Job ID = 1290598 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,954,721 reads read : 31,909,442 reads written : 15,954,721 reads 0-length : 15,954,721 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: 00:03:19 15954721 reads; of these: 15954721 (100.00%) were unpaired; of these: 1960764 (12.29%) aligned 0 times 12802713 (80.24%) aligned exactly 1 time 1191244 (7.47%) aligned >1 times 87.71% overall alignment rate Time searching: 00:03:19 Overall time: 00:03:19 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] 6471315 / 13993957 = 0.4624 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 @ Sat, 01 Jun 2019 21:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.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 @ Sat, 01 Jun 2019 21:51:52: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:52: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.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 @ Sat, 01 Jun 2019 21:51:52: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:52: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.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 @ Sat, 01 Jun 2019 21:51:52: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:52: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:59: 1000000 INFO @ Sat, 01 Jun 2019 21:52:00: 1000000 INFO @ Sat, 01 Jun 2019 21:52:02: 1000000 INFO @ Sat, 01 Jun 2019 21:52:06: 2000000 INFO @ Sat, 01 Jun 2019 21:52:08: 2000000 INFO @ Sat, 01 Jun 2019 21:52:12: 2000000 INFO @ Sat, 01 Jun 2019 21:52:13: 3000000 INFO @ Sat, 01 Jun 2019 21:52:15: 3000000 INFO @ Sat, 01 Jun 2019 21:52:20: 4000000 INFO @ Sat, 01 Jun 2019 21:52:21: 3000000 INFO @ Sat, 01 Jun 2019 21:52:23: 4000000 INFO @ Sat, 01 Jun 2019 21:52:27: 5000000 INFO @ Sat, 01 Jun 2019 21:52:31: 4000000 INFO @ Sat, 01 Jun 2019 21:52:31: 5000000 INFO @ Sat, 01 Jun 2019 21:52:34: 6000000 INFO @ Sat, 01 Jun 2019 21:52:39: 6000000 INFO @ Sat, 01 Jun 2019 21:52:40: 5000000 INFO @ Sat, 01 Jun 2019 21:52:41: 7000000 INFO @ Sat, 01 Jun 2019 21:52:45: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:45: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:45: #1 total tags in treatment: 7522642 INFO @ Sat, 01 Jun 2019 21:52:45: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:45: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:45: #1 tags after filtering in treatment: 7522642 INFO @ Sat, 01 Jun 2019 21:52:45: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:45: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:45: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:45: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:47: #2 number of paired peaks: 6072 INFO @ Sat, 01 Jun 2019 21:52:47: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:47: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:47: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:47: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:47: #2 predicted fragment length is 212 bps INFO @ Sat, 01 Jun 2019 21:52:47: #2 alternative fragment length(s) may be 4,212 bps INFO @ Sat, 01 Jun 2019 21:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.20_model.r INFO @ Sat, 01 Jun 2019 21:52:47: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:47: 7000000 INFO @ Sat, 01 Jun 2019 21:52:50: 6000000 INFO @ Sat, 01 Jun 2019 21:52:51: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:52:51: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:52:51: #1 total tags in treatment: 7522642 INFO @ Sat, 01 Jun 2019 21:52:51: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:51: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:52:51: #1 tags after filtering in treatment: 7522642 INFO @ Sat, 01 Jun 2019 21:52:51: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:51: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:51: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:51: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:52: #2 number of paired peaks: 6072 INFO @ Sat, 01 Jun 2019 21:52:52: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:53: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:53: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:53: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:53: #2 predicted fragment length is 212 bps INFO @ Sat, 01 Jun 2019 21:52:53: #2 alternative fragment length(s) may be 4,212 bps INFO @ Sat, 01 Jun 2019 21:52:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.10_model.r INFO @ Sat, 01 Jun 2019 21:52:53: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:53:00: 7000000 INFO @ Sat, 01 Jun 2019 21:53:05: #1 tag size is determined as 51 bps INFO @ Sat, 01 Jun 2019 21:53:05: #1 tag size = 51 INFO @ Sat, 01 Jun 2019 21:53:05: #1 total tags in treatment: 7522642 INFO @ Sat, 01 Jun 2019 21:53:05: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:53:05: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sat, 01 Jun 2019 21:53:05: #1 tags after filtering in treatment: 7522642 INFO @ Sat, 01 Jun 2019 21:53:05: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:53:05: #1 finished! INFO @ Sat, 01 Jun 2019 21:53:05: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:53:05: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:53:06: #2 number of paired peaks: 6072 INFO @ Sat, 01 Jun 2019 21:53:06: start model_add_line... INFO @ Sat, 01 Jun 2019 21:53:06: start X-correlation... INFO @ Sat, 01 Jun 2019 21:53:06: end of X-cor INFO @ Sat, 01 Jun 2019 21:53:06: #2 finished! INFO @ Sat, 01 Jun 2019 21:53:06: #2 predicted fragment length is 212 bps INFO @ Sat, 01 Jun 2019 21:53:06: #2 alternative fragment length(s) may be 4,212 bps INFO @ Sat, 01 Jun 2019 21:53:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.05_model.r INFO @ Sat, 01 Jun 2019 21:53:06: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:53:06: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:53:13: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:17: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:26: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:26: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:26: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.20_summits.bed INFO @ Sat, 01 Jun 2019 21:53:26: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1404 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.10_summits.bed INFO @ Sat, 01 Jun 2019 21:53:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (4569 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:31: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:43: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:43: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:43: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4082369/SRX4082369.05_summits.bed INFO @ Sat, 01 Jun 2019 21:53:43: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (7993 records, 4 fields): 16 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。