Job ID = 2590056 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,259,739 reads read : 16,259,739 reads written : 16,259,739 rm: cannot remove ‘[DSE]RR*’: 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: 00:03:04 16259739 reads; of these: 16259739 (100.00%) were unpaired; of these: 2800873 (17.23%) aligned 0 times 11249624 (69.19%) aligned exactly 1 time 2209242 (13.59%) aligned >1 times 82.77% overall alignment rate Time searching: 00:03:04 Overall time: 00:03:04 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] 4378937 / 13458866 = 0.3254 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 @ Mon, 12 Aug 2019 19:33:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.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 @ Mon, 12 Aug 2019 19:33:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:33:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:33:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.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 @ Mon, 12 Aug 2019 19:33:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:33:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.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 @ Mon, 12 Aug 2019 19:33:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 19:33:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 19:33:23: 1000000 INFO @ Mon, 12 Aug 2019 19:33:23: 1000000 INFO @ Mon, 12 Aug 2019 19:33:24: 1000000 INFO @ Mon, 12 Aug 2019 19:33:30: 2000000 INFO @ Mon, 12 Aug 2019 19:33:31: 2000000 INFO @ Mon, 12 Aug 2019 19:33:31: 2000000 INFO @ Mon, 12 Aug 2019 19:33:37: 3000000 INFO @ Mon, 12 Aug 2019 19:33:38: 3000000 INFO @ Mon, 12 Aug 2019 19:33:40: 3000000 INFO @ Mon, 12 Aug 2019 19:33:44: 4000000 INFO @ Mon, 12 Aug 2019 19:33:45: 4000000 INFO @ Mon, 12 Aug 2019 19:33:47: 4000000 INFO @ Mon, 12 Aug 2019 19:33:50: 5000000 INFO @ Mon, 12 Aug 2019 19:33:51: 5000000 INFO @ Mon, 12 Aug 2019 19:33:55: 5000000 INFO @ Mon, 12 Aug 2019 19:33:57: 6000000 INFO @ Mon, 12 Aug 2019 19:33:58: 6000000 INFO @ Mon, 12 Aug 2019 19:34:03: 6000000 INFO @ Mon, 12 Aug 2019 19:34:05: 7000000 INFO @ Mon, 12 Aug 2019 19:34:06: 7000000 INFO @ Mon, 12 Aug 2019 19:34:12: 8000000 INFO @ Mon, 12 Aug 2019 19:34:12: 7000000 INFO @ Mon, 12 Aug 2019 19:34:12: 8000000 INFO @ Mon, 12 Aug 2019 19:34:18: 9000000 INFO @ Mon, 12 Aug 2019 19:34:19: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:34:19: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:34:19: #1 total tags in treatment: 9079929 INFO @ Mon, 12 Aug 2019 19:34:19: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:34:19: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:34:19: #1 tags after filtering in treatment: 9079929 INFO @ Mon, 12 Aug 2019 19:34:19: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:34:19: #1 finished! INFO @ Mon, 12 Aug 2019 19:34:19: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:34:19: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:34:19: 9000000 INFO @ Mon, 12 Aug 2019 19:34:20: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:34:20: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:34:20: #1 total tags in treatment: 9079929 INFO @ Mon, 12 Aug 2019 19:34:20: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:34:20: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:34:20: 8000000 INFO @ Mon, 12 Aug 2019 19:34:20: #1 tags after filtering in treatment: 9079929 INFO @ Mon, 12 Aug 2019 19:34:20: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:34:20: #1 finished! INFO @ Mon, 12 Aug 2019 19:34:20: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:34:20: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:34:20: #2 number of paired peaks: 698 WARNING @ Mon, 12 Aug 2019 19:34:20: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Mon, 12 Aug 2019 19:34:20: start model_add_line... INFO @ Mon, 12 Aug 2019 19:34:20: start X-correlation... INFO @ Mon, 12 Aug 2019 19:34:20: end of X-cor INFO @ Mon, 12 Aug 2019 19:34:20: #2 finished! INFO @ Mon, 12 Aug 2019 19:34:20: #2 predicted fragment length is 144 bps INFO @ Mon, 12 Aug 2019 19:34:20: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 12 Aug 2019 19:34:20: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.10_model.r INFO @ Mon, 12 Aug 2019 19:34:20: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:34:20: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:34:21: #2 number of paired peaks: 698 WARNING @ Mon, 12 Aug 2019 19:34:21: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Mon, 12 Aug 2019 19:34:21: start model_add_line... INFO @ Mon, 12 Aug 2019 19:34:21: start X-correlation... INFO @ Mon, 12 Aug 2019 19:34:21: end of X-cor INFO @ Mon, 12 Aug 2019 19:34:21: #2 finished! INFO @ Mon, 12 Aug 2019 19:34:21: #2 predicted fragment length is 144 bps INFO @ Mon, 12 Aug 2019 19:34:21: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 12 Aug 2019 19:34:21: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.20_model.r INFO @ Mon, 12 Aug 2019 19:34:21: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:34:21: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:34:27: 9000000 INFO @ Mon, 12 Aug 2019 19:34:28: #1 tag size is determined as 42 bps INFO @ Mon, 12 Aug 2019 19:34:28: #1 tag size = 42 INFO @ Mon, 12 Aug 2019 19:34:28: #1 total tags in treatment: 9079929 INFO @ Mon, 12 Aug 2019 19:34:28: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 19:34:28: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 19:34:28: #1 tags after filtering in treatment: 9079929 INFO @ Mon, 12 Aug 2019 19:34:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 19:34:28: #1 finished! INFO @ Mon, 12 Aug 2019 19:34:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 19:34:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 19:34:29: #2 number of paired peaks: 698 WARNING @ Mon, 12 Aug 2019 19:34:29: Fewer paired peaks (698) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 698 pairs to build model! INFO @ Mon, 12 Aug 2019 19:34:29: start model_add_line... INFO @ Mon, 12 Aug 2019 19:34:29: start X-correlation... INFO @ Mon, 12 Aug 2019 19:34:29: end of X-cor INFO @ Mon, 12 Aug 2019 19:34:29: #2 finished! INFO @ Mon, 12 Aug 2019 19:34:29: #2 predicted fragment length is 144 bps INFO @ Mon, 12 Aug 2019 19:34:29: #2 alternative fragment length(s) may be 144 bps INFO @ Mon, 12 Aug 2019 19:34:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.05_model.r INFO @ Mon, 12 Aug 2019 19:34:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 19:34:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 19:34:47: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:34:48: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:34:56: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 19:35:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.10_peaks.xls INFO @ Mon, 12 Aug 2019 19:35:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:35:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.10_summits.bed INFO @ Mon, 12 Aug 2019 19:35:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1332 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:35:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.20_peaks.xls INFO @ Mon, 12 Aug 2019 19:35:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:35:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.20_summits.bed INFO @ Mon, 12 Aug 2019 19:35:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (738 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 19:35:09: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.05_peaks.xls INFO @ Mon, 12 Aug 2019 19:35:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 19:35:09: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX494900/SRX494900.05_summits.bed INFO @ Mon, 12 Aug 2019 19:35:09: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2173 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。