Job ID = 1290673 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 6,387,040 reads read : 6,387,040 reads written : 6,387,040 spots read : 6,285,680 reads read : 6,285,680 reads written : 6,285,680 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: 00:01:47 12672720 reads; of these: 12672720 (100.00%) were unpaired; of these: 1759451 (13.88%) aligned 0 times 9461842 (74.66%) aligned exactly 1 time 1451427 (11.45%) aligned >1 times 86.12% overall alignment rate Time searching: 00:01:47 Overall time: 00:01:47 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] 1248385 / 10913269 = 0.1144 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 22:01:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.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 22:01:21: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:01:21: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:01:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.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 22:01:21: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:01:21: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:01:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.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 22:01:21: #1 read tag files... INFO @ Sat, 01 Jun 2019 22:01:21: #1 read treatment tags... INFO @ Sat, 01 Jun 2019 22:01:28: 1000000 INFO @ Sat, 01 Jun 2019 22:01:29: 1000000 INFO @ Sat, 01 Jun 2019 22:01:29: 1000000 INFO @ Sat, 01 Jun 2019 22:01:35: 2000000 INFO @ Sat, 01 Jun 2019 22:01:37: 2000000 INFO @ Sat, 01 Jun 2019 22:01:37: 2000000 INFO @ Sat, 01 Jun 2019 22:01:42: 3000000 INFO @ Sat, 01 Jun 2019 22:01:45: 3000000 INFO @ Sat, 01 Jun 2019 22:01:45: 3000000 INFO @ Sat, 01 Jun 2019 22:01:49: 4000000 INFO @ Sat, 01 Jun 2019 22:01:53: 4000000 INFO @ Sat, 01 Jun 2019 22:01:54: 4000000 INFO @ Sat, 01 Jun 2019 22:01:56: 5000000 INFO @ Sat, 01 Jun 2019 22:02:00: 5000000 INFO @ Sat, 01 Jun 2019 22:02:02: 5000000 INFO @ Sat, 01 Jun 2019 22:02:03: 6000000 INFO @ Sat, 01 Jun 2019 22:02:08: 6000000 INFO @ Sat, 01 Jun 2019 22:02:10: 7000000 INFO @ Sat, 01 Jun 2019 22:02:10: 6000000 INFO @ Sat, 01 Jun 2019 22:02:15: 7000000 INFO @ Sat, 01 Jun 2019 22:02:17: 8000000 INFO @ Sat, 01 Jun 2019 22:02:18: 7000000 INFO @ Sat, 01 Jun 2019 22:02:23: 8000000 INFO @ Sat, 01 Jun 2019 22:02:24: 9000000 INFO @ Sat, 01 Jun 2019 22:02:26: 8000000 INFO @ Sat, 01 Jun 2019 22:02:28: #1 tag size is determined as 27 bps INFO @ Sat, 01 Jun 2019 22:02:28: #1 tag size = 27 INFO @ Sat, 01 Jun 2019 22:02:28: #1 total tags in treatment: 9664884 INFO @ Sat, 01 Jun 2019 22:02:28: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:28: #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 22:02:28: #1 tags after filtering in treatment: 9664884 INFO @ Sat, 01 Jun 2019 22:02:28: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:28: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:28: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:28: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:29: #2 number of paired peaks: 1231 INFO @ Sat, 01 Jun 2019 22:02:29: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:29: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:29: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:29: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:29: #2 predicted fragment length is 101 bps INFO @ Sat, 01 Jun 2019 22:02:29: #2 alternative fragment length(s) may be 4,101 bps INFO @ Sat, 01 Jun 2019 22:02:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.20_model.r INFO @ Sat, 01 Jun 2019 22:02:29: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:29: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:30: 9000000 INFO @ Sat, 01 Jun 2019 22:02:35: 9000000 INFO @ Sat, 01 Jun 2019 22:02:35: #1 tag size is determined as 27 bps INFO @ Sat, 01 Jun 2019 22:02:35: #1 tag size = 27 INFO @ Sat, 01 Jun 2019 22:02:35: #1 total tags in treatment: 9664884 INFO @ Sat, 01 Jun 2019 22:02:35: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:35: #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 22:02:35: #1 tags after filtering in treatment: 9664884 INFO @ Sat, 01 Jun 2019 22:02:35: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:35: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:35: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:35: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:36: #2 number of paired peaks: 1231 INFO @ Sat, 01 Jun 2019 22:02:36: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:36: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:36: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:36: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:36: #2 predicted fragment length is 101 bps INFO @ Sat, 01 Jun 2019 22:02:36: #2 alternative fragment length(s) may be 4,101 bps INFO @ Sat, 01 Jun 2019 22:02:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.05_model.r INFO @ Sat, 01 Jun 2019 22:02:36: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:40: #1 tag size is determined as 27 bps INFO @ Sat, 01 Jun 2019 22:02:40: #1 tag size = 27 INFO @ Sat, 01 Jun 2019 22:02:40: #1 total tags in treatment: 9664884 INFO @ Sat, 01 Jun 2019 22:02:40: #1 user defined the maximum tags... INFO @ Sat, 01 Jun 2019 22:02:40: #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 22:02:40: #1 tags after filtering in treatment: 9664884 INFO @ Sat, 01 Jun 2019 22:02:40: #1 Redundant rate of treatment: 0.00 INFO @ Sat, 01 Jun 2019 22:02:40: #1 finished! INFO @ Sat, 01 Jun 2019 22:02:40: #2 Build Peak Model... INFO @ Sat, 01 Jun 2019 22:02:40: #2 looking for paired plus/minus strand peaks... INFO @ Sat, 01 Jun 2019 22:02:41: #2 number of paired peaks: 1231 INFO @ Sat, 01 Jun 2019 22:02:41: start model_add_line... INFO @ Sat, 01 Jun 2019 22:02:41: start X-correlation... INFO @ Sat, 01 Jun 2019 22:02:41: end of X-cor INFO @ Sat, 01 Jun 2019 22:02:41: #2 finished! INFO @ Sat, 01 Jun 2019 22:02:41: #2 predicted fragment length is 101 bps INFO @ Sat, 01 Jun 2019 22:02:41: #2 alternative fragment length(s) may be 4,101 bps INFO @ Sat, 01 Jun 2019 22:02:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.10_model.r INFO @ Sat, 01 Jun 2019 22:02:41: #3 Call peaks... INFO @ Sat, 01 Jun 2019 22:02:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sat, 01 Jun 2019 22:02:58: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:03:05: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:03:10: #3 Call peaks for each chromosome... INFO @ Sat, 01 Jun 2019 22:03:12: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.20_peaks.xls INFO @ Sat, 01 Jun 2019 22:03:12: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.20_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:03:12: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.20_summits.bed INFO @ Sat, 01 Jun 2019 22:03:12: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (746 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:03:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.05_peaks.xls INFO @ Sat, 01 Jun 2019 22:03:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.05_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:03:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.05_summits.bed INFO @ Sat, 01 Jun 2019 22:03:19: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4963 records, 4 fields): 15 millis CompletedMACS2peakCalling INFO @ Sat, 01 Jun 2019 22:03:23: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.10_peaks.xls INFO @ Sat, 01 Jun 2019 22:03:23: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.10_peaks.narrowPeak INFO @ Sat, 01 Jun 2019 22:03:23: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX005651/SRX005651.10_summits.bed INFO @ Sat, 01 Jun 2019 22:03:23: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2416 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。