Job ID = 2589185 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,277,607 reads read : 3,277,607 reads written : 3,277,607 spots read : 3,599,838 reads read : 3,599,838 reads written : 3,599,838 rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107568.sra.cache’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR107569.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 6877445 reads; of these: 6877445 (100.00%) were unpaired; of these: 365126 (5.31%) aligned 0 times 5723320 (83.22%) aligned exactly 1 time 788999 (11.47%) aligned >1 times 94.69% 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] 1032296 / 6512319 = 0.1585 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 17:08:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.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 17:08:55: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:08:55: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:08:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.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 17:08:56: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:08:56: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:08:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.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 17:08:57: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:08:57: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:09:05: 1000000 INFO @ Mon, 12 Aug 2019 17:09:05: 1000000 INFO @ Mon, 12 Aug 2019 17:09:06: 1000000 INFO @ Mon, 12 Aug 2019 17:09:14: 2000000 INFO @ Mon, 12 Aug 2019 17:09:14: 2000000 INFO @ Mon, 12 Aug 2019 17:09:15: 2000000 INFO @ Mon, 12 Aug 2019 17:09:22: 3000000 INFO @ Mon, 12 Aug 2019 17:09:23: 3000000 INFO @ Mon, 12 Aug 2019 17:09:24: 3000000 INFO @ Mon, 12 Aug 2019 17:09:31: 4000000 INFO @ Mon, 12 Aug 2019 17:09:33: 4000000 INFO @ Mon, 12 Aug 2019 17:09:33: 4000000 INFO @ Mon, 12 Aug 2019 17:09:40: 5000000 INFO @ Mon, 12 Aug 2019 17:09:41: 5000000 INFO @ Mon, 12 Aug 2019 17:09:42: 5000000 INFO @ Mon, 12 Aug 2019 17:09:44: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:09:44: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:09:44: #1 total tags in treatment: 5480023 INFO @ Mon, 12 Aug 2019 17:09:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:09:44: #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 17:09:44: #1 tags after filtering in treatment: 5480023 INFO @ Mon, 12 Aug 2019 17:09:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:09:44: #1 finished! INFO @ Mon, 12 Aug 2019 17:09:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:09:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:09:45: #2 number of paired peaks: 1443 INFO @ Mon, 12 Aug 2019 17:09:45: start model_add_line... INFO @ Mon, 12 Aug 2019 17:09:45: start X-correlation... INFO @ Mon, 12 Aug 2019 17:09:45: end of X-cor INFO @ Mon, 12 Aug 2019 17:09:45: #2 finished! INFO @ Mon, 12 Aug 2019 17:09:45: #2 predicted fragment length is 137 bps INFO @ Mon, 12 Aug 2019 17:09:45: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 12 Aug 2019 17:09:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.10_model.r INFO @ Mon, 12 Aug 2019 17:09:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:09:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:09:45: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:09:45: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:09:45: #1 total tags in treatment: 5480023 INFO @ Mon, 12 Aug 2019 17:09:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:09:45: #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 17:09:45: #1 tags after filtering in treatment: 5480023 INFO @ Mon, 12 Aug 2019 17:09:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:09:45: #1 finished! INFO @ Mon, 12 Aug 2019 17:09:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:09:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:09:46: #2 number of paired peaks: 1443 INFO @ Mon, 12 Aug 2019 17:09:46: start model_add_line... INFO @ Mon, 12 Aug 2019 17:09:46: start X-correlation... INFO @ Mon, 12 Aug 2019 17:09:46: end of X-cor INFO @ Mon, 12 Aug 2019 17:09:46: #2 finished! INFO @ Mon, 12 Aug 2019 17:09:46: #2 predicted fragment length is 137 bps INFO @ Mon, 12 Aug 2019 17:09:46: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 12 Aug 2019 17:09:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.20_model.r INFO @ Mon, 12 Aug 2019 17:09:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:09:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:09:47: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:09:47: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:09:47: #1 total tags in treatment: 5480023 INFO @ Mon, 12 Aug 2019 17:09:47: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:09:47: #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 17:09:47: #1 tags after filtering in treatment: 5480023 INFO @ Mon, 12 Aug 2019 17:09:47: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:09:47: #1 finished! INFO @ Mon, 12 Aug 2019 17:09:47: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:09:47: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:09:47: #2 number of paired peaks: 1443 INFO @ Mon, 12 Aug 2019 17:09:47: start model_add_line... INFO @ Mon, 12 Aug 2019 17:09:47: start X-correlation... INFO @ Mon, 12 Aug 2019 17:09:47: end of X-cor INFO @ Mon, 12 Aug 2019 17:09:47: #2 finished! INFO @ Mon, 12 Aug 2019 17:09:47: #2 predicted fragment length is 137 bps INFO @ Mon, 12 Aug 2019 17:09:47: #2 alternative fragment length(s) may be 137 bps INFO @ Mon, 12 Aug 2019 17:09:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.05_model.r INFO @ Mon, 12 Aug 2019 17:09:47: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:09:47: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:10:03: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:04: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:05: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.10_summits.bed INFO @ Mon, 12 Aug 2019 17:10:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:12: Done! INFO @ Mon, 12 Aug 2019 17:10:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.20_summits.bed INFO @ Mon, 12 Aug 2019 17:10:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2438 records, 4 fields): 5 millis CompletedMACS2peakCalling pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4961 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:10:13: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:10:14: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:10:14: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX043992/SRX043992.05_summits.bed INFO @ Mon, 12 Aug 2019 17:10:14: Done! pass1 - making usageList (7 chroms): 5 millis pass2 - checking and writing primary data (7429 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。