Job ID = 1293108 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 27,642,393 reads read : 27,642,393 reads written : 27,642,393 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: 00:04:15 27642393 reads; of these: 27642393 (100.00%) were unpaired; of these: 9016971 (32.62%) aligned 0 times 15335321 (55.48%) aligned exactly 1 time 3290101 (11.90%) aligned >1 times 67.38% overall alignment rate Time searching: 00:04:15 Overall time: 00:04:15 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] 3260535 / 18625422 = 0.1751 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 22:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.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 22:05:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:05:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.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 22:05:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:05:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:29: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.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 22:05:29: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:05:29: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:05:36: 1000000 INFO @ Sun, 02 Jun 2019 22:05:36: 1000000 INFO @ Sun, 02 Jun 2019 22:05:37: 1000000 INFO @ Sun, 02 Jun 2019 22:05:43: 2000000 INFO @ Sun, 02 Jun 2019 22:05:44: 2000000 INFO @ Sun, 02 Jun 2019 22:05:45: 2000000 INFO @ Sun, 02 Jun 2019 22:05:49: 3000000 INFO @ Sun, 02 Jun 2019 22:05:51: 3000000 INFO @ Sun, 02 Jun 2019 22:05:53: 3000000 INFO @ Sun, 02 Jun 2019 22:05:56: 4000000 INFO @ Sun, 02 Jun 2019 22:05:58: 4000000 INFO @ Sun, 02 Jun 2019 22:06:01: 4000000 INFO @ Sun, 02 Jun 2019 22:06:03: 5000000 INFO @ Sun, 02 Jun 2019 22:06:06: 5000000 INFO @ Sun, 02 Jun 2019 22:06:08: 5000000 INFO @ Sun, 02 Jun 2019 22:06:10: 6000000 INFO @ Sun, 02 Jun 2019 22:06:14: 6000000 INFO @ Sun, 02 Jun 2019 22:06:16: 6000000 INFO @ Sun, 02 Jun 2019 22:06:17: 7000000 INFO @ Sun, 02 Jun 2019 22:06:21: 7000000 INFO @ Sun, 02 Jun 2019 22:06:24: 8000000 INFO @ Sun, 02 Jun 2019 22:06:24: 7000000 INFO @ Sun, 02 Jun 2019 22:06:29: 8000000 INFO @ Sun, 02 Jun 2019 22:06:30: 9000000 INFO @ Sun, 02 Jun 2019 22:06:32: 8000000 INFO @ Sun, 02 Jun 2019 22:06:36: 9000000 INFO @ Sun, 02 Jun 2019 22:06:37: 10000000 INFO @ Sun, 02 Jun 2019 22:06:39: 9000000 INFO @ Sun, 02 Jun 2019 22:06:44: 10000000 INFO @ Sun, 02 Jun 2019 22:06:44: 11000000 INFO @ Sun, 02 Jun 2019 22:06:47: 10000000 INFO @ Sun, 02 Jun 2019 22:06:51: 12000000 INFO @ Sun, 02 Jun 2019 22:06:52: 11000000 INFO @ Sun, 02 Jun 2019 22:06:55: 11000000 INFO @ Sun, 02 Jun 2019 22:06:58: 13000000 INFO @ Sun, 02 Jun 2019 22:06:59: 12000000 INFO @ Sun, 02 Jun 2019 22:07:02: 12000000 INFO @ Sun, 02 Jun 2019 22:07:05: 14000000 INFO @ Sun, 02 Jun 2019 22:07:07: 13000000 INFO @ Sun, 02 Jun 2019 22:07:10: 13000000 INFO @ Sun, 02 Jun 2019 22:07:12: 15000000 INFO @ Sun, 02 Jun 2019 22:07:14: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:07:14: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:07:14: #1 total tags in treatment: 15364887 INFO @ Sun, 02 Jun 2019 22:07:14: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:07:14: #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 22:07:15: #1 tags after filtering in treatment: 15364887 INFO @ Sun, 02 Jun 2019 22:07:15: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:07:15: #1 finished! INFO @ Sun, 02 Jun 2019 22:07:15: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:07:15: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:07:15: 14000000 INFO @ Sun, 02 Jun 2019 22:07:16: #2 number of paired peaks: 470 WARNING @ Sun, 02 Jun 2019 22:07:16: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 02 Jun 2019 22:07:16: start model_add_line... INFO @ Sun, 02 Jun 2019 22:07:16: start X-correlation... INFO @ Sun, 02 Jun 2019 22:07:16: end of X-cor INFO @ Sun, 02 Jun 2019 22:07:16: #2 finished! INFO @ Sun, 02 Jun 2019 22:07:16: #2 predicted fragment length is 112 bps INFO @ Sun, 02 Jun 2019 22:07:16: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 02 Jun 2019 22:07:16: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.10_model.r INFO @ Sun, 02 Jun 2019 