Job ID = 1292208 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 7,439,152 reads read : 7,439,152 reads written : 7,439,152 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: 00:01:17 7439152 reads; of these: 7439152 (100.00%) were unpaired; of these: 318213 (4.28%) aligned 0 times 5971478 (80.27%) aligned exactly 1 time 1149461 (15.45%) aligned >1 times 95.72% overall alignment rate Time searching: 00:01:17 Overall time: 00:01:17 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] 899774 / 7120939 = 0.1264 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 17:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.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 17:42:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:42:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.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 17:42:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:42:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:42:52: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.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 17:42:52: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:42:52: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:42:59: 1000000 INFO @ Sun, 02 Jun 2019 17:43:00: 1000000 INFO @ Sun, 02 Jun 2019 17:43:01: 1000000 INFO @ Sun, 02 Jun 2019 17:43:06: 2000000 INFO @ Sun, 02 Jun 2019 17:43:07: 2000000 INFO @ Sun, 02 Jun 2019 17:43:08: 2000000 INFO @ Sun, 02 Jun 2019 17:43:12: 3000000 INFO @ Sun, 02 Jun 2019 17:43:14: 3000000 INFO @ Sun, 02 Jun 2019 17:43:16: 3000000 INFO @ Sun, 02 Jun 2019 17:43:18: 4000000 INFO @ Sun, 02 Jun 2019 17:43:20: 4000000 INFO @ Sun, 02 Jun 2019 17:43:23: 4000000 INFO @ Sun, 02 Jun 2019 17:43:25: 5000000 INFO @ Sun, 02 Jun 2019 17:43:27: 5000000 INFO @ Sun, 02 Jun 2019 17:43:31: 5000000 INFO @ Sun, 02 Jun 2019 17:43:31: 6000000 INFO @ Sun, 02 Jun 2019 17:43:33: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:43:33: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:43:33: #1 total tags in treatment: 6221165 INFO @ Sun, 02 Jun 2019 17:43:33: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:43:33: #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 17:43:33: #1 tags after filtering in treatment: 6221165 INFO @ Sun, 02 Jun 2019 17:43:33: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:43:33: #1 finished! INFO @ Sun, 02 Jun 2019 17:43:33: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:43:33: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:43:33: 6000000 INFO @ Sun, 02 Jun 2019 17:43:33: #2 number of paired peaks: 460 WARNING @ Sun, 02 Jun 2019 17:43:33: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 02 Jun 2019 17:43:33: start model_add_line... INFO @ Sun, 02 Jun 2019 17:43:33: start X-correlation... INFO @ Sun, 02 Jun 2019 17:43:33: end of X-cor INFO @ Sun, 02 Jun 2019 17:43:33: #2 finished! INFO @ Sun, 02 Jun 2019 17:43:33: #2 predicted fragment length is 76 bps INFO @ Sun, 02 Jun 2019 17:43:33: #2 alternative fragment length(s) may be 4,40,76,88,116,120,590 bps INFO @ Sun, 02 Jun 2019 17:43:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.10_model.r INFO @ Sun, 02 Jun 2019 17:43:33: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:43:33: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:43:34: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:43:34: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:43:34: #1 total tags in treatment: 6221165 INFO @ Sun, 02 Jun 2019 17:43:34: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:43:34: #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 17:43:35: #1 tags after filtering in treatment: 6221165 INFO @ Sun, 02 Jun 2019 17:43:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:43:35: #1 finished! INFO @ Sun, 02 Jun 2019 17:43:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:43:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:43:35: #2 number of paired peaks: 460 WARNING @ Sun, 02 Jun 2019 17:43:35: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 02 Jun 2019 17:43:35: start model_add_line... INFO @ Sun, 02 Jun 2019 17:43:35: start X-correlation... INFO @ Sun, 02 Jun 2019 17:43:35: end of X-cor INFO @ Sun, 02 Jun 2019 17:43:35: #2 finished! INFO @ Sun, 02 Jun 2019 17:43:35: #2 predicted fragment length is 76 bps INFO @ Sun, 02 Jun 2019 17:43:35: #2 alternative fragment length(s) may be 4,40,76,88,116,120,590 bps INFO @ Sun, 02 Jun 2019 17:43:35: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.05_model.r INFO @ Sun, 02 Jun 2019 17:43:35: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:43:35: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:43:38: 6000000 INFO @ Sun, 02 Jun 2019 17:43:40: #1 tag size is determined as 32 bps INFO @ Sun, 02 Jun 2019 17:43:40: #1 tag size = 32 INFO @ Sun, 02 Jun 2019 17:43:40: #1 total tags in treatment: 6221165 INFO @ Sun, 02 Jun 2019 17:43:40: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:43:40: #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 17:43:40: #1 tags after filtering in treatment: 6221165 INFO @ Sun, 02 Jun 2019 17:43:40: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:43:40: #1 finished! INFO @ Sun, 02 Jun 2019 17:43:40: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:43:40: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:43:41: #2 number of paired peaks: 460 WARNING @ Sun, 02 Jun 2019 17:43:41: Fewer paired peaks (460) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 460 pairs to build model! INFO @ Sun, 02 Jun 2019 17:43:41: start model_add_line... INFO @ Sun, 02 Jun 2019 17:43:41: start X-correlation... INFO @ Sun, 02 Jun 2019 17:43:41: end of X-cor INFO @ Sun, 02 Jun 2019 17:43:41: #2 finished! INFO @ Sun, 02 Jun 2019 17:43:41: #2 predicted fragment length is 76 bps INFO @ Sun, 02 Jun 2019 17:43:41: #2 alternative fragment length(s) may be 4,40,76,88,116,120,590 bps INFO @ Sun, 02 Jun 2019 17:43:41: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.20_model.r INFO @ Sun, 02 Jun 2019 17:43:41: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:43:41: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:43:52: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:43:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:43:59: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:44:01: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:44:01: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:44:01: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.10_summits.bed INFO @ Sun, 02 Jun 2019 17:44:01: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (553 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:44:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:44:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:44:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.05_summits.bed INFO @ Sun, 02 Jun 2019 17:44:03: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1151 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:44:08: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:44:08: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:44:08: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX331244/SRX331244.20_summits.bed INFO @ Sun, 02 Jun 2019 17:44:08: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (216 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。