Job ID = 2590236 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 29,916,745 reads read : 29,916,745 reads written : 29,916,745 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: 00:10:26 29916745 reads; of these: 29916745 (100.00%) were unpaired; of these: 795037 (2.66%) aligned 0 times 26154519 (87.42%) aligned exactly 1 time 2967189 (9.92%) aligned >1 times 97.34% overall alignment rate Time searching: 00:10:26 Overall time: 00:10:26 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 12 files... [bam_rmdupse_core] 6403380 / 29121708 = 0.2199 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 20:51:15: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.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 20:51:15: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:15: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:16: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.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 20:51:16: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:16: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.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 20:51:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:51:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:51:23: 1000000 INFO @ Mon, 12 Aug 2019 20:51:24: 1000000 INFO @ Mon, 12 Aug 2019 20:51:26: 1000000 INFO @ Mon, 12 Aug 2019 20:51:31: 2000000 INFO @ Mon, 12 Aug 2019 20:51:33: 2000000 INFO @ Mon, 12 Aug 2019 20:51:33: 2000000 INFO @ Mon, 12 Aug 2019 20:51:39: 3000000 INFO @ Mon, 12 Aug 2019 20:51:41: 3000000 INFO @ Mon, 12 Aug 2019 20:51:41: 3000000 INFO @ Mon, 12 Aug 2019 20:51:46: 4000000 INFO @ Mon, 12 Aug 2019 20:51:49: 4000000 INFO @ Mon, 12 Aug 2019 20:51:50: 4000000 INFO @ Mon, 12 Aug 2019 20:51:54: 5000000 INFO @ Mon, 12 Aug 2019 20:51:56: 5000000 INFO @ Mon, 12 Aug 2019 20:51:58: 5000000 INFO @ Mon, 12 Aug 2019 20:52:01: 6000000 INFO @ Mon, 12 Aug 2019 20:52:04: 6000000 INFO @ Mon, 12 Aug 2019 20:52:06: 6000000 INFO @ Mon, 12 Aug 2019 20:52:09: 7000000 INFO @ Mon, 12 Aug 2019 20:52:11: 7000000 INFO @ Mon, 12 Aug 2019 20:52:14: 7000000 INFO @ Mon, 12 Aug 2019 20:52:17: 8000000 INFO @ Mon, 12 Aug 2019 20:52:19: 8000000 INFO @ Mon, 12 Aug 2019 20:52:23: 8000000 INFO @ Mon, 12 Aug 2019 20:52:24: 9000000 INFO @ Mon, 12 Aug 2019 20:52:26: 9000000 INFO @ Mon, 12 Aug 2019 20:52:31: 9000000 INFO @ Mon, 12 Aug 2019 20:52:32: 10000000 INFO @ Mon, 12 Aug 2019 20:52:34: 10000000 INFO @ Mon, 12 Aug 2019 20:52:39: 11000000 INFO @ Mon, 12 Aug 2019 20:52:40: 10000000 INFO @ Mon, 12 Aug 2019 20:52:42: 11000000 INFO @ Mon, 12 Aug 2019 20:52:47: 12000000 INFO @ Mon, 12 Aug 2019 20:52:48: 11000000 INFO @ Mon, 12 Aug 2019 20:52:49: 12000000 INFO @ Mon, 12 Aug 2019 20:52:55: 13000000 INFO @ Mon, 12 Aug 2019 20:52:56: 12000000 INFO @ Mon, 12 Aug 2019 20:52:57: 13000000 INFO @ Mon, 12 Aug 2019 20:53:02: 14000000 INFO @ Mon, 12 Aug 2019 20:53:04: 14000000 INFO @ Mon, 12 Aug 2019 20:53:05: 13000000 INFO @ Mon, 12 Aug 2019 20:53:10: 15000000 INFO @ Mon, 12 Aug 2019 20:53:12: 15000000 INFO @ Mon, 12 Aug 2019 20:53:13: 14000000 INFO @ Mon, 12 Aug 2019 20:53:17: 16000000 INFO @ Mon, 12 Aug 2019 20:53:20: 16000000 INFO @ Mon, 12 Aug 2019 20:53:21: 15000000 INFO @ Mon, 12 Aug 2019 20:53:25: 17000000 INFO @ Mon, 12 Aug 2019 20:53:27: 17000000 INFO @ Mon, 12 Aug 2019 20:53:30: 16000000 INFO @ Mon, 12 Aug 2019 20:53:32: 18000000 INFO @ Mon, 12 Aug 2019 20:53:35: 18000000 INFO @ Mon, 12 Aug 2019 20:53:38: 17000000 INFO @ Mon, 12 Aug 2019 20:53:40: 19000000 INFO @ Mon, 12 Aug 2019 20:53:42: 19000000 INFO @ Mon, 12 Aug 2019 20:53:46: 18000000 INFO @ Mon, 12 Aug 2019 20:53:48: 20000000 INFO @ Mon, 12 Aug 2019 20:53:50: 20000000 INFO @ Mon, 12 Aug 2019 20:53:55: 19000000 INFO @ Mon, 12 Aug 2019 20:53:55: 21000000 INFO @ Mon, 12 Aug 2019 20:53:57: 21000000 INFO @ Mon, 12 Aug 2019 20:54:03: 22000000 INFO @ Mon, 12 Aug 2019 20:54:03: 20000000 INFO @ Mon, 12 Aug 2019 20:54:05: 22000000 INFO @ Mon, 12 Aug 2019 20:54:08: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:54:08: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:54:08: #1 total tags in treatment: 22718328 INFO @ Mon, 12 Aug 2019 20:54:08: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:54:08: #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 20:54:09: #1 tags after filtering in treatment: 22718328 INFO @ Mon, 12 Aug 2019 20:54:09: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:54:09: #1 finished! INFO @ Mon, 12 Aug 2019 20:54:09: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:54:09: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:54:11: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:54:11: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:54:11: #1 total tags in treatment: 22718328 INFO @ Mon, 12 