Job ID = 1292312 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,464,299 reads read : 9,464,299 reads written : 9,464,299 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: 00:02:09 9464299 reads; of these: 9464299 (100.00%) were unpaired; of these: 1408727 (14.88%) aligned 0 times 5348577 (56.51%) aligned exactly 1 time 2706995 (28.60%) aligned >1 times 85.12% overall alignment rate Time searching: 00:02:09 Overall time: 00:02:09 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] 5065323 / 8055572 = 0.6288 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 18:01:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.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 18:01:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.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 18:01:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:32: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.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 18:01:32: #1 read tag files... INFO @ Sun, 02 Jun 2019 18:01:32: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 18:01:40: 1000000 INFO @ Sun, 02 Jun 2019 18:01:41: 1000000 INFO @ Sun, 02 Jun 2019 18:01:41: 1000000 INFO @ Sun, 02 Jun 2019 18:01:49: 2000000 INFO @ Sun, 02 Jun 2019 18:01:50: 2000000 INFO @ Sun, 02 Jun 2019 18:01:50: 2000000 INFO @ Sun, 02 Jun 2019 18:01:57: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:01:57: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:01:57: #1 total tags in treatment: 2990249 INFO @ Sun, 02 Jun 2019 18:01:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:01:57: #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 18:01:57: #1 tags after filtering in treatment: 2990249 INFO @ Sun, 02 Jun 2019 18:01:57: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:01:57: #1 finished! INFO @ Sun, 02 Jun 2019 18:01:57: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:01:57: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:01:58: #2 number of paired peaks: 5302 INFO @ Sun, 02 Jun 2019 18:01:58: start model_add_line... INFO @ Sun, 02 Jun 2019 18:01:58: start X-correlation... INFO @ Sun, 02 Jun 2019 18:01:58: end of X-cor INFO @ Sun, 02 Jun 2019 18:01:58: #2 finished! INFO @ Sun, 02 Jun 2019 18:01:58: #2 predicted fragment length is 197 bps INFO @ Sun, 02 Jun 2019 18:01:58: #2 alternative fragment length(s) may be 2,197 bps INFO @ Sun, 02 Jun 2019 18:01:58: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.20_model.r INFO @ Sun, 02 Jun 2019 18:01:58: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:01:58: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:01:59: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:01:59: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:01:59: #1 total tags in treatment: 2990249 INFO @ Sun, 02 Jun 2019 18:01:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:01:59: #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 18:01:59: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 18:01:59: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 18:01:59: #1 total tags in treatment: 2990249 INFO @ Sun, 02 Jun 2019 18:01:59: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 18:01:59: #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 18:01:59: #1 tags after filtering in treatment: 2990249 INFO @ Sun, 02 Jun 2019 18:01:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:01:59: #1 finished! INFO @ Sun, 02 Jun 2019 18:01:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:01:59: #1 tags after filtering in treatment: 2990249 INFO @ Sun, 02 Jun 2019 18:01:59: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 18:01:59: #1 finished! INFO @ Sun, 02 Jun 2019 18:01:59: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 18:01:59: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 18:01:59: #2 number of paired peaks: 5302 INFO @ Sun, 02 Jun 2019 18:01:59: start model_add_line... INFO @ Sun, 02 Jun 2019 18:01:59: #2 number of paired peaks: 5302 INFO @ Sun, 02 Jun 2019 18:01:59: start model_add_line... INFO @ Sun, 02 Jun 2019 18:01:59: start X-correlation... INFO @ Sun, 02 Jun 2019 18:01:59: start X-correlation... INFO @ Sun, 02 Jun 2019 18:01:59: end of X-cor INFO @ Sun, 02 Jun 2019 18:01:59: #2 finished! INFO @ Sun, 02 Jun 2019 18:01:59: #2 predicted fragment length is 197 bps INFO @ Sun, 02 Jun 2019 18:01:59: #2 alternative fragment length(s) may be 2,197 bps INFO @ Sun, 02 Jun 2019 18:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.10_model.r INFO @ Sun, 02 Jun 2019 18:01:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:01:59: end of X-cor INFO @ Sun, 02 Jun 2019 18:01:59: #2 finished! INFO @ Sun, 02 Jun 2019 18:01:59: #2 predicted fragment length is 197 bps INFO @ Sun, 02 Jun 2019 18:01:59: #2 alternative fragment length(s) may be 2,197 bps INFO @ Sun, 02 Jun 2019 18:01:59: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.05_model.r INFO @ Sun, 02 Jun 2019 18:01:59: #3 Call peaks... INFO @ Sun, 02 Jun 2019 18:01:59: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 18:02:10: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:02:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:02:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:02:15: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:02:15: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:02:15: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.20_summits.bed INFO @ Sun, 02 Jun 2019 18:02:15: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (213 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:02:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:02:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:02:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:02:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.10_summits.bed INFO @ Sun, 02 Jun 2019 18:02:17: Done! INFO @ Sun, 02 Jun 2019 18:02:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:02:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331336/SRX331336.05_summits.bed INFO @ Sun, 02 Jun 2019 18:02:17: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (560 records, 4 fields): 3 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1189 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。