Job ID = 1291668 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 87,175,889 reads read : 87,175,889 reads written : 87,175,889 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: 00:00:00 Multiseed full-index search: 00:20:49 87175889 reads; of these: 87175889 (100.00%) were unpaired; of these: 11335932 (13.00%) aligned 0 times 62757751 (71.99%) aligned exactly 1 time 13082206 (15.01%) aligned >1 times 87.00% overall alignment rate Time searching: 00:20:49 Overall time: 00:20:49 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 32 files... [bam_rmdupse_core] 43526051 / 75839957 = 0.5739 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 @ Sun, 02 Jun 2019 16:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.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 @ Sun, 02 Jun 2019 16:58:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:58:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.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 @ Sun, 02 Jun 2019 16:58:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:58:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:58:03: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.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 @ Sun, 02 Jun 2019 16:58:03: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:58:03: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:58:12: 1000000 INFO @ Sun, 02 Jun 2019 16:58:13: 1000000 INFO @ Sun, 02 Jun 2019 16:58:14: 1000000 INFO @ Sun, 02 Jun 2019 16:58:20: 2000000 INFO @ Sun, 02 Jun 2019 16:58:23: 2000000 INFO @ Sun, 02 Jun 2019 16:58:23: 2000000 INFO @ Sun, 02 Jun 2019 16:58:29: 3000000 INFO @ Sun, 02 Jun 2019 16:58:32: 3000000 INFO @ Sun, 02 Jun 2019 16:58:33: 3000000 INFO @ Sun, 02 Jun 2019 16:58:37: 4000000 INFO @ Sun, 02 Jun 2019 16:58:42: 4000000 INFO @ Sun, 02 Jun 2019 16:58:42: 4000000 INFO @ Sun, 02 Jun 2019 16:58:45: 5000000 INFO @ Sun, 02 Jun 2019 16:58:51: 5000000 INFO @ Sun, 02 Jun 2019 16:58:51: 5000000 INFO @ Sun, 02 Jun 2019 16:58:53: 6000000 INFO @ Sun, 02 Jun 2019 16:58:59: 6000000 INFO @ Sun, 02 Jun 2019 16:59:00: 6000000 INFO @ Sun, 02 Jun 2019 16:59:01: 7000000 INFO @ Sun, 02 Jun 2019 16:59:08: 8000000 INFO @ Sun, 02 Jun 2019 16:59:08: 7000000 INFO @ Sun, 02 Jun 2019 16:59:10: 7000000 INFO @ Sun, 02 Jun 2019 16:59:17: 9000000 INFO @ Sun, 02 Jun 2019 16:59:17: 8000000 INFO @ Sun, 02 Jun 2019 16:59:20: 8000000 INFO @ Sun, 02 Jun 2019 16:59:25: 9000000 INFO @ Sun, 02 Jun 2019 16:59:25: 10000000 INFO @ Sun, 02 Jun 2019 16:59:29: 9000000 INFO @ Sun, 02 Jun 2019 16:59:34: 11000000 INFO @ Sun, 02 Jun 2019 16:59:34: 10000000 INFO @ Sun, 02 Jun 2019 16:59:38: 10000000 INFO @ Sun, 02 Jun 2019 16:59:41: 12000000 INFO @ Sun, 02 Jun 2019 16:59:44: 11000000 INFO @ Sun, 02 Jun 2019 16:59:48: 11000000 INFO @ Sun, 02 Jun 2019 16:59:49: 13000000 INFO @ Sun, 02 Jun 2019 16:59:52: 12000000 INFO @ Sun, 02 Jun 2019 16:59:57: 14000000 INFO @ Sun, 02 Jun 2019 16:59:57: 12000000 INFO @ Sun, 02 Jun 2019 17:00:01: 13000000 INFO @ Sun, 02 Jun 2019 17:00:05: 15000000 INFO @ Sun, 02 Jun 2019 17:00:06: 13000000 INFO @ Sun, 02 Jun 2019 17:00:10: 14000000 INFO @ Sun, 02 Jun 2019 17:00:13: 16000000 INFO @ Sun, 02 Jun 2019 17:00:15: 14000000 INFO @ Sun, 02 Jun 2019 17:00:18: 15000000 INFO @ Sun, 02 Jun 2019 17:00:22: 17000000 INFO @ Sun, 02 Jun 2019 17:00:24: 15000000 INFO @ Sun, 02 Jun 2019 17:00:27: 16000000 INFO @ Sun, 02 Jun 2019 17:00:29: 18000000 INFO @ Sun, 02 Jun 2019 17:00:33: 16000000 INFO @ Sun, 02 Jun 2019 17:00:36: 17000000 INFO @ Sun, 02 Jun 2019 17:00:37: 19000000 INFO @ Sun, 02 Jun 2019 17:00:43: 17000000 INFO @ Sun, 02 Jun 2019 17:00:44: 18000000 INFO @ Sun, 02 Jun 2019 17:00:45: 