22:07:16: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:07:16: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:07:18: 14000000 INFO @ Sun, 02 Jun 2019 22:07:22: 15000000 INFO @ Sun, 02 Jun 2019 22:07:25: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:07:25: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:07:25: #1 total tags in treatment: 15364887 INFO @ Sun, 02 Jun 2019 22:07:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:07:25: #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 22:07:25: #1 tags after filtering in treatment: 15364887 INFO @ Sun, 02 Jun 2019 22:07:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:07:25: #1 finished! INFO @ Sun, 02 Jun 2019 22:07:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:07:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:07:26: 15000000 INFO @ Sun, 02 Jun 2019 22:07:27: #2 number of paired peaks: 470 WARNING @ Sun, 02 Jun 2019 22:07:27: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 02 Jun 2019 22:07:27: start model_add_line... INFO @ Sun, 02 Jun 2019 22:07:27: start X-correlation... INFO @ Sun, 02 Jun 2019 22:07:27: end of X-cor INFO @ Sun, 02 Jun 2019 22:07:27: #2 finished! INFO @ Sun, 02 Jun 2019 22:07:27: #2 predicted fragment length is 112 bps INFO @ Sun, 02 Jun 2019 22:07:27: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 02 Jun 2019 22:07:27: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.20_model.r INFO @ Sun, 02 Jun 2019 22:07:27: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:07:27: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:07:29: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 22:07:29: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 22:07:29: #1 total tags in treatment: 15364887 INFO @ Sun, 02 Jun 2019 22:07:29: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:07:29: #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 22:07:29: #1 tags after filtering in treatment: 15364887 INFO @ Sun, 02 Jun 2019 22:07:29: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:07:29: #1 finished! INFO @ Sun, 02 Jun 2019 22:07:29: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:07:29: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:07:31: #2 number of paired peaks: 470 WARNING @ Sun, 02 Jun 2019 22:07:31: Fewer paired peaks (470) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 470 pairs to build model! INFO @ Sun, 02 Jun 2019 22:07:31: start model_add_line... INFO @ Sun, 02 Jun 2019 22:07:31: start X-correlation... INFO @ Sun, 02 Jun 2019 22:07:31: end of X-cor INFO @ Sun, 02 Jun 2019 22:07:31: #2 finished! INFO @ Sun, 02 Jun 2019 22:07:31: #2 predicted fragment length is 112 bps INFO @ Sun, 02 Jun 2019 22:07:31: #2 alternative fragment length(s) may be 112 bps INFO @ Sun, 02 Jun 2019 22:07:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.05_model.r INFO @ Sun, 02 Jun 2019 22:07:31: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:07:31: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:07:57: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:08:08: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:08:11: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:08:17: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:08:17: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:08:17: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.10_summits.bed INFO @ Sun, 02 Jun 2019 22:08:17: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1962 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:08:28: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:08:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:08:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.20_summits.bed INFO @ Sun, 02 Jun 2019 22:08:28: Done! pass1 - making usageList (6 chroms): 2 millis pass2 - checking and writing primary data (1334 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:08:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:08:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:08:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX529220/SRX529220.05_summits.bed INFO @ Sun, 02 Jun 2019 22:08:30: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (2767 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。