Job ID = 1292991 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 24,711,238 reads read : 24,711,238 reads written : 24,711,238 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: 00:06:24 24711238 reads; of these: 24711238 (100.00%) were unpaired; of these: 2023185 (8.19%) aligned 0 times 19222900 (77.79%) aligned exactly 1 time 3465153 (14.02%) aligned >1 times 91.81% overall alignment rate Time searching: 00:06:24 Overall time: 00:06:24 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] 9301717 / 22688053 = 0.4100 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 21:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.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 21:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.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 21:29:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:29:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:29:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:29:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:29:20: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.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 21:29:20: #1 read tag files... INFO @ Sun, 02 Jun 2019 21:29:20: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 21:29:28: 1000000 INFO @ Sun, 02 Jun 2019 21:29:30: 1000000 INFO @ Sun, 02 Jun 2019 21:29:30: 1000000 INFO @ Sun, 02 Jun 2019 21:29:35: 2000000 INFO @ Sun, 02 Jun 2019 21:29:39: 2000000 INFO @ Sun, 02 Jun 2019 21:29:40: 2000000 INFO @ Sun, 02 Jun 2019 21:29:41: 3000000 INFO @ Sun, 02 Jun 2019 21:29:48: 4000000 INFO @ Sun, 02 Jun 2019 21:29:49: 3000000 INFO @ Sun, 02 Jun 2019 21:29:49: 3000000 INFO @ Sun, 02 Jun 2019 21:29:55: 5000000 INFO @ Sun, 02 Jun 2019 21:29:58: 4000000 INFO @ Sun, 02 Jun 2019 21:29:59: 4000000 INFO @ Sun, 02 Jun 2019 21:30:03: 6000000 INFO @ Sun, 02 Jun 2019 21:30:07: 5000000 INFO @ Sun, 02 Jun 2019 21:30:08: 5000000 INFO @ Sun, 02 Jun 2019 21:30:09: 7000000 INFO @ Sun, 02 Jun 2019 21:30:16: 8000000 INFO @ Sun, 02 Jun 2019 21:30:17: 6000000 INFO @ Sun, 02 Jun 2019 21:30:18: 6000000 INFO @ Sun, 02 Jun 2019 21:30:23: 9000000 INFO @ Sun, 02 Jun 2019 21:30:25: 7000000 INFO @ Sun, 02 Jun 2019 21:30:27: 7000000 INFO @ Sun, 02 Jun 2019 21:30:30: 10000000 INFO @ Sun, 02 Jun 2019 21:30:34: 8000000 INFO @ Sun, 02 Jun 2019 21:30:35: 8000000 INFO @ Sun, 02 Jun 2019 21:30:37: 11000000 INFO @ Sun, 02 Jun 2019 21:30:43: 9000000 INFO @ Sun, 02 Jun 2019 21:30:44: 12000000 INFO @ Sun, 02 Jun 2019 21:30:44: 9000000 INFO @ Sun, 02 Jun 2019 21:30:50: 13000000 INFO @ Sun, 02 Jun 2019 21:30:52: 10000000 INFO @ Sun, 02 Jun 2019 21:30:53: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:30:53: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:30:53: #1 total tags in treatment: 13386336 INFO @ Sun, 02 Jun 2019 21:30:53: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:30:53: #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 21:30:53: 10000000 INFO @ Sun, 02 Jun 2019 21:30:53: #1 tags after filtering in treatment: 13386336 INFO @ Sun, 02 Jun 2019 21:30:53: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:30:53: #1 finished! INFO @ Sun, 02 Jun 2019 21:30:53: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:30:53: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:30:54: #2 number of paired peaks: 648 WARNING @ Sun, 02 Jun 2019 21:30:54: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Sun, 02 Jun 2019 21:30:54: start model_add_line... INFO @ Sun, 02 Jun 2019 21:30:55: start X-correlation... INFO @ Sun, 02 Jun 2019 21:30:55: end of X-cor INFO @ Sun, 02 Jun 2019 21:30:55: #2 finished! INFO @ Sun, 02 Jun 2019 21:30:55: #2 predicted fragment length is 139 bps INFO @ Sun, 02 Jun 2019 21:30:55: #2 alternative fragment length(s) may be 3,139 bps INFO @ Sun, 02 Jun 2019 21:30:55: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.10_model.r INFO @ Sun, 02 Jun 2019 21:30:55: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:30:55: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:31:01: 11000000 INFO @ Sun, 02 Jun 2019 21:31:02: 11000000 INFO @ Sun, 02 Jun 2019 21:31:10: 12000000 INFO @ Sun, 02 Jun 2019 21:31:11: 12000000 INFO @ Sun, 02 Jun 2019 21:31:18: 13000000 INFO @ Sun, 02 Jun 2019 21:31:20: 13000000 INFO @ Sun, 02 Jun 2019 21:31:22: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:31:22: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:31:22: #1 total tags in treatment: 13386336 INFO @ Sun, 02 Jun 2019 21:31:22: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:31:22: #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 21:31:22: #1 tags after filtering in treatment: 13386336 INFO @ Sun, 02 Jun 2019 21:31:22: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:31:22: #1 finished! INFO @ Sun, 02 Jun 2019 21:31:22: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:31:22: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:31:23: #1 tag size is determined as 51 bps INFO @ Sun, 02 Jun 2019 21:31:23: #1 tag size = 51 INFO @ Sun, 02 Jun 2019 21:31:23: #1 total tags in treatment: 13386336 INFO @ Sun, 02 Jun 2019 21:31:23: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 21:31:23: #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 21:31:23: #1 tags after filtering in treatment: 13386336 INFO @ Sun, 02 Jun 2019 21:31:23: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 21:31:23: #1 finished! INFO @ Sun, 02 Jun 2019 21:31:23: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 21:31:23: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 21:31:23: #2 number of paired peaks: 648 WARNING @ Sun, 02 Jun 2019 21:31:23: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Sun, 02 Jun 2019 21:31:23: start model_add_line... INFO @ Sun, 02 Jun 2019 21:31:23: start X-correlation... INFO @ Sun, 02 Jun 2019 21:31:23: end of X-cor INFO @ Sun, 02 Jun 2019 21:31:23: #2 finished! INFO @ Sun, 02 Jun 2019 21:31:23: #2 predicted fragment length is 139 bps INFO @ Sun, 02 Jun 2019 21:31:23: #2 alternative fragment length(s) may be 3,139 bps INFO @ Sun, 02 Jun 2019 21:31:23: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.20_model.r INFO @ Sun, 02 Jun 2019 21:31:23: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:31:23: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:31:24: #2 number of paired peaks: 648 WARNING @ Sun, 02 Jun 2019 21:31:24: Fewer paired peaks (648) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 648 pairs to build model! INFO @ Sun, 02 Jun 2019 21:31:24: start model_add_line... INFO @ Sun, 02 Jun 2019 21:31:25: start X-correlation... INFO @ Sun, 02 Jun 2019 21:31:25: end of X-cor INFO @ Sun, 02 Jun 2019 21:31:25: #2 finished! INFO @ Sun, 02 Jun 2019 21:31:25: #2 predicted fragment length is 139 bps INFO @ Sun, 02 Jun 2019 21:31:25: #2 alternative fragment length(s) may be 3,139 bps INFO @ Sun, 02 Jun 2019 21:31:25: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.05_model.r INFO @ Sun, 02 Jun 2019 21:31:25: #3 Call peaks... INFO @ Sun, 02 Jun 2019 21:31:25: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 21:31:33: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:31:50: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.10_peaks.xls INFO @ Sun, 02 Jun 2019 21:31:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:31:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.10_summits.bed INFO @ Sun, 02 Jun 2019 21:31:50: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (1184 records, 4 fields): 4 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:32:02: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:32:03: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 21:32:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.20_peaks.xls INFO @ Sun, 02 Jun 2019 21:32:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:32:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.20_summits.bed INFO @ Sun, 02 Jun 2019 21:32:19: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (494 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 21:32:20: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.05_peaks.xls INFO @ Sun, 02 Jun 2019 21:32:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 21:32:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5020767/SRX5020767.05_summits.bed INFO @ Sun, 02 Jun 2019 21:32:20: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2592 records, 4 fields): 5 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。