00:03: #1 tags after filtering in treatment: 10977371 INFO @ Sun, 02 Jun 2019 20:00:03: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:00:03: #1 finished! INFO @ Sun, 02 Jun 2019 20:00:03: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:00:03: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:00:04: #2 number of paired peaks: 950 WARNING @ Sun, 02 Jun 2019 20:00:04: Fewer paired peaks (950) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 950 pairs to build model! INFO @ Sun, 02 Jun 2019 20:00:04: start model_add_line... INFO @ Sun, 02 Jun 2019 20:00:04: start X-correlation... INFO @ Sun, 02 Jun 2019 20:00:04: end of X-cor INFO @ Sun, 02 Jun 2019 20:00:04: #2 finished! INFO @ Sun, 02 Jun 2019 20:00:04: #2 predicted fragment length is 197 bps INFO @ Sun, 02 Jun 2019 20:00:04: #2 alternative fragment length(s) may be 3,174,197 bps INFO @ Sun, 02 Jun 2019 20:00:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.10_model.r INFO @ Sun, 02 Jun 2019 20:00:04: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:00:04: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:00:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:00:18: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.20_summits.bed INFO @ Sun, 02 Jun 2019 20:00:34: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (535 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:00:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:00:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:00:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.05_summits.bed INFO @ Sun, 02 Jun 2019 20:00:34: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5521 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:00:37: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:00:52: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:00:52: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:00:52: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494855/SRX494855.10_summits.bed INFO @ Sun, 02 Jun 2019 20:00:52: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2337 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。