20000000 INFO @ Sun, 02 Jun 2019 17:00:52: 18000000 INFO @ Sun, 02 Jun 2019 17:00:53: 21000000 INFO @ Sun, 02 Jun 2019 17:00:53: 19000000 INFO @ Sun, 02 Jun 2019 17:01:00: 22000000 INFO @ Sun, 02 Jun 2019 17:01:01: 19000000 INFO @ Sun, 02 Jun 2019 17:01:01: 20000000 INFO @ Sun, 02 Jun 2019 17:01:08: 23000000 INFO @ Sun, 02 Jun 2019 17:01:10: 21000000 INFO @ Sun, 02 Jun 2019 17:01:10: 20000000 INFO @ Sun, 02 Jun 2019 17:01:16: 24000000 INFO @ Sun, 02 Jun 2019 17:01:18: 22000000 INFO @ Sun, 02 Jun 2019 17:01:19: 21000000 INFO @ Sun, 02 Jun 2019 17:01:24: 25000000 INFO @ Sun, 02 Jun 2019 17:01:26: 23000000 INFO @ Sun, 02 Jun 2019 17:01:28: 22000000 INFO @ Sun, 02 Jun 2019 17:01:32: 26000000 INFO @ Sun, 02 Jun 2019 17:01:35: 24000000 INFO @ Sun, 02 Jun 2019 17:01:37: 23000000 INFO @ Sun, 02 Jun 2019 17:01:39: 27000000 INFO @ Sun, 02 Jun 2019 17:01:43: 25000000 INFO @ Sun, 02 Jun 2019 17:01:45: 24000000 INFO @ Sun, 02 Jun 2019 17:01:47: 28000000 INFO @ Sun, 02 Jun 2019 17:01:51: 26000000 INFO @ Sun, 02 Jun 2019 17:01:53: 25000000 INFO @ Sun, 02 Jun 2019 17:01:54: 29000000 INFO @ Sun, 02 Jun 2019 17:02:00: 27000000 INFO @ Sun, 02 Jun 2019 17:02:01: 30000000 INFO @ Sun, 02 Jun 2019 17:02:02: 26000000 INFO @ Sun, 02 Jun 2019 17:02:08: 28000000 INFO @ Sun, 02 Jun 2019 17:02:10: 31000000 INFO @ Sun, 02 Jun 2019 17:02:11: 27000000 INFO @ Sun, 02 Jun 2019 17:02:16: 29000000 INFO @ Sun, 02 Jun 2019 17:02:18: 32000000 INFO @ Sun, 02 Jun 2019 17:02:20: 28000000 INFO @ Sun, 02 Jun 2019 17:02:21: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:02:21: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:02:21: #1 total tags in treatment: 32313906 INFO @ Sun, 02 Jun 2019 17:02:21: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:02:21: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:02:21: #1 tags after filtering in treatment: 32313906 INFO @ Sun, 02 Jun 2019 17:02:21: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:02:21: #1 finished! INFO @ Sun, 02 Jun 2019 17:02:21: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:02:21: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:02:24: 30000000 INFO @ Sun, 02 Jun 2019 17:02:24: #2 number of paired peaks: 226 WARNING @ Sun, 02 Jun 2019 17:02:24: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sun, 02 Jun 2019 17:02:24: start model_add_line... INFO @ Sun, 02 Jun 2019 17:02:24: start X-correlation... INFO @ Sun, 02 Jun 2019 17:02:24: end of X-cor INFO @ Sun, 02 Jun 2019 17:02:24: #2 finished! INFO @ Sun, 02 Jun 2019 17:02:24: #2 predicted fragment length is 313 bps INFO @ Sun, 02 Jun 2019 17:02:24: #2 alternative fragment length(s) may be 1,79,142,193,213,235,248,269,288,296,313,349,405,469,494,528 bps INFO @ Sun, 02 Jun 2019 17:02:24: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.05_model.r INFO @ Sun, 02 Jun 2019 17:02:24: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:02:24: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:02:28: 29000000 INFO @ Sun, 02 Jun 2019 17:02:33: 31000000 INFO @ Sun, 02 Jun 2019 17:02:37: 30000000 INFO @ Sun, 02 Jun 2019 17:02:41: 32000000 INFO @ Sun, 02 Jun 2019 17:02:44: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:02:44: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:02:44: #1 total tags in treatment: 32313906 INFO @ Sun, 02 Jun 2019 17:02:44: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:02:44: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:02:44: #1 tags after filtering in treatment: 32313906 INFO @ Sun, 02 Jun 2019 17:02:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:02:44: #1 finished! INFO @ Sun, 02 Jun 2019 17:02:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:02:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:02:45: 