Job ID = 4178398 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 16,470,012 reads read : 16,470,012 reads written : 16,470,012 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: 00:03:42 16470012 reads; of these: 16470012 (100.00%) were unpaired; of these: 908760 (5.52%) aligned 0 times 13203437 (80.17%) aligned exactly 1 time 2357815 (14.32%) aligned >1 times 94.48% overall alignment rate Time searching: 00:03:42 Overall time: 00:03:42 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] 2036352 / 15561252 = 0.1309 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 05 Dec 2019 12:30:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.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 @ Thu, 05 Dec 2019 12:30:27: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:27: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:30:37: 1000000 INFO @ Thu, 05 Dec 2019 12:30:47: 2000000 INFO @ Thu, 05 Dec 2019 12:30:56: 3000000 INFO @ Thu, 05 Dec 2019 12:30:56: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.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 @ Thu, 05 Dec 2019 12:30:56: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:30:56: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:31:05: 4000000 INFO @ Thu, 05 Dec 2019 12:31:07: 1000000 INFO @ Thu, 05 Dec 2019 12:31:15: 5000000 INFO @ Thu, 05 Dec 2019 12:31:17: 2000000 BedGraph に変換中... INFO @ Thu, 05 Dec 2019 12:31:25: 6000000 INFO @ Thu, 05 Dec 2019 12:31:28: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.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 @ Thu, 05 Dec 2019 12:31:28: #1 read tag files... INFO @ Thu, 05 Dec 2019 12:31:28: #1 read treatment tags... INFO @ Thu, 05 Dec 2019 12:31:28: 3000000 INFO @ Thu, 05 Dec 2019 12:31:34: 7000000 INFO @ Thu, 05 Dec 2019 12:31:36: 1000000 INFO @ Thu, 05 Dec 2019 12:31:40: 4000000 INFO @ Thu, 05 Dec 2019 12:31:44: 8000000 INFO @ Thu, 05 Dec 2019 12:31:44: 2000000 INFO @ Thu, 05 Dec 2019 12:31:51: 5000000 INFO @ Thu, 05 Dec 2019 12:31:53: 3000000 INFO @ Thu, 05 Dec 2019 12:31:53: 9000000 INFO @ Thu, 05 Dec 2019 12:32:01: 4000000 INFO @ Thu, 05 Dec 2019 12:32:02: 6000000 INFO @ Thu, 05 Dec 2019 12:32:03: 10000000 INFO @ Thu, 05 Dec 2019 12:32:09: 5000000 INFO @ Thu, 05 Dec 2019 12:32:12: 11000000 INFO @ Thu, 05 Dec 2019 12:32:13: 7000000 INFO @ Thu, 05 Dec 2019 12:32:18: 6000000 INFO @ Thu, 05 Dec 2019 12:32:23: 12000000 INFO @ Thu, 05 Dec 2019 12:32:25: 8000000 INFO @ Thu, 05 Dec 2019 12:32:28: 7000000 INFO @ Thu, 05 Dec 2019 12:32:34: 13000000 INFO @ Thu, 05 Dec 2019 12:32:39: 8000000 INFO @ Thu, 05 Dec 2019 12:32:40: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:32:40: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:32:40: #1 total tags in treatment: 13524900 INFO @ Thu, 05 Dec 2019 12:32:40: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:32:40: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:32:40: 9000000 INFO @ Thu, 05 Dec 2019 12:32:40: #1 tags after filtering in treatment: 13524900 INFO @ Thu, 05 Dec 2019 12:32:40: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:32:40: #1 finished! INFO @ Thu, 05 Dec 2019 12:32:40: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:32:40: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:32:41: #2 number of paired peaks: 548 WARNING @ Thu, 05 Dec 2019 12:32:41: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Thu, 05 Dec 2019 12:32:41: start model_add_line... INFO @ Thu, 05 Dec 2019 12:32:41: start X-correlation... INFO @ Thu, 05 Dec 2019 12:32:41: end of X-cor INFO @ Thu, 05 Dec 2019 12:32:41: #2 finished! INFO @ Thu, 05 Dec 2019 12:32:41: #2 predicted fragment length is 122 bps INFO @ Thu, 05 Dec 2019 12:32:41: #2 alternative fragment length(s) may be 122 bps INFO @ Thu, 05 Dec 2019 12:32:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.05_model.r INFO @ Thu, 05 Dec 2019 12:32:41: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:32:41: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:32:50: 9000000 INFO @ Thu, 05 Dec 2019 12:32:51: 10000000 INFO @ Thu, 05 Dec 2019 12:33:00: 10000000 INFO @ Thu, 05 Dec 2019 12:33:04: 11000000 INFO @ Thu, 05 Dec 2019 12:33:11: 11000000 INFO @ Thu, 05 Dec 2019 12:33:17: 12000000 INFO @ Thu, 05 Dec 2019 12:33:22: 12000000 INFO @ Thu, 05 Dec 2019 12:33:23: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:33:30: 13000000 INFO @ Thu, 05 Dec 2019 12:33:32: 13000000 INFO @ Thu, 05 Dec 2019 12:33:35: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:33:35: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:33:35: #1 total tags in treatment: 13524900 INFO @ Thu, 05 Dec 2019 12:33:35: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:33:35: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:33:35: #1 tags after filtering in treatment: 13524900 INFO @ Thu, 05 Dec 2019 12:33:35: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:33:35: #1 finished! INFO @ Thu, 05 Dec 2019 12:33:35: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:33:35: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:33:37: #2 number of paired peaks: 548 WARNING @ Thu, 05 Dec 2019 12:33:37: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Thu, 05 Dec 2019 12:33:37: start model_add_line... INFO @ Thu, 05 Dec 2019 12:33:37: start X-correlation... INFO @ Thu, 05 Dec 2019 12:33:37: end of X-cor INFO @ Thu, 05 Dec 2019 12:33:37: #2 finished! INFO @ Thu, 05 Dec 2019 12:33:37: #2 predicted fragment length is 122 bps INFO @ Thu, 05 Dec 2019 12:33:37: #2 alternative fragment length(s) may be 122 bps INFO @ Thu, 05 Dec 2019 12:33:37: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.10_model.r INFO @ Thu, 05 Dec 2019 12:33:37: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:33:37: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:33:37: #1 tag size is determined as 50 bps INFO @ Thu, 05 Dec 2019 12:33:37: #1 tag size = 50 INFO @ Thu, 05 Dec 2019 12:33:37: #1 total tags in treatment: 13524900 INFO @ Thu, 05 Dec 2019 12:33:37: #1 user defined the maximum tags... INFO @ Thu, 05 Dec 2019 12:33:37: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 05 Dec 2019 12:33:38: #1 tags after filtering in treatment: 13524900 INFO @ Thu, 05 Dec 2019 12:33:38: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 05 Dec 2019 12:33:38: #1 finished! INFO @ Thu, 05 Dec 2019 12:33:38: #2 Build Peak Model... INFO @ Thu, 05 Dec 2019 12:33:38: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 05 Dec 2019 12:33:39: #2 number of paired peaks: 548 WARNING @ Thu, 05 Dec 2019 12:33:39: Fewer paired peaks (548) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 548 pairs to build model! INFO @ Thu, 05 Dec 2019 12:33:39: start model_add_line... INFO @ Thu, 05 Dec 2019 12:33:39: start X-correlation... INFO @ Thu, 05 Dec 2019 12:33:39: end of X-cor INFO @ Thu, 05 Dec 2019 12:33:39: #2 finished! INFO @ Thu, 05 Dec 2019 12:33:39: #2 predicted fragment length is 122 bps INFO @ Thu, 05 Dec 2019 12:33:39: #2 alternative fragment length(s) may be 122 bps INFO @ Thu, 05 Dec 2019 12:33:39: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.20_model.r INFO @ Thu, 05 Dec 2019 12:33:39: #3 Call peaks... INFO @ Thu, 05 Dec 2019 12:33:39: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 05 Dec 2019 12:33:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.05_peaks.xls INFO @ Thu, 05 Dec 2019 12:33:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.05_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:33:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.05_summits.bed INFO @ Thu, 05 Dec 2019 12:33:44: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (5232 records, 4 fields): 21 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:34:15: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:34:18: #3 Call peaks for each chromosome... INFO @ Thu, 05 Dec 2019 12:34:34: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.10_peaks.xls INFO @ Thu, 05 Dec 2019 12:34:34: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.10_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:34:34: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.10_summits.bed INFO @ Thu, 05 Dec 2019 12:34:34: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (3610 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Thu, 05 Dec 2019 12:34:37: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.20_peaks.xls INFO @ Thu, 05 Dec 2019 12:34:37: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.20_peaks.narrowPeak INFO @ Thu, 05 Dec 2019 12:34:37: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX4107876/SRX4107876.20_summits.bed INFO @ Thu, 05 Dec 2019 12:34:37: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2101 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。