Job ID = 1293250 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 11,146,393 reads read : 11,146,393 reads written : 11,146,393 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: 00:00:01 Multiseed full-index search: 00:03:16 11146393 reads; of these: 11146393 (100.00%) were unpaired; of these: 241084 (2.16%) aligned 0 times 9595881 (86.09%) aligned exactly 1 time 1309428 (11.75%) aligned >1 times 97.84% overall alignment rate Time searching: 00:03:17 Overall time: 00:03:17 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_sort_core] merging from 8 files... [bam_rmdupse_core] 8244283 / 10905309 = 0.7560 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 22:34:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.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 22:34:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:34:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:34:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.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 22:34:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:34:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:34:09: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.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 22:34:09: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:34:09: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:34:19: 1000000 INFO @ Sun, 02 Jun 2019 22:34:19: 1000000 INFO @ Sun, 02 Jun 2019 22:34:22: 1000000 INFO @ Sun, 02 Jun 2019 22:34:29: 2000000 INFO @ Sun, 02 Jun 2019 22:34:29: 2000000 INFO @ Sun, 02 Jun 2019 22:34:35: 2000000 INFO @ Sun, 02 Jun 2019 22:34:36: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:34:36: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:34:36: #1 total tags in treatment: 2661026 INFO @ Sun, 02 Jun 2019 22:34:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:34:36: #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 22:34:36: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:34:36: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:34:36: #1 total tags in treatment: 2661026 INFO @ Sun, 02 Jun 2019 22:34:36: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:34:36: #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 22:34:36: #1 tags after filtering in treatment: 2661026 INFO @ Sun, 02 Jun 2019 22:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:34:36: #1 finished! INFO @ Sun, 02 Jun 2019 22:34:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:34:36: #1 tags after filtering in treatment: 2661026 INFO @ Sun, 02 Jun 2019 22:34:36: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:34:36: #1 finished! INFO @ Sun, 02 Jun 2019 22:34:36: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:34:36: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:34:36: #2 number of paired peaks: 2318 INFO @ Sun, 02 Jun 2019 22:34:36: start model_add_line... INFO @ Sun, 02 Jun 2019 22:34:36: #2 number of paired peaks: 2318 INFO @ Sun, 02 Jun 2019 22:34:36: start model_add_line... INFO @ Sun, 02 Jun 2019 22:34:36: start X-correlation... INFO @ Sun, 02 Jun 2019 22:34:36: start X-correlation... INFO @ Sun, 02 Jun 2019 22:34:36: end of X-cor INFO @ Sun, 02 Jun 2019 22:34:36: #2 finished! INFO @ Sun, 02 Jun 2019 22:34:36: #2 predicted fragment length is 151 bps INFO @ Sun, 02 Jun 2019 22:34:36: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 02 Jun 2019 22:34:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.05_model.r INFO @ Sun, 02 Jun 2019 22:34:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:34:36: end of X-cor INFO @ Sun, 02 Jun 2019 22:34:36: #2 finished! INFO @ Sun, 02 Jun 2019 22:34:36: #2 predicted fragment length is 151 bps INFO @ Sun, 02 Jun 2019 22:34:36: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 02 Jun 2019 22:34:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.20_model.r INFO @ Sun, 02 Jun 2019 22:34:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:34:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:34:43: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:34:43: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:34:43: #1 total tags in treatment: 2661026 INFO @ Sun, 02 Jun 2019 22:34:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:34:43: #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 22:34:43: #1 tags after filtering in treatment: 2661026 INFO @ Sun, 02 Jun 2019 22:34:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:34:43: #1 finished! INFO @ Sun, 02 Jun 2019 22:34:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:34:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:34:43: #2 number of paired peaks: 2318 INFO @ Sun, 02 Jun 2019 22:34:43: start model_add_line... INFO @ Sun, 02 Jun 2019 22:34:43: start X-correlation... INFO @ Sun, 02 Jun 2019 22:34:44: end of X-cor INFO @ Sun, 02 Jun 2019 22:34:44: #2 finished! INFO @ Sun, 02 Jun 2019 22:34:44: #2 predicted fragment length is 151 bps INFO @ Sun, 02 Jun 2019 22:34:44: #2 alternative fragment length(s) may be 151 bps INFO @ Sun, 02 Jun 2019 22:34:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.10_model.r INFO @ Sun, 02 Jun 2019 22:34:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:34:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:34:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:34:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:34:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:34:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:34:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.20_summits.bed INFO @ Sun, 02 Jun 2019 22:34:49: Done! INFO @ Sun, 02 Jun 2019 22:34:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.05_peaks.xls pass1 - making usageList (6 chroms): 1 millis INFO @ Sun, 02 Jun 2019 22:34:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:34:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.05_summits.bed pass2 - checking and writing primary data (293 records, 4 fields): 25 millis INFO @ Sun, 02 Jun 2019 22:34:49: Done! CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2065 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:34:53: #3 Call peaks for each chromosome... BedGraph に変換しました。 BigWig に変換中... INFO @ Sun, 02 Jun 2019 22:34:57: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:34:57: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:34:57: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX554735/SRX554735.10_summits.bed INFO @ Sun, 02 Jun 2019 22:34:57: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (822 records, 4 fields): 4 millis CompletedMACS2peakCalling BigWig に変換しました。