Job ID = 2589210 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 1,762,709 reads read : 1,762,709 reads written : 1,762,709 spots read : 1,417,977 reads read : 1,417,977 reads written : 1,417,977 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107598.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107599.sra.cache’: 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: 00:00:23 3180686 reads; of these: 3180686 (100.00%) were unpaired; of these: 1726786 (54.29%) aligned 0 times 1269039 (39.90%) aligned exactly 1 time 184861 (5.81%) aligned >1 times 45.71% overall alignment rate Time searching: 00:00:23 Overall time: 00:00:23 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] 392327 / 1453900 = 0.2698 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 @ Mon, 12 Aug 2019 17:10:10: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.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 @ Mon, 12 Aug 2019 17:10:10: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:10:10: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:10:11: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.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 @ Mon, 12 Aug 2019 17:10:11: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:10:11: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:10:12: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.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 @ Mon, 12 Aug 2019 17:10:12: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:10:12: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:10:18: 1000000 INFO @ Mon, 12 Aug 2019 17:10:18: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:10:18: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:10:18: #1 total tags in treatment: 1061573 INFO @ Mon, 12 Aug 2019 17:10:18: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:10:18: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:10:18: #1 tags after filtering in treatment: 1061573 INFO @ Mon, 12 Aug 2019 17:10:18: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:10:18: #1 finished! INFO @ Mon, 12 Aug 2019 17:10:18: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:10:18: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:10:18: #2 number of paired peaks: 3385 INFO @ Mon, 12 Aug 2019 17:10:18: start model_add_line... INFO @ Mon, 12 Aug 2019 17:10:18: start X-correlation... INFO @ Mon, 12 Aug 2019 17:10:18: end of X-cor INFO @ Mon, 12 Aug 2019 17:10:18: #2 finished! INFO @ Mon, 12 Aug 2019 17:10:18: #2 predicted fragment length is 167 bps INFO @ Mon, 12 Aug 2019 17:10:18: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 12 Aug 2019 17:10:18: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.05_model.r INFO @ Mon, 12 Aug 2019 17:10:18: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:10:18: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:19: 1000000 INFO @ Mon, 12 Aug 2019 17:10:19: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:10:19: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:10:19: #1 total tags in treatment: 1061573 INFO @ Mon, 12 Aug 2019 17:10:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:10:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:10:19: #1 tags after filtering in treatment: 1061573 INFO @ Mon, 12 Aug 2019 17:10:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:10:19: #1 finished! INFO @ Mon, 12 Aug 2019 17:10:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:10:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:10:19: #2 number of paired peaks: 3385 INFO @ Mon, 12 Aug 2019 17:10:19: start model_add_line... INFO @ Mon, 12 Aug 2019 17:10:20: start X-correlation... INFO @ Mon, 12 Aug 2019 17:10:20: end of X-cor INFO @ Mon, 12 Aug 2019 17:10:20: #2 finished! INFO @ Mon, 12 Aug 2019 17:10:20: #2 predicted fragment length is 167 bps INFO @ Mon, 12 Aug 2019 17:10:20: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 12 Aug 2019 17:10:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.10_model.r INFO @ Mon, 12 Aug 2019 17:10:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:10:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:20: 1000000 INFO @ Mon, 12 Aug 2019 17:10:20: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:10:20: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:10:20: #1 total tags in treatment: 1061573 INFO @ Mon, 12 Aug 2019 17:10:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:10:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 17:10:21: #1 tags after filtering in treatment: 1061573 INFO @ Mon, 12 Aug 2019 17:10:21: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:10:21: #1 finished! INFO @ Mon, 12 Aug 2019 17:10:21: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:10:21: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:10:21: #2 number of paired peaks: 3385 INFO @ Mon, 12 Aug 2019 17:10:21: start model_add_line... INFO @ Mon, 12 Aug 2019 17:10:21: start X-correlation... INFO @ Mon, 12 Aug 2019 17:10:21: end of X-cor INFO @ Mon, 12 Aug 2019 17:10:21: #2 finished! INFO @ Mon, 12 Aug 2019 17:10:21: #2 predicted fragment length is 167 bps INFO @ Mon, 12 Aug 2019 17:10:21: #2 alternative fragment length(s) may be 167 bps INFO @ Mon, 12 Aug 2019 17:10:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.20_model.r INFO @ Mon, 12 Aug 2019 17:10:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:10:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:22: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:23: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:24: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.05_summits.bed INFO @ Mon, 12 Aug 2019 17:10:24: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4036 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:10:24: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.10_summits.bed INFO @ Mon, 12 Aug 2019 17:10:25: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2031 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:10:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX044016/SRX044016.20_summits.bed INFO @ Mon, 12 Aug 2019 17:10:26: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (584 records, 4 fields): 4 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。