Job ID = 1292999 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,153,575 reads read : 15,153,575 reads written : 15,153,575 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: 00:02:49 15153575 reads; of these: 15153575 (100.00%) were unpaired; of these: 5992981 (39.55%) aligned 0 times 7656439 (50.53%) aligned exactly 1 time 1504155 (9.93%) aligned >1 times 60.45% overall alignment rate Time searching: 00:02:49 Overall time: 00:02:49 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] 3756351 / 9160594 = 0.4101 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 21:21:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.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 21:21:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:21:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:21:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.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 21:21:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:21:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:21:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.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 21:21:10: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:21:10: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:21:19: 1000000 INFO @ Sun, 02 Jun 2019 21:21:21: 1000000 INFO @ Sun, 02 Jun 2019 21:21:22: 1000000 INFO @ Sun, 02 Jun 2019 21:21:28: 2000000 INFO @ Sun, 02 Jun 2019 21:21:33: 2000000 INFO @ Sun, 02 Jun 2019 21:21:34: 2000000 INFO @ Sun, 02 Jun 2019 21:21:37: 3000000 INFO @ Sun, 02 Jun 2019 21:21:43: 3000000 INFO @ Sun, 02 Jun 2019 21:21:45: 3000000 INFO @ Sun, 02 Jun 2019 21:21:45: 4000000 INFO @ Sun, 02 Jun 2019 21:21:54: 4000000 INFO @ Sun, 02 Jun 2019 21:21:54: 5000000 INFO @ Sun, 02 Jun 2019 21:21:56: 4000000 INFO @ Sun, 02 Jun 2019 21:21:57: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:21:57: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:21:57: #1 total tags in treatment: 5404243 INFO @ Sun, 02 Jun 2019 21:21:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:21:57: #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 21:21:58: #1 tags after filtering in treatment: 5404243 INFO @ Sun, 02 Jun 2019 21:21:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:21:58: #1 finished! INFO @ Sun, 02 Jun 2019 21:21:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:21:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:21:58: #2 number of paired peaks: 898 WARNING @ Sun, 02 Jun 2019 21:21:58: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Sun, 02 Jun 2019 21:21:58: start model_add_line... INFO @ Sun, 02 Jun 2019 21:21:58: start X-correlation... INFO @ Sun, 02 Jun 2019 21:21:58: end of X-cor INFO @ Sun, 02 Jun 2019 21:21:58: #2 finished! INFO @ Sun, 02 Jun 2019 21:21:58: #2 predicted fragment length is 156 bps INFO @ Sun, 02 Jun 2019 21:21:58: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 02 Jun 2019 21:21:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.05_model.r INFO @ Sun, 02 Jun 2019 21:21:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:21:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:22:05: 5000000 INFO @ Sun, 02 Jun 2019 21:22:08: 5000000 INFO @ Sun, 02 Jun 2019 21:22:09: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:22:09: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:22:09: #1 total tags in treatment: 5404243 INFO @ Sun, 02 Jun 2019 21:22:09: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:22:09: #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 21:22:09: #1 tags after filtering in treatment: 5404243 INFO @ Sun, 02 Jun 2019 21:22:09: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:22:09: #1 finished! INFO @ Sun, 02 Jun 2019 21:22:09: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:22:09: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:22:09: #2 number of paired peaks: 898 WARNING @ Sun, 02 Jun 2019 21:22:09: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Sun, 02 Jun 2019 21:22:09: start model_add_line... INFO @ Sun, 02 Jun 2019 21:22:09: start X-correlation... INFO @ Sun, 02 Jun 2019 21:22:09: end of X-cor INFO @ Sun, 02 Jun 2019 21:22:09: #2 finished! INFO @ Sun, 02 Jun 2019 21:22:09: #2 predicted fragment length is 156 bps INFO @ Sun, 02 Jun 2019 21:22:09: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 02 Jun 2019 21:22:09: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.20_model.r INFO @ Sun, 02 Jun 2019 21:22:09: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:22:09: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:22:12: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 21:22:12: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 21:22:12: #1 total tags in treatment: 5404243 INFO @ Sun, 02 Jun 2019 21:22:12: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:22:12: #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 21:22:12: #1 tags after filtering in treatment: 5404243 INFO @ Sun, 02 Jun 2019 21:22:12: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:22:12: #1 finished! INFO @ Sun, 02 Jun 2019 21:22:12: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:22:12: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:22:12: #2 number of paired peaks: 898 WARNING @ Sun, 02 Jun 2019 21:22:12: Fewer paired peaks (898) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 898 pairs to build model! INFO @ Sun, 02 Jun 2019 21:22:12: start model_add_line... INFO @ Sun, 02 Jun 2019 21:22:12: start X-correlation... INFO @ Sun, 02 Jun 2019 21:22:12: end of X-cor INFO @ Sun, 02 Jun 2019 21:22:12: #2 finished! INFO @ Sun, 02 Jun 2019 21:22:12: #2 predicted fragment length is 156 bps INFO @ Sun, 02 Jun 2019 21:22:12: #2 alternative fragment length(s) may be 156 bps INFO @ Sun, 02 Jun 2019 21:22:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.10_model.r INFO @ Sun, 02 Jun 2019 21:22:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:22:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:22:15: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:22:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:22:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:22:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.05_summits.bed INFO @ Sun, 02 Jun 2019 21:22:23: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3151 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:22:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:22:31: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:22:35: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:22:35: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:22:35: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.20_summits.bed INFO @ Sun, 02 Jun 2019 21:22:35: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (793 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:22:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:22:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:22:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020773/SRX5020773.10_summits.bed INFO @ Sun, 02 Jun 2019 21:22:39: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1736 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。