Job ID = 1290606 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,907,024 reads read : 15,907,024 reads written : 15,907,024 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: 00:00:01 Multiseed full-index search: 00:03:01 15907024 reads; of these: 15907024 (100.00%) were unpaired; of these: 1690425 (10.63%) aligned 0 times 11628236 (73.10%) aligned exactly 1 time 2588363 (16.27%) aligned >1 times 89.37% overall alignment rate Time searching: 00:03:02 Overall time: 00:03:02 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] 4583917 / 14216599 = 0.3224 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 21:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.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 21:51:31: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:31: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.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 21:51:31: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:31: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:31: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.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 21:51:31: #1 read tag files... INFO @ Sat, 01 Jun 2019 21:51:31: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 21:51:39: 1000000 INFO @ Sat, 01 Jun 2019 21:51:40: 1000000 INFO @ Sat, 01 Jun 2019 21:51:40: 1000000 INFO @ Sat, 01 Jun 2019 21:51:47: 2000000 INFO @ Sat, 01 Jun 2019 21:51:48: 2000000 INFO @ Sat, 01 Jun 2019 21:51:48: 2000000 INFO @ Sat, 01 Jun 2019 21:51:54: 3000000 INFO @ Sat, 01 Jun 2019 21:51:57: 3000000 INFO @ Sat, 01 Jun 2019 21:51:57: 3000000 INFO @ Sat, 01 Jun 2019 21:52:02: 4000000 INFO @ Sat, 01 Jun 2019 21:52:05: 4000000 INFO @ Sat, 01 Jun 2019 21:52:05: 4000000 INFO @ Sat, 01 Jun 2019 21:52:10: 5000000 INFO @ Sat, 01 Jun 2019 21:52:14: 5000000 INFO @ Sat, 01 Jun 2019 21:52:14: 5000000 INFO @ Sat, 01 Jun 2019 21:52:18: 6000000 INFO @ Sat, 01 Jun 2019 21:52:22: 6000000 INFO @ Sat, 01 Jun 2019 21:52:23: 6000000 INFO @ Sat, 01 Jun 2019 21:52:25: 7000000 INFO @ Sat, 01 Jun 2019 21:52:31: 7000000 INFO @ Sat, 01 Jun 2019 21:52:31: 7000000 INFO @ Sat, 01 Jun 2019 21:52:33: 8000000 INFO @ Sat, 01 Jun 2019 21:52:39: 8000000 INFO @ Sat, 01 Jun 2019 21:52:40: 8000000 INFO @ Sat, 01 Jun 2019 21:52:41: 9000000 INFO @ Sat, 01 Jun 2019 21:52:46: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 21:52:46: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 21:52:46: #1 total tags in treatment: 9632682 INFO @ Sat, 01 Jun 2019 21:52:46: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:46: #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 21:52:46: #1 tags after filtering in treatment: 9632682 INFO @ Sat, 01 Jun 2019 21:52:46: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:46: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:46: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:46: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:47: #2 number of paired peaks: 1484 INFO @ Sat, 01 Jun 2019 21:52:47: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:47: 9000000 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 144 bps INFO @ Sat, 01 Jun 2019 21:52:47: #2 alternative fragment length(s) may be 144 bps INFO @ Sat, 01 Jun 2019 21:52:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.20_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 21:52:48: 9000000 INFO @ Sat, 01 Jun 2019 21:52:52: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 21:52:52: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 21:52:52: #1 total tags in treatment: 9632682 INFO @ Sat, 01 Jun 2019 21:52:52: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:52: #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 21:52:53: #1 tags after filtering in treatment: 9632682 INFO @ Sat, 01 Jun 2019 21:52:53: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:53: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:53: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:53: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:54: #2 number of paired peaks: 1484 INFO @ Sat, 01 Jun 2019 21:52:54: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:54: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:54: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:54: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:54: #2 predicted fragment length is 144 bps INFO @ Sat, 01 Jun 2019 21:52:54: #2 alternative fragment length(s) may be 144 bps INFO @ Sat, 01 Jun 2019 21:52:54: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.05_model.r INFO @ Sat, 01 Jun 2019 21:52:54: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:54: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:52:54: #1 tag size is determined as 36 bps INFO @ Sat, 01 Jun 2019 21:52:54: #1 tag size = 36 INFO @ Sat, 01 Jun 2019 21:52:54: #1 total tags in treatment: 9632682 INFO @ Sat, 01 Jun 2019 21:52:54: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 21:52:54: #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 21:52:54: #1 tags after filtering in treatment: 9632682 INFO @ Sat, 01 Jun 2019 21:52:54: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 21:52:54: #1 finished! INFO @ Sat, 01 Jun 2019 21:52:54: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 21:52:54: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 21:52:55: #2 number of paired peaks: 1484 INFO @ Sat, 01 Jun 2019 21:52:55: start model_add_line... INFO @ Sat, 01 Jun 2019 21:52:55: start X-correlation... INFO @ Sat, 01 Jun 2019 21:52:55: end of X-cor INFO @ Sat, 01 Jun 2019 21:52:55: #2 finished! INFO @ Sat, 01 Jun 2019 21:52:55: #2 predicted fragment length is 144 bps INFO @ Sat, 01 Jun 2019 21:52:55: #2 alternative fragment length(s) may be 144 bps INFO @ Sat, 01 Jun 2019 21:52:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.10_model.r INFO @ Sat, 01 Jun 2019 21:52:55: #3 Call peaks... INFO @ Sat, 01 Jun 2019 21:52:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 21:53:19: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:24: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:25: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 21:53:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.20_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.20_summits.bed INFO @ Sat, 01 Jun 2019 21:53:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2552 records, 4 fields): 9 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.05_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.05_summits.bed INFO @ Sat, 01 Jun 2019 21:53:38: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (4529 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 21:53:39: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.10_peaks.xls INFO @ Sat, 01 Jun 2019 21:53:39: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 21:53:39: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX059233/SRX059233.10_summits.bed INFO @ Sat, 01 Jun 2019 21:53:39: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3449 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。