Job ID = 2589313 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 9,851,248 reads read : 9,851,248 reads written : 9,851,248 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘/home/okishinya/ncbi/public/sra/SRR217395.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: 00:01:47 9851248 reads; of these: 9851248 (100.00%) were unpaired; of these: 1064006 (10.80%) aligned 0 times 7397946 (75.10%) aligned exactly 1 time 1389296 (14.10%) aligned >1 times 89.20% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 1075812 / 8787242 = 0.1224 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 17:26:47: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.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 17:26:47: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:26:47: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:26:48: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.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 17:26:48: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:26:48: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:26:49: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.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 17:26:49: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:26:49: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:26:54: 1000000 INFO @ Mon, 12 Aug 2019 17:26:56: 1000000 INFO @ Mon, 12 Aug 2019 17:26:57: 1000000 INFO @ Mon, 12 Aug 2019 17:27:01: 2000000 INFO @ Mon, 12 Aug 2019 17:27:03: 2000000 INFO @ Mon, 12 Aug 2019 17:27:04: 2000000 INFO @ Mon, 12 Aug 2019 17:27:07: 3000000 INFO @ Mon, 12 Aug 2019 17:27:10: 3000000 INFO @ Mon, 12 Aug 2019 17:27:11: 3000000 INFO @ Mon, 12 Aug 2019 17:27:14: 4000000 INFO @ Mon, 12 Aug 2019 17:27:18: 4000000 INFO @ Mon, 12 Aug 2019 17:27:19: 4000000 INFO @ Mon, 12 Aug 2019 17:27:20: 5000000 INFO @ Mon, 12 Aug 2019 17:27:25: 5000000 INFO @ Mon, 12 Aug 2019 17:27:26: 5000000 INFO @ Mon, 12 Aug 2019 17:27:27: 6000000 INFO @ Mon, 12 Aug 2019 17:27:32: 6000000 INFO @ Mon, 12 Aug 2019 17:27:33: 6000000 INFO @ Mon, 12 Aug 2019 17:27:34: 7000000 INFO @ Mon, 12 Aug 2019 17:27:38: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:27:38: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:27:38: #1 total tags in treatment: 7711430 INFO @ Mon, 12 Aug 2019 17:27:38: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:27:38: #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 17:27:38: #1 tags after filtering in treatment: 7711430 INFO @ Mon, 12 Aug 2019 17:27:38: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:27:38: #1 finished! INFO @ Mon, 12 Aug 2019 17:27:38: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:27:38: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:27:39: 7000000 INFO @ Mon, 12 Aug 2019 17:27:39: #2 number of paired peaks: 432 WARNING @ Mon, 12 Aug 2019 17:27:39: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Mon, 12 Aug 2019 17:27:39: start model_add_line... INFO @ Mon, 12 Aug 2019 17:27:39: start X-correlation... INFO @ Mon, 12 Aug 2019 17:27:39: end of X-cor INFO @ Mon, 12 Aug 2019 17:27:39: #2 finished! INFO @ Mon, 12 Aug 2019 17:27:39: #2 predicted fragment length is 84 bps INFO @ Mon, 12 Aug 2019 17:27:39: #2 alternative fragment length(s) may be 3,52,84 bps INFO @ Mon, 12 Aug 2019 17:27:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.05_model.r INFO @ Mon, 12 Aug 2019 17:27:39: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:27:39: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:27:40: 7000000 INFO @ Mon, 12 Aug 2019 17:27:44: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:27:44: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:27:44: #1 total tags in treatment: 7711430 INFO @ Mon, 12 Aug 2019 17:27:44: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:27:44: #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 17:27:44: #1 tags after filtering in treatment: 7711430 INFO @ Mon, 12 Aug 2019 17:27:44: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:27:44: #1 finished! INFO @ Mon, 12 Aug 2019 17:27:44: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:27:44: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:27:45: #2 number of paired peaks: 432 WARNING @ Mon, 12 Aug 2019 17:27:45: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Mon, 12 Aug 2019 17:27:45: start model_add_line... INFO @ Mon, 12 Aug 2019 17:27:45: start X-correlation... INFO @ Mon, 12 Aug 2019 17:27:45: end of X-cor INFO @ Mon, 12 Aug 2019 17:27:45: #2 finished! INFO @ Mon, 12 Aug 2019 17:27:45: #2 predicted fragment length is 84 bps INFO @ Mon, 12 Aug 2019 17:27:45: #2 alternative fragment length(s) may be 3,52,84 bps INFO @ Mon, 12 Aug 2019 17:27:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.10_model.r INFO @ Mon, 12 Aug 2019 17:27:45: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:27:45: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:27:45: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:27:45: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:27:45: #1 total tags in treatment: 7711430 INFO @ Mon, 12 Aug 2019 17:27:45: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:27:45: #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 17:27:45: #1 tags after filtering in treatment: 7711430 INFO @ Mon, 12 Aug 2019 17:27:45: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:27:45: #1 finished! INFO @ Mon, 12 Aug 2019 17:27:45: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:27:45: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:27:46: #2 number of paired peaks: 432 WARNING @ Mon, 12 Aug 2019 17:27:46: Fewer paired peaks (432) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 432 pairs to build model! INFO @ Mon, 12 Aug 2019 17:27:46: start model_add_line... INFO @ Mon, 12 Aug 2019 17:27:46: start X-correlation... INFO @ Mon, 12 Aug 2019 17:27:46: end of X-cor INFO @ Mon, 12 Aug 2019 17:27:46: #2 finished! INFO @ Mon, 12 Aug 2019 17:27:46: #2 predicted fragment length is 84 bps INFO @ Mon, 12 Aug 2019 17:27:46: #2 alternative fragment length(s) may be 3,52,84 bps INFO @ Mon, 12 Aug 2019 17:27:46: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.20_model.r INFO @ Mon, 12 Aug 2019 17:27:46: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:27:46: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:28:01: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:28:07: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:28:08: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:28:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:28:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:28:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.05_summits.bed INFO @ Mon, 12 Aug 2019 17:28:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2135 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:28:18: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:28:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:28:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.10_summits.bed INFO @ Mon, 12 Aug 2019 17:28:18: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1006 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:28:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:28:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:28:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX065689/SRX065689.20_summits.bed INFO @ Mon, 12 Aug 2019 17:28:19: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (347 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。