Job ID = 1291823 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,944,143 reads read : 13,944,143 reads written : 13,944,143 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: 00:02:50 13944143 reads; of these: 13944143 (100.00%) were unpaired; of these: 2407938 (17.27%) aligned 0 times 9744570 (69.88%) aligned exactly 1 time 1791635 (12.85%) aligned >1 times 82.73% overall alignment rate Time searching: 00:02:50 Overall time: 00:02:50 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] 5120186 / 11536205 = 0.4438 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 16:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.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 16:41:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:41:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.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 16:41:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:41:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:41:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.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 16:41:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:41:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:41:44: 1000000 INFO @ Sun, 02 Jun 2019 16:41:45: 1000000 INFO @ Sun, 02 Jun 2019 16:41:45: 1000000 INFO @ Sun, 02 Jun 2019 16:41:51: 2000000 INFO @ Sun, 02 Jun 2019 16:41:52: 2000000 INFO @ Sun, 02 Jun 2019 16:41:53: 2000000 INFO @ Sun, 02 Jun 2019 16:41:58: 3000000 INFO @ Sun, 02 Jun 2019 16:41:59: 3000000 INFO @ Sun, 02 Jun 2019 16:42:00: 3000000 INFO @ Sun, 02 Jun 2019 16:42:05: 4000000 INFO @ Sun, 02 Jun 2019 16:42:06: 4000000 INFO @ Sun, 02 Jun 2019 16:42:08: 4000000 INFO @ Sun, 02 Jun 2019 16:42:11: 5000000 INFO @ Sun, 02 Jun 2019 16:42:12: 5000000 INFO @ Sun, 02 Jun 2019 16:42:15: 5000000 INFO @ Sun, 02 Jun 2019 16:42:18: 6000000 INFO @ Sun, 02 Jun 2019 16:42:19: 6000000 INFO @ Sun, 02 Jun 2019 16:42:20: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:42:20: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:42:20: #1 total tags in treatment: 6416019 INFO @ Sun, 02 Jun 2019 16:42:20: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:42:20: #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 16:42:20: #1 tags after filtering in treatment: 6416019 INFO @ Sun, 02 Jun 2019 16:42:20: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:42:20: #1 finished! INFO @ Sun, 02 Jun 2019 16:42:20: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:42:20: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:42:21: #2 number of paired peaks: 1357 INFO @ Sun, 02 Jun 2019 16:42:21: start model_add_line... INFO @ Sun, 02 Jun 2019 16:42:21: start X-correlation... INFO @ Sun, 02 Jun 2019 16:42:21: end of X-cor INFO @ Sun, 02 Jun 2019 16:42:21: #2 finished! INFO @ Sun, 02 Jun 2019 16:42:21: #2 predicted fragment length is 214 bps INFO @ Sun, 02 Jun 2019 16:42:21: #2 alternative fragment length(s) may be 214 bps INFO @ Sun, 02 Jun 2019 16:42:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.05_model.r INFO @ Sun, 02 Jun 2019 16:42:21: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:42:21: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:42:22: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:42:22: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:42:22: #1 total tags in treatment: 6416019 INFO @ Sun, 02 Jun 2019 16:42:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:42:22: #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 16:42:22: #1 tags after filtering in treatment: 6416019 INFO @ Sun, 02 Jun 2019 16:42:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:42:22: #1 finished! INFO @ Sun, 02 Jun 2019 16:42:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:42:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:42:23: 6000000 INFO @ Sun, 02 Jun 2019 16:42:23: #2 number of paired peaks: 1357 INFO @ Sun, 02 Jun 2019 16:42:23: start model_add_line... INFO @ Sun, 02 Jun 2019 16:42:23: start X-correlation... INFO @ Sun, 02 Jun 2019 16:42:23: end of X-cor INFO @ Sun, 02 Jun 2019 16:42:23: #2 finished! INFO @ Sun, 02 Jun 2019 16:42:23: #2 predicted fragment length is 214 bps INFO @ Sun, 02 Jun 2019 16:42:23: #2 alternative fragment length(s) may be 214 bps INFO @ Sun, 02 Jun 2019 16:42:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.20_model.r INFO @ Sun, 02 Jun 2019 16:42:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:42:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:42:26: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 16:42:26: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 16:42:26: #1 total tags in treatment: 6416019 INFO @ Sun, 02 Jun 2019 16:42:26: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:42:26: #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 16:42:26: #1 tags after filtering in treatment: 6416019 INFO @ Sun, 02 Jun 2019 16:42:26: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:42:26: #1 finished! INFO @ Sun, 02 Jun 2019 16:42:26: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:42:26: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:42:27: #2 number of paired peaks: 1357 INFO @ Sun, 02 Jun 2019 16:42:27: start model_add_line... INFO @ Sun, 02 Jun 2019 16:42:27: start X-correlation... INFO @ Sun, 02 Jun 2019 16:42:27: end of X-cor INFO @ Sun, 02 Jun 2019 16:42:27: #2 finished! INFO @ Sun, 02 Jun 2019 16:42:27: #2 predicted fragment length is 214 bps INFO @ Sun, 02 Jun 2019 16:42:27: #2 alternative fragment length(s) may be 214 bps INFO @ Sun, 02 Jun 2019 16:42:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.10_model.r INFO @ Sun, 02 Jun 2019 16:42:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:42:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:42:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:42:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:42:49: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:42:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:42:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:42:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.05_summits.bed INFO @ Sun, 02 Jun 2019 16:42:54: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3175 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:42:55: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:42:55: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:42:55: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.20_summits.bed INFO @ Sun, 02 Jun 2019 16:42:55: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (999 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:42:58: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:42:58: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:42:58: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257662/SRX257662.10_summits.bed INFO @ Sun, 02 Jun 2019 16:42:58: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1862 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。