Aug 2019 20:54:11: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:54:11: #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 20:54:11: #2 number of paired peaks: 785 WARNING @ Mon, 12 Aug 2019 20:54:11: Fewer paired peaks (785) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 785 pairs to build model! INFO @ Mon, 12 Aug 2019 20:54:11: start model_add_line... INFO @ Mon, 12 Aug 2019 20:54:11: start X-correlation... INFO @ Mon, 12 Aug 2019 20:54:11: end of X-cor INFO @ Mon, 12 Aug 2019 20:54:11: #2 finished! INFO @ Mon, 12 Aug 2019 20:54:11: #2 predicted fragment length is 191 bps INFO @ Mon, 12 Aug 2019 20:54:11: #2 alternative fragment length(s) may be 3,191 bps INFO @ Mon, 12 Aug 2019 20:54:11: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.05_model.r INFO @ Mon, 12 Aug 2019 20:54:11: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:54:11: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:54:11: #1 tags after filtering in treatment: 22718328 INFO @ Mon, 12 Aug 2019 20:54:11: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:54:11: #1 finished! INFO @ Mon, 12 Aug 2019 20:54:11: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:54:11: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:54:11: 21000000 INFO @ Mon, 12 Aug 2019 20:54:13: #2 number of paired peaks: 785 WARNING @ Mon, 12 Aug 2019 20:54:13: Fewer paired peaks (785) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 785 pairs to build model! INFO @ Mon, 12 Aug 2019 20:54:13: start model_add_line... INFO @ Mon, 12 Aug 2019 20:54:13: start X-correlation... INFO @ Mon, 12 Aug 2019 20:54:14: end of X-cor INFO @ Mon, 12 Aug 2019 20:54:14: #2 finished! INFO @ Mon, 12 Aug 2019 20:54:14: #2 predicted fragment length is 191 bps INFO @ Mon, 12 Aug 2019 20:54:14: #2 alternative fragment length(s) may be 3,191 bps INFO @ Mon, 12 Aug 2019 20:54:14: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.20_model.r INFO @ Mon, 12 Aug 2019 20:54:14: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:54:14: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:54:19: 22000000 INFO @ Mon, 12 Aug 2019 20:54:26: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:54:26: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:54:26: #1 total tags in treatment: 22718328 INFO @ Mon, 12 Aug 2019 20:54:26: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:54:26: #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 20:54:26: #1 tags after filtering in treatment: 22718328 INFO @ Mon, 12 Aug 2019 20:54:26: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:54:26: #1 finished! INFO @ Mon, 12 Aug 2019 20:54:26: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:54:26: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:54:28: #2 number of paired peaks: 785 WARNING @ Mon, 12 Aug 2019 20:54:28: Fewer paired peaks (785) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 785 pairs to build model! INFO @ Mon, 12 Aug 2019 20:54:28: start model_add_line... INFO @ Mon, 12 Aug 2019 20:54:28: start X-correlation... INFO @ Mon, 12 Aug 2019 20:54:28: end of X-cor INFO @ Mon, 12 Aug 2019 20:54:28: #2 finished! INFO @ Mon, 12 Aug 2019 20:54:28: #2 predicted fragment length is 191 bps INFO @ Mon, 12 Aug 2019 20:54:28: #2 alternative fragment length(s) may be 3,191 bps INFO @ Mon, 12 Aug 2019 20:54:28: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.10_model.r INFO @ Mon, 12 Aug 2019 20:54:28: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:54:28: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:55:16: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:55:19: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:55:33: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:55:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:55:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:55:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.05_summits.bed INFO @ Mon, 12 Aug 2019 20:55:42: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (7634 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:55:44: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:55:44: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:55:44: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.20_summits.bed INFO @ Mon, 12 Aug 2019 20:55:44: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (2510 records, 4 fields): 7 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:55:59: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:55:59: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:55:59: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985670/SRX5985670.10_summits.bed INFO @ Mon, 12 Aug 2019 20:55:59: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (4972 records, 4 fields): 8 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。