Job ID = 1292922 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 10,825,090 reads read : 10,825,090 reads written : 10,825,090 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: 00:02:28 10825090 reads; of these: 10825090 (100.00%) were unpaired; of these: 885528 (8.18%) aligned 0 times 8382888 (77.44%) aligned exactly 1 time 1556674 (14.38%) aligned >1 times 91.82% overall alignment rate Time searching: 00:02:28 Overall time: 00:02:28 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_sort_core] merging from 8 files... [bam_rmdupse_core] 775947 / 9939562 = 0.0781 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 21:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.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 21:09:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.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 21:09:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:30: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.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 21:09:30: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:09:30: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:09:37: 1000000 INFO @ Sun, 02 Jun 2019 21:09:38: 1000000 INFO @ Sun, 02 Jun 2019 21:09:38: 1000000 INFO @ Sun, 02 Jun 2019 21:09:43: 2000000 INFO @ Sun, 02 Jun 2019 21:09:45: 2000000 INFO @ Sun, 02 Jun 2019 21:09:46: 2000000 INFO @ Sun, 02 Jun 2019 21:09:50: 3000000 INFO @ Sun, 02 Jun 2019 21:09:53: 3000000 INFO @ Sun, 02 Jun 2019 21:09:53: 3000000 INFO @ Sun, 02 Jun 2019 21:09:57: 4000000 INFO @ Sun, 02 Jun 2019 21:10:00: 4000000 INFO @ Sun, 02 Jun 2019 21:10:01: 4000000 INFO @ Sun, 02 Jun 2019 21:10:03: 5000000 INFO @ Sun, 02 Jun 2019 21:10:08: 5000000 INFO @ Sun, 02 Jun 2019 21:10:08: 5000000 INFO @ Sun, 02 Jun 2019 21:10:11: 6000000 INFO @ Sun, 02 Jun 2019 21:10:15: 6000000 INFO @ Sun, 02 Jun 2019 21:10:16: 6000000 INFO @ Sun, 02 Jun 2019 21:10:18: 7000000 INFO @ Sun, 02 Jun 2019 21:10:23: 7000000 INFO @ Sun, 02 Jun 2019 21:10:23: 7000000 INFO @ Sun, 02 Jun 2019 21:10:24: 8000000 INFO @ Sun, 02 Jun 2019 21:10:31: 8000000 INFO @ Sun, 02 Jun 2019 21:10:31: 8000000 INFO @ Sun, 02 Jun 2019 21:10:31: 9000000 INFO @ Sun, 02 Jun 2019 21:10:32: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:32: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:32: #1 total tags in treatment: 9163615 INFO @ Sun, 02 Jun 2019 21:10:32: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:32: #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 21:10:32: #1 tags after filtering in treatment: 9163615 INFO @ Sun, 02 Jun 2019 21:10:32: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:32: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:32: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:32: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:33: #2 number of paired peaks: 425 WARNING @ Sun, 02 Jun 2019 21:10:33: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:33: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:33: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:33: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:33: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:33: #2 predicted fragment length is 132 bps INFO @ Sun, 02 Jun 2019 21:10:33: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 02 Jun 2019 21:10:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.10_model.r INFO @ Sun, 02 Jun 2019 21:10:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:38: 9000000 INFO @ Sun, 02 Jun 2019 21:10:38: 9000000 INFO @ Sun, 02 Jun 2019 21:10:39: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:39: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:39: #1 total tags in treatment: 9163615 INFO @ Sun, 02 Jun 2019 21:10:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:39: #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 21:10:39: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:10:39: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:10:39: #1 total tags in treatment: 9163615 INFO @ Sun, 02 Jun 2019 21:10:39: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:10:39: #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 21:10:39: #1 tags after filtering in treatment: 9163615 INFO @ Sun, 02 Jun 2019 21:10:39: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:39: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:39: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:39: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:40: #1 tags after filtering in treatment: 9163615 INFO @ Sun, 02 Jun 2019 21:10:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:10:40: #1 finished! INFO @ Sun, 02 Jun 2019 21:10:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:10:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:10:40: #2 number of paired peaks: 425 WARNING @ Sun, 02 Jun 2019 21:10:40: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:40: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:40: #2 number of paired peaks: 425 WARNING @ Sun, 02 Jun 2019 21:10:40: Fewer paired peaks (425) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 425 pairs to build model! INFO @ Sun, 02 Jun 2019 21:10:40: start model_add_line... INFO @ Sun, 02 Jun 2019 21:10:40: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:40: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:40: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:40: #2 predicted fragment length is 132 bps INFO @ Sun, 02 Jun 2019 21:10:40: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 02 Jun 2019 21:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.20_model.r INFO @ Sun, 02 Jun 2019 21:10:40: start X-correlation... INFO @ Sun, 02 Jun 2019 21:10:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:10:40: end of X-cor INFO @ Sun, 02 Jun 2019 21:10:40: #2 finished! INFO @ Sun, 02 Jun 2019 21:10:40: #2 predicted fragment length is 132 bps INFO @ Sun, 02 Jun 2019 21:10:40: #2 alternative fragment length(s) may be 132 bps INFO @ Sun, 02 Jun 2019 21:10:40: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.05_model.r INFO @ Sun, 02 Jun 2019 21:10:40: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:10:40: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:11:00: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:11:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:11:07: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:11:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:11:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:11:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.10_summits.bed INFO @ Sun, 02 Jun 2019 21:11:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1131 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:11:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:11:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:11:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.20_summits.bed INFO @ Sun, 02 Jun 2019 21:11:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (329 records, 4 fields): 1 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:11:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:11:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:11:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020715/SRX5020715.05_summits.bed INFO @ Sun, 02 Jun 2019 21:11:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2829 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。