Job ID = 2589258 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 5,037,643 reads read : 5,037,643 reads written : 5,037,643 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217334.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: 00:00:34 5037643 reads; of these: 5037643 (100.00%) were unpaired; of these: 2810353 (55.79%) aligned 0 times 1973485 (39.17%) aligned exactly 1 time 253805 (5.04%) aligned >1 times 44.21% overall alignment rate Time searching: 00:00:34 Overall time: 00:00:34 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] 174691 / 2227290 = 0.0784 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 17:16:26: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.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 17:16:26: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:16:26: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:16:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.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 17:16:27: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:16:27: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:16:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.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 17:16:28: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:16:28: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:16:33: 1000000 INFO @ Mon, 12 Aug 2019 17:16:36: 1000000 INFO @ Mon, 12 Aug 2019 17:16:37: 1000000 INFO @ Mon, 12 Aug 2019 17:16:40: 2000000 INFO @ Mon, 12 Aug 2019 17:16:40: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:16:40: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:16:40: #1 total tags in treatment: 2052599 INFO @ Mon, 12 Aug 2019 17:16:40: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:16:40: #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 17:16:40: #1 tags after filtering in treatment: 2052599 INFO @ Mon, 12 Aug 2019 17:16:40: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:16:40: #1 finished! INFO @ Mon, 12 Aug 2019 17:16:40: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:16:40: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:16:41: #2 number of paired peaks: 3043 INFO @ Mon, 12 Aug 2019 17:16:41: start model_add_line... INFO @ Mon, 12 Aug 2019 17:16:41: start X-correlation... INFO @ Mon, 12 Aug 2019 17:16:41: end of X-cor INFO @ Mon, 12 Aug 2019 17:16:41: #2 finished! INFO @ Mon, 12 Aug 2019 17:16:41: #2 predicted fragment length is 137 bps INFO @ Mon, 12 Aug 2019 17:16:41: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 12 Aug 2019 17:16:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.05_model.r INFO @ Mon, 12 Aug 2019 17:16:41: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:16:41: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:16:44: 2000000 INFO @ Mon, 12 Aug 2019 17:16:44: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:16:44: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:16:44: #1 total tags in treatment: 2052599 INFO @ Mon, 12 Aug 2019 17:16:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:16:44: #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 17:16:44: #1 tags after filtering in treatment: 2052599 INFO @ Mon, 12 Aug 2019 17:16:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:16:44: #1 finished! INFO @ Mon, 12 Aug 2019 17:16:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:16:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:16:44: #2 number of paired peaks: 3043 INFO @ Mon, 12 Aug 2019 17:16:44: start model_add_line... INFO @ Mon, 12 Aug 2019 17:16:44: start X-correlation... INFO @ Mon, 12 Aug 2019 17:16:44: end of X-cor INFO @ Mon, 12 Aug 2019 17:16:44: #2 finished! INFO @ Mon, 12 Aug 2019 17:16:44: #2 predicted fragment length is 137 bps INFO @ Mon, 12 Aug 2019 17:16:44: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 12 Aug 2019 17:16:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.20_model.r INFO @ Mon, 12 Aug 2019 17:16:44: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:16:44: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:16:47: 2000000 INFO @ Mon, 12 Aug 2019 17:16:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:16:48: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:16:48: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:16:48: #1 total tags in treatment: 2052599 INFO @ Mon, 12 Aug 2019 17:16:48: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:16:48: #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 17:16:48: #1 tags after filtering in treatment: 2052599 INFO @ Mon, 12 Aug 2019 17:16:48: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:16:48: #1 finished! INFO @ Mon, 12 Aug 2019 17:16:48: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:16:48: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:16:48: #2 number of paired peaks: 3043 INFO @ Mon, 12 Aug 2019 17:16:48: start model_add_line... INFO @ Mon, 12 Aug 2019 17:16:48: start X-correlation... INFO @ Mon, 12 Aug 2019 17:16:48: end of X-cor INFO @ Mon, 12 Aug 2019 17:16:48: #2 finished! INFO @ Mon, 12 Aug 2019 17:16:48: #2 predicted fragment length is 137 bps INFO @ Mon, 12 Aug 2019 17:16:48: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 12 Aug 2019 17:16:48: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.10_model.r INFO @ Mon, 12 Aug 2019 17:16:48: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:16:48: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:16:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:16:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:16:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.05_summits.bed INFO @ Mon, 12 Aug 2019 17:16:51: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (5958 records, 4 fields): 14 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:16:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:16:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:16:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:16:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.20_summits.bed INFO @ Mon, 12 Aug 2019 17:16:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1332 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:16:55: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:16:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:16:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:16:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065628/SRX065628.10_summits.bed INFO @ Mon, 12 Aug 2019 17:16:59: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3429 records, 4 fields): 9 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。