Job ID = 1293162 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,713,630 reads read : 11,427,260 reads written : 5,713,630 reads 0-length : 5,713,630 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: 00:01:29 5713630 reads; of these: 5713630 (100.00%) were unpaired; of these: 192650 (3.37%) aligned 0 times 4764168 (83.38%) aligned exactly 1 time 756812 (13.25%) aligned >1 times 96.63% overall alignment rate Time searching: 00:01:29 Overall time: 00:01:29 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] 2309029 / 5520980 = 0.4182 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 22:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.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 22:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.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 22:05:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:05:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:05:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:13: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.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 22:05:13: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:05:13: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:20: 1000000 INFO @ Sun, 02 Jun 2019 22:05:22: 1000000 INFO @ Sun, 02 Jun 2019 22:05:23: 1000000 INFO @ Sun, 02 Jun 2019 22:05:27: 2000000 INFO @ Sun, 02 Jun 2019 22:05:31: 2000000 INFO @ Sun, 02 Jun 2019 22:05:32: 2000000 INFO @ Sun, 02 Jun 2019 22:05:35: 3000000 INFO @ Sun, 02 Jun 2019 22:05:37: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:05:37: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:05:37: #1 total tags in treatment: 3211951 INFO @ Sun, 02 Jun 2019 22:05:37: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:37: #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 22:05:37: #1 tags after filtering in treatment: 3211951 INFO @ Sun, 02 Jun 2019 22:05:37: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:37: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:37: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:37: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:37: #2 number of paired peaks: 2950 INFO @ Sun, 02 Jun 2019 22:05:37: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:37: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:37: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:37: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:37: #2 predicted fragment length is 150 bps INFO @ Sun, 02 Jun 2019 22:05:37: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 02 Jun 2019 22:05:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.10_model.r INFO @ Sun, 02 Jun 2019 22:05:37: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:37: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:41: 3000000 INFO @ Sun, 02 Jun 2019 22:05:41: 3000000 INFO @ Sun, 02 Jun 2019 22:05:43: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:05:43: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:05:43: #1 total tags in treatment: 3211951 INFO @ Sun, 02 Jun 2019 22:05:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:43: #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 22:05:43: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 22:05:43: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 22:05:43: #1 total tags in treatment: 3211951 INFO @ Sun, 02 Jun 2019 22:05:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:05:43: #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 22:05:43: #1 tags after filtering in treatment: 3211951 INFO @ Sun, 02 Jun 2019 22:05:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:43: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:43: #1 tags after filtering in treatment: 3211951 INFO @ Sun, 02 Jun 2019 22:05:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:05:43: #1 finished! INFO @ Sun, 02 Jun 2019 22:05:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:05:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:05:43: #2 number of paired peaks: 2950 INFO @ Sun, 02 Jun 2019 22:05:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:43: #2 number of paired peaks: 2950 INFO @ Sun, 02 Jun 2019 22:05:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:05:43: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:43: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:43: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:43: #2 predicted fragment length is 150 bps INFO @ Sun, 02 Jun 2019 22:05:43: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 02 Jun 2019 22:05:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.05_model.r INFO @ Sun, 02 Jun 2019 22:05:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:43: start X-correlation... INFO @ Sun, 02 Jun 2019 22:05:43: end of X-cor INFO @ Sun, 02 Jun 2019 22:05:43: #2 finished! INFO @ Sun, 02 Jun 2019 22:05:43: #2 predicted fragment length is 150 bps INFO @ Sun, 02 Jun 2019 22:05:43: #2 alternative fragment length(s) may be 150 bps INFO @ Sun, 02 Jun 2019 22:05:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.20_model.r INFO @ Sun, 02 Jun 2019 22:05:43: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:05:43: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:05:48: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.10_summits.bed INFO @ Sun, 02 Jun 2019 22:05:53: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3411 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.20_summits.bed INFO @ Sun, 02 Jun 2019 22:05:59: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2203 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:05:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:05:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:05:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402727/SRX5402727.05_summits.bed INFO @ Sun, 02 Jun 2019 22:05:59: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4407 records, 4 fields): 7 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。