Job ID = 1292341 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,765,284 reads read : 13,765,284 reads written : 13,765,284 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: 00:02:38 13765284 reads; of these: 13765284 (100.00%) were unpaired; of these: 1747116 (12.69%) aligned 0 times 10018791 (72.78%) aligned exactly 1 time 1999377 (14.52%) aligned >1 times 87.31% overall alignment rate Time searching: 00:02:38 Overall time: 00:02:38 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] 2639070 / 12018168 = 0.2196 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 17:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.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 17:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.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 17:58:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:21: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.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 17:58:21: #1 read tag files... INFO @ Sun, 02 Jun 2019 17:58:21: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 17:58:28: 1000000 INFO @ Sun, 02 Jun 2019 17:58:29: 1000000 INFO @ Sun, 02 Jun 2019 17:58:30: 1000000 INFO @ Sun, 02 Jun 2019 17:58:35: 2000000 INFO @ Sun, 02 Jun 2019 17:58:37: 2000000 INFO @ Sun, 02 Jun 2019 17:58:39: 2000000 INFO @ Sun, 02 Jun 2019 17:58:41: 3000000 INFO @ Sun, 02 Jun 2019 17:58:45: 3000000 INFO @ Sun, 02 Jun 2019 17:58:48: 3000000 INFO @ Sun, 02 Jun 2019 17:58:48: 4000000 INFO @ Sun, 02 Jun 2019 17:58:53: 4000000 INFO @ Sun, 02 Jun 2019 17:58:55: 5000000 INFO @ Sun, 02 Jun 2019 17:58:56: 4000000 INFO @ Sun, 02 Jun 2019 17:59:01: 5000000 INFO @ Sun, 02 Jun 2019 17:59:02: 6000000 INFO @ Sun, 02 Jun 2019 17:59:05: 5000000 INFO @ Sun, 02 Jun 2019 17:59:09: 6000000 INFO @ Sun, 02 Jun 2019 17:59:09: 7000000 INFO @ Sun, 02 Jun 2019 17:59:14: 6000000 INFO @ Sun, 02 Jun 2019 17:59:16: 8000000 INFO @ Sun, 02 Jun 2019 17:59:16: 7000000 INFO @ Sun, 02 Jun 2019 17:59:22: 9000000 INFO @ Sun, 02 Jun 2019 17:59:23: 7000000 INFO @ Sun, 02 Jun 2019 17:59:24: 8000000 INFO @ Sun, 02 Jun 2019 17:59:25: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 17:59:25: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 17:59:25: #1 total tags in treatment: 9379098 INFO @ Sun, 02 Jun 2019 17:59:25: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:59:25: #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 17:59:25: #1 tags after filtering in treatment: 9379098 INFO @ Sun, 02 Jun 2019 17:59:25: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:59:25: #1 finished! INFO @ Sun, 02 Jun 2019 17:59:25: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:59:25: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:59:26: #2 number of paired peaks: 977 WARNING @ Sun, 02 Jun 2019 17:59:26: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Sun, 02 Jun 2019 17:59:26: start model_add_line... INFO @ Sun, 02 Jun 2019 17:59:26: start X-correlation... INFO @ Sun, 02 Jun 2019 17:59:26: end of X-cor INFO @ Sun, 02 Jun 2019 17:59:26: #2 finished! INFO @ Sun, 02 Jun 2019 17:59:26: #2 predicted fragment length is 146 bps INFO @ Sun, 02 Jun 2019 17:59:26: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 02 Jun 2019 17:59:26: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.10_model.r INFO @ Sun, 02 Jun 2019 17:59:26: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:59:26: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:59:31: 8000000 INFO @ Sun, 02 Jun 2019 17:59:32: 9000000 INFO @ Sun, 02 Jun 2019 17:59:35: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 17:59:35: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 17:59:35: #1 total tags in treatment: 9379098 INFO @ Sun, 02 Jun 2019 17:59:35: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:59:35: #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 17:59:35: #1 tags after filtering in treatment: 9379098 INFO @ Sun, 02 Jun 2019 17:59:35: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:59:35: #1 finished! INFO @ Sun, 02 Jun 2019 17:59:35: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:59:35: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:59:36: #2 number of paired peaks: 977 WARNING @ Sun, 02 Jun 2019 17:59:36: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Sun, 02 Jun 2019 17:59:36: start model_add_line... INFO @ Sun, 02 Jun 2019 17:59:36: start X-correlation... INFO @ Sun, 02 Jun 2019 17:59:36: end of X-cor INFO @ Sun, 02 Jun 2019 17:59:36: #2 finished! INFO @ Sun, 02 Jun 2019 17:59:36: #2 predicted fragment length is 146 bps INFO @ Sun, 02 Jun 2019 17:59:36: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 02 Jun 2019 17:59:36: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.05_model.r INFO @ Sun, 02 Jun 2019 17:59:36: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:59:36: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:59:39: 9000000 INFO @ Sun, 02 Jun 2019 17:59:43: #1 tag size is determined as 36 bps INFO @ Sun, 02 Jun 2019 17:59:43: #1 tag size = 36 INFO @ Sun, 02 Jun 2019 17:59:43: #1 total tags in treatment: 9379098 INFO @ Sun, 02 Jun 2019 17:59:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:59:43: #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 17:59:43: #1 tags after filtering in treatment: 9379098 INFO @ Sun, 02 Jun 2019 17:59:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:59:43: #1 finished! INFO @ Sun, 02 Jun 2019 17:59:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:59:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:59:44: #2 number of paired peaks: 977 WARNING @ Sun, 02 Jun 2019 17:59:44: Fewer paired peaks (977) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 977 pairs to build model! INFO @ Sun, 02 Jun 2019 17:59:44: start model_add_line... INFO @ Sun, 02 Jun 2019 17:59:44: start X-correlation... INFO @ Sun, 02 Jun 2019 17:59:44: end of X-cor INFO @ Sun, 02 Jun 2019 17:59:44: #2 finished! INFO @ Sun, 02 Jun 2019 17:59:44: #2 predicted fragment length is 146 bps INFO @ Sun, 02 Jun 2019 17:59:44: #2 alternative fragment length(s) may be 146 bps INFO @ Sun, 02 Jun 2019 17:59:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.20_model.r INFO @ Sun, 02 Jun 2019 17:59:44: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:59:44: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:59:54: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:00:05: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:00:07: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.10_peaks.xls INFO @ Sun, 02 Jun 2019 18:00:07: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:00:07: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.10_summits.bed INFO @ Sun, 02 Jun 2019 18:00:07: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (3851 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:00:12: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 18:00:19: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.05_peaks.xls INFO @ Sun, 02 Jun 2019 18:00:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:00:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.05_summits.bed INFO @ Sun, 02 Jun 2019 18:00:19: Done! pass1 - making usageList (7 chroms): 3 millis pass2 - checking and writing primary data (5269 records, 4 fields): 11 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 18:00:25: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.20_peaks.xls INFO @ Sun, 02 Jun 2019 18:00:25: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 18:00:25: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX335101/SRX335101.20_summits.bed INFO @ Sun, 02 Jun 2019 18:00:25: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (2560 records, 4 fields): 6 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。