Job ID = 1291667 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 3,551,601 reads read : 3,551,601 reads written : 3,551,601 spots read : 3,581,775 reads read : 3,581,775 reads written : 3,581,775 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: 00:01:38 7133376 reads; of these: 7133376 (100.00%) were unpaired; of these: 2878454 (40.35%) aligned 0 times 3565524 (49.98%) aligned exactly 1 time 689398 (9.66%) aligned >1 times 59.65% overall alignment rate Time searching: 00:01:38 Overall time: 00:01:38 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] 917064 / 4254922 = 0.2155 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 16:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.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 16:16:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:16:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.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 16:16:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:16:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:16:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.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 16:16:37: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:16:37: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:16:46: 1000000 INFO @ Sun, 02 Jun 2019 16:16:47: 1000000 INFO @ Sun, 02 Jun 2019 16:16:48: 1000000 INFO @ Sun, 02 Jun 2019 16:16:55: 2000000 INFO @ Sun, 02 Jun 2019 16:16:58: 2000000 INFO @ Sun, 02 Jun 2019 16:16:59: 2000000 INFO @ Sun, 02 Jun 2019 16:17:04: 3000000 INFO @ Sun, 02 Jun 2019 16:17:07: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:17:07: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:17:07: #1 total tags in treatment: 3337858 INFO @ Sun, 02 Jun 2019 16:17:07: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:17:07: #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 16:17:07: #1 tags after filtering in treatment: 3337858 INFO @ Sun, 02 Jun 2019 16:17:07: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:17:07: #1 finished! INFO @ Sun, 02 Jun 2019 16:17:07: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:17:07: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:17:07: #2 number of paired peaks: 2782 INFO @ Sun, 02 Jun 2019 16:17:07: start model_add_line... INFO @ Sun, 02 Jun 2019 16:17:07: start X-correlation... INFO @ Sun, 02 Jun 2019 16:17:07: end of X-cor INFO @ Sun, 02 Jun 2019 16:17:07: #2 finished! INFO @ Sun, 02 Jun 2019 16:17:07: #2 predicted fragment length is 290 bps INFO @ Sun, 02 Jun 2019 16:17:07: #2 alternative fragment length(s) may be 290 bps INFO @ Sun, 02 Jun 2019 16:17:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.05_model.r INFO @ Sun, 02 Jun 2019 16:17:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:17:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:17:08: 3000000 INFO @ Sun, 02 Jun 2019 16:17:10: 3000000 INFO @ Sun, 02 Jun 2019 16:17:11: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:17:11: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:17:11: #1 total tags in treatment: 3337858 INFO @ Sun, 02 Jun 2019 16:17:11: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:17:11: #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 16:17:11: #1 tags after filtering in treatment: 3337858 INFO @ Sun, 02 Jun 2019 16:17:11: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:17:11: #1 finished! INFO @ Sun, 02 Jun 2019 16:17:11: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:17:11: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:17:12: #2 number of paired peaks: 2782 INFO @ Sun, 02 Jun 2019 16:17:12: start model_add_line... INFO @ Sun, 02 Jun 2019 16:17:12: start X-correlation... INFO @ Sun, 02 Jun 2019 16:17:12: end of X-cor INFO @ Sun, 02 Jun 2019 16:17:12: #2 finished! INFO @ Sun, 02 Jun 2019 16:17:12: #2 predicted fragment length is 290 bps INFO @ Sun, 02 Jun 2019 16:17:12: #2 alternative fragment length(s) may be 290 bps INFO @ Sun, 02 Jun 2019 16:17:12: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.10_model.r INFO @ Sun, 02 Jun 2019 16:17:12: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:17:12: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:17:13: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 16:17:13: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 16:17:13: #1 total tags in treatment: 3337858 INFO @ Sun, 02 Jun 2019 16:17:13: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 16:17:13: #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 16:17:13: #1 tags after filtering in treatment: 3337858 INFO @ Sun, 02 Jun 2019 16:17:13: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 16:17:13: #1 finished! INFO @ Sun, 02 Jun 2019 16:17:13: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 16:17:13: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 16:17:14: #2 number of paired peaks: 2782 INFO @ Sun, 02 Jun 2019 16:17:14: start model_add_line... INFO @ Sun, 02 Jun 2019 16:17:14: start X-correlation... INFO @ Sun, 02 Jun 2019 16:17:14: end of X-cor INFO @ Sun, 02 Jun 2019 16:17:14: #2 finished! INFO @ Sun, 02 Jun 2019 16:17:14: #2 predicted fragment length is 290 bps INFO @ Sun, 02 Jun 2019 16:17:14: #2 alternative fragment length(s) may be 290 bps INFO @ Sun, 02 Jun 2019 16:17:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.20_model.r INFO @ Sun, 02 Jun 2019 16:17:14: #3 Call peaks... INFO @ Sun, 02 Jun 2019 16:17:14: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 16:17:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:17:26: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:17:27: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 16:17:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.05_peaks.xls INFO @ Sun, 02 Jun 2019 16:17:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:17:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.05_summits.bed INFO @ Sun, 02 Jun 2019 16:17:28: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4217 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:17:32: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.10_peaks.xls INFO @ Sun, 02 Jun 2019 16:17:32: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:17:32: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.10_summits.bed INFO @ Sun, 02 Jun 2019 16:17:32: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2929 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 16:17:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.20_peaks.xls INFO @ Sun, 02 Jun 2019 16:17:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 16:17:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769995/SRX1769995.20_summits.bed INFO @ Sun, 02 Jun 2019 16:17:33: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (1949 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。