Job ID = 1292160 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,375,307 reads read : 8,375,307 reads written : 8,375,307 rm: cannot remove ‘[DSE]RR*’: No such file or directory rm: cannot remove ‘fastqDump_tmp*’: 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: 00:01:23 8375307 reads; of these: 8375307 (100.00%) were unpaired; of these: 781186 (9.33%) aligned 0 times 6298955 (75.21%) aligned exactly 1 time 1295166 (15.46%) aligned >1 times 90.67% overall alignment rate Time searching: 00:01:23 Overall time: 00:01:23 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] 1233497 / 7594121 = 0.1624 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 @ Sun, 02 Jun 2019 17:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.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 @ Sun, 02 Jun 2019 17:37:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:37:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.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 @ Sun, 02 Jun 2019 17:37:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:37:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:37:45: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.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 @ Sun, 02 Jun 2019 17:37:45: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:37:45: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:37:51: 1000000 INFO @ Sun, 02 Jun 2019 17:37:52: 1000000 INFO @ Sun, 02 Jun 2019 17:37:52: 1000000 INFO @ Sun, 02 Jun 2019 17:37:57: 2000000 INFO @ Sun, 02 Jun 2019 17:37:58: 2000000 INFO @ Sun, 02 Jun 2019 17:37:58: 2000000 INFO @ Sun, 02 Jun 2019 17:38:03: 3000000 INFO @ Sun, 02 Jun 2019 17:38:04: 3000000 INFO @ Sun, 02 Jun 2019 17:38:04: 3000000 INFO @ Sun, 02 Jun 2019 17:38:09: 4000000 INFO @ Sun, 02 Jun 2019 17:38:10: 4000000 INFO @ Sun, 02 Jun 2019 17:38:10: 4000000 INFO @ Sun, 02 Jun 2019 17:38:14: 5000000 INFO @ Sun, 02 Jun 2019 17:38:16: 5000000 INFO @ Sun, 02 Jun 2019 17:38:16: 5000000 INFO @ Sun, 02 Jun 2019 17:38:20: 6000000 INFO @ Sun, 02 Jun 2019 17:38:22: 6000000 INFO @ Sun, 02 Jun 2019 17:38:22: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:38:22: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:38:22: #1 total tags in treatment: 6360624 INFO @ Sun, 02 Jun 2019 17:38:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:38:22: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:38:22: #1 tags after filtering in treatment: 6360624 INFO @ Sun, 02 Jun 2019 17:38:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:38:22: #1 finished! INFO @ Sun, 02 Jun 2019 17:38:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:38:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:38:23: 6000000 INFO @ Sun, 02 Jun 2019 17:38:23: #2 number of paired peaks: 609 WARNING @ Sun, 02 Jun 2019 17:38:23: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Sun, 02 Jun 2019 17:38:23: start model_add_line... INFO @ Sun, 02 Jun 2019 17:38:23: start X-correlation... INFO @ Sun, 02 Jun 2019 17:38:23: end of X-cor INFO @ Sun, 02 Jun 2019 17:38:23: #2 finished! INFO @ Sun, 02 Jun 2019 17:38:23: #2 predicted fragment length is 123 bps INFO @ Sun, 02 Jun 2019 17:38:23: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 02 Jun 2019 17:38:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.05_model.r INFO @ Sun, 02 Jun 2019 17:38:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:38:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:38:25: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:38:25: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:38:25: #1 total tags in treatment: 6360624 INFO @ Sun, 02 Jun 2019 17:38:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:38:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:38:25: #1 tags after filtering in treatment: 6360624 INFO @ Sun, 02 Jun 2019 17:38:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:38:25: #1 finished! INFO @ Sun, 02 Jun 2019 17:38:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:38:25: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:38:25: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:38:25: #1 total tags in treatment: 6360624 INFO @ Sun, 02 Jun 2019 17:38:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:38:25: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:38:25: #1 tags after filtering in treatment: 6360624 INFO @ Sun, 02 Jun 2019 17:38:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:38:25: #1 finished! INFO @ Sun, 02 Jun 2019 17:38:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:38:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:38:25: #2 number of paired peaks: 609 WARNING @ Sun, 02 Jun 2019 17:38:25: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Sun, 02 Jun 2019 17:38:25: start model_add_line... INFO @ Sun, 02 Jun 2019 17:38:25: start X-correlation... INFO @ Sun, 02 Jun 2019 17:38:25: end of X-cor INFO @ Sun, 02 Jun 2019 17:38:25: #2 finished! INFO @ Sun, 02 Jun 2019 17:38:25: #2 predicted fragment length is 123 bps INFO @ Sun, 02 Jun 2019 17:38:25: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 02 Jun 2019 17:38:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.20_model.r INFO @ Sun, 02 Jun 2019 17:38:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:38:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:38:26: #2 number of paired peaks: 609 WARNING @ Sun, 02 Jun 2019 17:38:26: Fewer paired peaks (609) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 609 pairs to build model! INFO @ Sun, 02 Jun 2019 17:38:26: start model_add_line... INFO @ Sun, 02 Jun 2019 17:38:26: start X-correlation... INFO @ Sun, 02 Jun 2019 17:38:26: end of X-cor INFO @ Sun, 02 Jun 2019 17:38:26: #2 finished! INFO @ Sun, 02 Jun 2019 17:38:26: #2 predicted fragment length is 123 bps INFO @ Sun, 02 Jun 2019 17:38:26: #2 alternative fragment length(s) may be 123 bps INFO @ Sun, 02 Jun 2019 17:38:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.10_model.r INFO @ Sun, 02 Jun 2019 17:38:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:38:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:38:42: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:38:44: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:38:45: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:38:51: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:38:51: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:38:51: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.05_summits.bed INFO @ Sun, 02 Jun 2019 17:38:51: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (3041 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:38:53: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:38:53: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:38:53: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.20_summits.bed INFO @ Sun, 02 Jun 2019 17:38:53: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (662 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:38:54: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:38:54: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:38:54: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331198/SRX331198.10_summits.bed INFO @ Sun, 02 Jun 2019 17:38:54: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1666 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。