31000000 INFO @ Sun, 02 Jun 2019 17:02:47: #2 number of paired peaks: 226 WARNING @ Sun, 02 Jun 2019 17:02:47: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sun, 02 Jun 2019 17:02:47: start model_add_line... INFO @ Sun, 02 Jun 2019 17:02:47: start X-correlation... INFO @ Sun, 02 Jun 2019 17:02:47: end of X-cor INFO @ Sun, 02 Jun 2019 17:02:47: #2 finished! INFO @ Sun, 02 Jun 2019 17:02:47: #2 predicted fragment length is 313 bps INFO @ Sun, 02 Jun 2019 17:02:47: #2 alternative fragment length(s) may be 1,79,142,193,213,235,248,269,288,296,313,349,405,469,494,528 bps INFO @ Sun, 02 Jun 2019 17:02:47: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.10_model.r INFO @ Sun, 02 Jun 2019 17:02:47: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:02:47: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:02:54: 32000000 INFO @ Sun, 02 Jun 2019 17:02:57: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:02:57: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:02:57: #1 total tags in treatment: 32313906 INFO @ Sun, 02 Jun 2019 17:02:57: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:02:57: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Sun, 02 Jun 2019 17:02:58: #1 tags after filtering in treatment: 32313906 INFO @ Sun, 02 Jun 2019 17:02:58: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:02:58: #1 finished! INFO @ Sun, 02 Jun 2019 17:02:58: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:02:58: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:03:00: #2 number of paired peaks: 226 WARNING @ Sun, 02 Jun 2019 17:03:00: Fewer paired peaks (226) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 226 pairs to build model! INFO @ Sun, 02 Jun 2019 17:03:00: start model_add_line... INFO @ Sun, 02 Jun 2019 17:03:01: start X-correlation... INFO @ Sun, 02 Jun 2019 17:03:01: end of X-cor INFO @ Sun, 02 Jun 2019 17:03:01: #2 finished! INFO @ Sun, 02 Jun 2019 17:03:01: #2 predicted fragment length is 313 bps INFO @ Sun, 02 Jun 2019 17:03:01: #2 alternative fragment length(s) may be 1,79,142,193,213,235,248,269,288,296,313,349,405,469,494,528 bps INFO @ Sun, 02 Jun 2019 17:03:01: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.20_model.r INFO @ Sun, 02 Jun 2019 17:03:01: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:03:01: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:04:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:04:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:04:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:04:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:04:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.05_summits.bed INFO @ Sun, 02 Jun 2019 17:04:45: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (7897 records, 4 fields): 16 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:04:46: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:05:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:05:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:05:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.10_summits.bed INFO @ Sun, 02 Jun 2019 17:05:08: Done! pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (5838 records, 4 fields): 13 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:05:21: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:05:21: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:05:21: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX1769996/SRX1769996.20_summits.bed INFO @ Sun, 02 Jun 2019 17:05:21: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3948 records, 4 fields): 11 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。