Job ID = 2589151 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,075,959 reads read : 7,075,959 reads written : 7,075,959 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107355.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: 00:01:05 7075959 reads; of these: 7075959 (100.00%) were unpaired; of these: 2616324 (36.97%) aligned 0 times 4006191 (56.62%) aligned exactly 1 time 453444 (6.41%) aligned >1 times 63.03% overall alignment rate Time searching: 00:01:05 Overall time: 00:01:05 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] 1467147 / 4459635 = 0.3290 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 17:03:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.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 17:03:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:02: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.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 17:03:02: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:02: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.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 17:03:03: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:03:03: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:03:10: 1000000 INFO @ Mon, 12 Aug 2019 17:03:10: 1000000 INFO @ Mon, 12 Aug 2019 17:03:10: 1000000 INFO @ Mon, 12 Aug 2019 17:03:18: 2000000 INFO @ Mon, 12 Aug 2019 17:03:18: 2000000 INFO @ Mon, 12 Aug 2019 17:03:18: 2000000 INFO @ Mon, 12 Aug 2019 17:03:26: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:03:26: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:03:26: #1 total tags in treatment: 2992488 INFO @ Mon, 12 Aug 2019 17:03:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:03:26: #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 17:03:26: #1 tags after filtering in treatment: 2992488 INFO @ Mon, 12 Aug 2019 17:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:03:26: #1 finished! INFO @ Mon, 12 Aug 2019 17:03:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:03:26: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:03:26: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:03:26: #1 total tags in treatment: 2992488 INFO @ Mon, 12 Aug 2019 17:03:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:03:26: #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 17:03:26: #1 tags after filtering in treatment: 2992488 INFO @ Mon, 12 Aug 2019 17:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:03:26: #1 finished! INFO @ Mon, 12 Aug 2019 17:03:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:03:26: #1 tag size is determined as 34 bps INFO @ Mon, 12 Aug 2019 17:03:26: #1 tag size = 34 INFO @ Mon, 12 Aug 2019 17:03:26: #1 total tags in treatment: 2992488 INFO @ Mon, 12 Aug 2019 17:03:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:03:26: #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 17:03:26: #1 tags after filtering in treatment: 2992488 INFO @ Mon, 12 Aug 2019 17:03:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:03:26: #1 finished! INFO @ Mon, 12 Aug 2019 17:03:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:03:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:03:26: #2 number of paired peaks: 3205 INFO @ Mon, 12 Aug 2019 17:03:26: start model_add_line... INFO @ Mon, 12 Aug 2019 17:03:26: start X-correlation... INFO @ Mon, 12 Aug 2019 17:03:26: end of X-cor INFO @ Mon, 12 Aug 2019 17:03:26: #2 finished! INFO @ Mon, 12 Aug 2019 17:03:26: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 17:03:26: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 17:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.20_model.r INFO @ Mon, 12 Aug 2019 17:03:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:03:26: #2 number of paired peaks: 3205 INFO @ Mon, 12 Aug 2019 17:03:26: start model_add_line... INFO @ Mon, 12 Aug 2019 17:03:26: start X-correlation... INFO @ Mon, 12 Aug 2019 17:03:26: end of X-cor INFO @ Mon, 12 Aug 2019 17:03:26: #2 finished! INFO @ Mon, 12 Aug 2019 17:03:26: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 17:03:26: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 17:03:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.05_model.r INFO @ Mon, 12 Aug 2019 17:03:26: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:03:26: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:03:26: #2 number of paired peaks: 3205 INFO @ Mon, 12 Aug 2019 17:03:26: start model_add_line... INFO @ Mon, 12 Aug 2019 17:03:26: start X-correlation... INFO @ Mon, 12 Aug 2019 17:03:27: end of X-cor INFO @ Mon, 12 Aug 2019 17:03:27: #2 finished! INFO @ Mon, 12 Aug 2019 17:03:27: #2 predicted fragment length is 128 bps INFO @ Mon, 12 Aug 2019 17:03:27: #2 alternative fragment length(s) may be 128 bps INFO @ Mon, 12 Aug 2019 17:03:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.10_model.r INFO @ Mon, 12 Aug 2019 17:03:27: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:03:27: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:03:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:03:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:03:37: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:03:41: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:03:41: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:03:41: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.20_summits.bed INFO @ Mon, 12 Aug 2019 17:03:41: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (278 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:03:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.05_summits.bed INFO @ Mon, 12 Aug 2019 17:03:42: Done! INFO @ Mon, 12 Aug 2019 17:03:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:03:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:03:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043880/SRX043880.10_summits.bed INFO @ Mon, 12 Aug 2019 17:03:42: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (2812 records, 4 fields): 6 millis CompletedMACS2peakCalling pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1022 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。