Job ID = 1291866 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 15,030,186 reads read : 15,030,186 reads written : 15,030,186 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: 00:04:00 15030186 reads; of these: 15030186 (100.00%) were unpaired; of these: 183648 (1.22%) aligned 0 times 12282777 (81.72%) aligned exactly 1 time 2563761 (17.06%) aligned >1 times 98.78% overall alignment rate Time searching: 00:04:00 Overall time: 00:04:00 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] 2221074 / 14846538 = 0.1496 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 16:59:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.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 16:59:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:59:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:59:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.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 16:59:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:59:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:59:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.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 16:59:17: #1 read tag files... INFO @ Sun, 02 Jun 2019 16:59:17: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 16:59:24: 1000000 INFO @ Sun, 02 Jun 2019 16:59:24: 1000000 INFO @ Sun, 02 Jun 2019 16:59:25: 1000000 INFO @ Sun, 02 Jun 2019 16:59:31: 2000000 INFO @ Sun, 02 Jun 2019 16:59:31: 2000000 INFO @ Sun, 02 Jun 2019 16:59:32: 2000000 INFO @ Sun, 02 Jun 2019 16:59:38: 3000000 INFO @ Sun, 02 Jun 2019 16:59:38: 3000000 INFO @ Sun, 02 Jun 2019 16:59:39: 3000000 INFO @ Sun, 02 Jun 2019 16:59:44: 4000000 INFO @ Sun, 02 Jun 2019 16:59:44: 4000000 INFO @ Sun, 02 Jun 2019 16:59:46: 4000000 INFO @ Sun, 02 Jun 2019 16:59:51: 5000000 INFO @ Sun, 02 Jun 2019 16:59:51: 5000000 INFO @ Sun, 02 Jun 2019 16:59:53: 5000000 INFO @ Sun, 02 Jun 2019 16:59:58: 6000000 INFO @ Sun, 02 Jun 2019 16:59:58: 6000000 INFO @ Sun, 02 Jun 2019 17:00:00: 6000000 INFO @ Sun, 02 Jun 2019 17:00:05: 7000000 INFO @ Sun, 02 Jun 2019 17:00:05: 7000000 INFO @ Sun, 02 Jun 2019 17:00:08: 7000000 INFO @ Sun, 02 Jun 2019 17:00:12: 8000000 INFO @ Sun, 02 Jun 2019 17:00:12: 8000000 INFO @ Sun, 02 Jun 2019 17:00:15: 8000000 INFO @ Sun, 02 Jun 2019 17:00:18: 9000000 INFO @ Sun, 02 Jun 2019 17:00:19: 9000000 INFO @ Sun, 02 Jun 2019 17:00:22: 9000000 INFO @ Sun, 02 Jun 2019 17:00:25: 10000000 INFO @ Sun, 02 Jun 2019 17:00:25: 10000000 INFO @ Sun, 02 Jun 2019 17:00:29: 10000000 INFO @ Sun, 02 Jun 2019 17:00:32: 11000000 INFO @ Sun, 02 Jun 2019 17:00:32: 11000000 INFO @ Sun, 02 Jun 2019 17:00:37: 11000000 INFO @ Sun, 02 Jun 2019 17:00:39: 12000000 INFO @ Sun, 02 Jun 2019 17:00:39: 12000000 INFO @ Sun, 02 Jun 2019 17:00:43: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:00:43: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:00:43: #1 total tags in treatment: 12625464 INFO @ Sun, 02 Jun 2019 17:00:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:00:43: #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 17:00:43: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:00:43: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:00:43: #1 total tags in treatment: 12625464 INFO @ Sun, 02 Jun 2019 17:00:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:00:43: #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 17:00:43: #1 tags after filtering in treatment: 12625464 INFO @ Sun, 02 Jun 2019 17:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:00:43: #1 finished! INFO @ Sun, 02 Jun 2019 17:00:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:00:43: #1 tags after filtering in treatment: 12625464 INFO @ Sun, 02 Jun 2019 17:00:43: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:00:43: #1 finished! INFO @ Sun, 02 Jun 2019 17:00:43: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:00:43: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:00:44: 12000000 INFO @ Sun, 02 Jun 2019 17:00:44: #2 number of paired peaks: 361 WARNING @ Sun, 02 Jun 2019 17:00:44: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sun, 02 Jun 2019 17:00:44: start model_add_line... INFO @ Sun, 02 Jun 2019 17:00:45: start X-correlation... INFO @ Sun, 02 Jun 2019 17:00:45: end of X-cor INFO @ Sun, 02 Jun 2019 17:00:45: #2 finished! INFO @ Sun, 02 Jun 2019 17:00:45: #2 predicted fragment length is 46 bps INFO @ Sun, 02 Jun 2019 17:00:45: #2 alternative fragment length(s) may be 2,46,517,545 bps INFO @ Sun, 02 Jun 2019 