Job ID = 1292768 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,863,744 reads read : 11,863,744 reads written : 11,863,744 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: 00:02:13 11863744 reads; of these: 11863744 (100.00%) were unpaired; of these: 1140756 (9.62%) aligned 0 times 9265096 (78.10%) aligned exactly 1 time 1457892 (12.29%) aligned >1 times 90.38% overall alignment rate Time searching: 00:02:13 Overall time: 00:02:13 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] 3202517 / 10722988 = 0.2987 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 20:27:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.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 20:27:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:27:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:27:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.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 20:27:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:27:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:27:44: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.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 20:27:44: #1 read tag files... INFO @ Sun, 02 Jun 2019 20:27:44: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 20:27:51: 1000000 INFO @ Sun, 02 Jun 2019 20:27:52: 1000000 INFO @ Sun, 02 Jun 2019 20:27:54: 1000000 INFO @ Sun, 02 Jun 2019 20:27:58: 2000000 INFO @ Sun, 02 Jun 2019 20:28:00: 2000000 INFO @ Sun, 02 Jun 2019 20:28:04: 2000000 INFO @ Sun, 02 Jun 2019 20:28:04: 3000000 INFO @ Sun, 02 Jun 2019 20:28:08: 3000000 INFO @ Sun, 02 Jun 2019 20:28:11: 4000000 INFO @ Sun, 02 Jun 2019 20:28:13: 3000000 INFO @ Sun, 02 Jun 2019 20:28:15: 4000000 INFO @ Sun, 02 Jun 2019 20:28:17: 5000000 INFO @ Sun, 02 Jun 2019 20:28:22: 5000000 INFO @ Sun, 02 Jun 2019 20:28:22: 4000000 INFO @ Sun, 02 Jun 2019 20:28:24: 6000000 INFO @ Sun, 02 Jun 2019 20:28:29: 6000000 INFO @ Sun, 02 Jun 2019 20:28:31: 7000000 INFO @ Sun, 02 Jun 2019 20:28:32: 5000000 INFO @ Sun, 02 Jun 2019 20:28:34: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:28:34: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:28:34: #1 total tags in treatment: 7520471 INFO @ Sun, 02 Jun 2019 20:28:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:28:34: #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 20:28:34: #1 tags after filtering in treatment: 7520471 INFO @ Sun, 02 Jun 2019 20:28:34: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:28:34: #1 finished! INFO @ Sun, 02 Jun 2019 20:28:34: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:28:34: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:28:35: #2 number of paired peaks: 3869 INFO @ Sun, 02 Jun 2019 20:28:35: start model_add_line... INFO @ Sun, 02 Jun 2019 20:28:36: start X-correlation... INFO @ Sun, 02 Jun 2019 20:28:36: end of X-cor INFO @ Sun, 02 Jun 2019 20:28:36: #2 finished! INFO @ Sun, 02 Jun 2019 20:28:36: #2 predicted fragment length is 261 bps INFO @ Sun, 02 Jun 2019 20:28:36: #2 alternative fragment length(s) may be 261 bps INFO @ Sun, 02 Jun 2019 20:28:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.20_model.r INFO @ Sun, 02 Jun 2019 20:28:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:28:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:28:37: 7000000 INFO @ Sun, 02 Jun 2019 20:28:40: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:28:40: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:28:40: #1 total tags in treatment: 7520471 INFO @ Sun, 02 Jun 2019 20:28:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:28:40: #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 20:28:41: #1 tags after filtering in treatment: 7520471 INFO @ Sun, 02 Jun 2019 20:28:41: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:28:41: #1 finished! INFO @ Sun, 02 Jun 2019 20:28:41: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:28:41: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:28:41: 6000000 INFO @ Sun, 02 Jun 2019 20:28:42: #2 number of paired peaks: 3869 INFO @ Sun, 02 Jun 2019 20:28:42: start model_add_line... INFO @ Sun, 02 Jun 2019 20:28:42: start X-correlation... INFO @ Sun, 02 Jun 2019 20:28:42: end of X-cor INFO @ Sun, 02 Jun 2019 20:28:42: #2 finished! INFO @ Sun, 02 Jun 2019 20:28:42: #2 predicted fragment length is 261 bps INFO @ Sun, 02 Jun 2019 20:28:42: #2 alternative fragment length(s) may be 261 bps INFO @ Sun, 02 Jun 2019 20:28:42: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.05_model.r INFO @ Sun, 02 Jun 2019 20:28:42: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:28:42: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:28:50: 7000000 INFO @ Sun, 02 Jun 2019 20:28:55: #1 tag size is determined as 42 bps INFO @ Sun, 02 Jun 2019 20:28:55: #1 tag size = 42 INFO @ Sun, 02 Jun 2019 20:28:55: #1 total tags in treatment: 7520471 INFO @ Sun, 02 Jun 2019 20:28:55: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 20:28:55: #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 20:28:55: #1 tags after filtering in treatment: 7520471 INFO @ Sun, 02 Jun 2019 20:28:55: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 20:28:55: #1 finished! INFO @ Sun, 02 Jun 2019 20:28:55: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 20:28:55: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 20:28:56: #2 number of paired peaks: 3869 INFO @ Sun, 02 Jun 2019 20:28:56: start model_add_line... INFO @ Sun, 02 Jun 2019 20:28:56: start X-correlation... INFO @ Sun, 02 Jun 2019 20:28:56: end of X-cor INFO @ Sun, 02 Jun 2019 20:28:56: #2 finished! INFO @ Sun, 02 Jun 2019 20:28:56: #2 predicted fragment length is 261 bps INFO @ Sun, 02 Jun 2019 20:28:56: #2 alternative fragment length(s) may be 261 bps INFO @ Sun, 02 Jun 2019 20:28:56: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.10_model.r INFO @ Sun, 02 Jun 2019 20:28:56: #3 Call peaks... INFO @ Sun, 02 Jun 2019 20:28:56: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 20:29:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:29:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:29:14: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.20_peaks.xls INFO @ Sun, 02 Jun 2019 20:29:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:29:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.20_summits.bed INFO @ Sun, 02 Jun 2019 20:29:14: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (3355 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:29:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.05_peaks.xls INFO @ Sun, 02 Jun 2019 20:29:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:29:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.05_summits.bed INFO @ Sun, 02 Jun 2019 20:29:20: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5123 records, 4 fields): 12 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 20:29:25: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 20:29:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.10_peaks.xls INFO @ Sun, 02 Jun 2019 20:29:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 20:29:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494992/SRX494992.10_summits.bed INFO @ Sun, 02 Jun 2019 20:29:37: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (4221 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。