17:00:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.10_model.r INFO @ Sun, 02 Jun 2019 17:00:45: #2 number of paired peaks: 361 WARNING @ Sun, 02 Jun 2019 17:00:45: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sun, 02 Jun 2019 17:00:45: start model_add_line... INFO @ Sun, 02 Jun 2019 17:00:45: start X-correlation... INFO @ Sun, 02 Jun 2019 17:00:45: end of X-cor INFO @ Sun, 02 Jun 2019 17:00:45: #2 finished! INFO @ Sun, 02 Jun 2019 17:00:45: #2 predicted fragment length is 46 bps INFO @ Sun, 02 Jun 2019 17:00:45: #2 alternative fragment length(s) may be 2,46,517,545 bps INFO @ Sun, 02 Jun 2019 17:00:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.20_model.r WARNING @ Sun, 02 Jun 2019 17:00:45: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:00:45: #2 You may need to consider one of the other alternative d(s): 2,46,517,545 WARNING @ Sun, 02 Jun 2019 17:00:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:00:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:00:45: #3 Pre-compute pvalue-qvalue table... WARNING @ Sun, 02 Jun 2019 17:00:45: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:00:45: #2 You may need to consider one of the other alternative d(s): 2,46,517,545 WARNING @ Sun, 02 Jun 2019 17:00:45: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:00:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:00:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:00:48: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 17:00:48: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 17:00:48: #1 total tags in treatment: 12625464 INFO @ Sun, 02 Jun 2019 17:00:48: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 17:00:48: #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 17:00:49: #1 tags after filtering in treatment: 12625464 INFO @ Sun, 02 Jun 2019 17:00:49: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 17:00:49: #1 finished! INFO @ Sun, 02 Jun 2019 17:00:49: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 17:00:49: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 17:00:50: #2 number of paired peaks: 361 WARNING @ Sun, 02 Jun 2019 17:00:50: Fewer paired peaks (361) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 361 pairs to build model! INFO @ Sun, 02 Jun 2019 17:00:50: start model_add_line... INFO @ Sun, 02 Jun 2019 17:00:50: start X-correlation... INFO @ Sun, 02 Jun 2019 17:00:50: end of X-cor INFO @ Sun, 02 Jun 2019 17:00:50: #2 finished! INFO @ Sun, 02 Jun 2019 17:00:50: #2 predicted fragment length is 46 bps INFO @ Sun, 02 Jun 2019 17:00:50: #2 alternative fragment length(s) may be 2,46,517,545 bps INFO @ Sun, 02 Jun 2019 17:00:50: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.05_model.r WARNING @ Sun, 02 Jun 2019 17:00:50: #2 Since the d (46) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 17:00:50: #2 You may need to consider one of the other alternative d(s): 2,46,517,545 WARNING @ Sun, 02 Jun 2019 17:00:50: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Sun, 02 Jun 2019 17:00:50: #3 Call peaks... INFO @ Sun, 02 Jun 2019 17:00:50: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 17:01:16: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:01:17: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:01:21: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 17:01:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.10_peaks.xls INFO @ Sun, 02 Jun 2019 17:01:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:01:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.10_summits.bed INFO @ Sun, 02 Jun 2019 17:01:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (499 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:01:33: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.20_peaks.xls INFO @ Sun, 02 Jun 2019 17:01:33: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:01:33: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.20_summits.bed INFO @ Sun, 02 Jun 2019 17:01:33: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (184 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 17:01:38: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.05_peaks.xls INFO @ Sun, 02 Jun 2019 17:01:38: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 17:01:38: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX257701/SRX257701.05_summits.bed INFO @ Sun, 02 Jun 2019 17:01:38: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (711 records, 4 fields): 3 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。