Job ID = 1293201 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 25,740,955 reads read : 25,740,955 reads written : 25,740,955 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: 00:07:14 25740955 reads; of these: 25740955 (100.00%) were unpaired; of these: 4546318 (17.66%) aligned 0 times 13379671 (51.98%) aligned exactly 1 time 7814966 (30.36%) aligned >1 times 82.34% overall alignment rate Time searching: 00:07:14 Overall time: 00:07:14 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] 6302520 / 21194637 = 0.2974 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 22:37:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.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 22:37:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:37:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:37:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.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 22:37:54: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:37:54: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:37:55: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.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 22:37:55: #1 read tag files... INFO @ Sun, 02 Jun 2019 22:37:55: #1 read treatment tags... INFO @ Sun, 02 Jun 2019 22:38:02: 1000000 INFO @ Sun, 02 Jun 2019 22:38:03: 1000000 INFO @ Sun, 02 Jun 2019 22:38:03: 1000000 INFO @ Sun, 02 Jun 2019 22:38:09: 2000000 INFO @ Sun, 02 Jun 2019 22:38:10: 2000000 INFO @ Sun, 02 Jun 2019 22:38:12: 2000000 INFO @ Sun, 02 Jun 2019 22:38:16: 3000000 INFO @ Sun, 02 Jun 2019 22:38:18: 3000000 INFO @ Sun, 02 Jun 2019 22:38:20: 3000000 INFO @ Sun, 02 Jun 2019 22:38:23: 4000000 INFO @ Sun, 02 Jun 2019 22:38:26: 4000000 INFO @ Sun, 02 Jun 2019 22:38:29: 4000000 INFO @ Sun, 02 Jun 2019 22:38:30: 5000000 INFO @ Sun, 02 Jun 2019 22:38:34: 5000000 INFO @ Sun, 02 Jun 2019 22:38:37: 5000000 INFO @ Sun, 02 Jun 2019 22:38:37: 6000000 INFO @ Sun, 02 Jun 2019 22:38:41: 6000000 INFO @ Sun, 02 Jun 2019 22:38:44: 7000000 INFO @ Sun, 02 Jun 2019 22:38:45: 6000000 INFO @ Sun, 02 Jun 2019 22:38:49: 7000000 INFO @ Sun, 02 Jun 2019 22:38:51: 8000000 INFO @ Sun, 02 Jun 2019 22:38:55: 7000000 INFO @ Sun, 02 Jun 2019 22:38:57: 8000000 INFO @ Sun, 02 Jun 2019 22:38:59: 9000000 INFO @ Sun, 02 Jun 2019 22:39:03: 8000000 INFO @ Sun, 02 Jun 2019 22:39:05: 9000000 INFO @ Sun, 02 Jun 2019 22:39:07: 10000000 INFO @ Sun, 02 Jun 2019 22:39:12: 9000000 INFO @ Sun, 02 Jun 2019 22:39:13: 10000000 INFO @ Sun, 02 Jun 2019 22:39:14: 11000000 INFO @ Sun, 02 Jun 2019 22:39:21: 10000000 INFO @ Sun, 02 Jun 2019 22:39:21: 11000000 INFO @ Sun, 02 Jun 2019 22:39:22: 12000000 INFO @ Sun, 02 Jun 2019 22:39:29: 12000000 INFO @ Sun, 02 Jun 2019 22:39:29: 13000000 INFO @ Sun, 02 Jun 2019 22:39:29: 11000000 INFO @ Sun, 02 Jun 2019 22:39:36: 13000000 INFO @ Sun, 02 Jun 2019 22:39:36: 14000000 INFO @ Sun, 02 Jun 2019 22:39:38: 12000000 INFO @ Sun, 02 Jun 2019 22:39:43: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:39:43: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:39:43: #1 total tags in treatment: 14892117 INFO @ Sun, 02 Jun 2019 22:39:43: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:39:43: #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 22:39:44: #1 tags after filtering in treatment: 14892117 INFO @ Sun, 02 Jun 2019 22:39:44: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:39:44: #1 finished! INFO @ Sun, 02 Jun 2019 22:39:44: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:39:44: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:39:44: 14000000 INFO @ Sun, 02 Jun 2019 22:39:45: #2 number of paired peaks: 2095 INFO @ Sun, 02 Jun 2019 22:39:45: start model_add_line... INFO @ Sun, 02 Jun 2019 22:39:45: start X-correlation... INFO @ Sun, 02 Jun 2019 22:39:45: end of X-cor INFO @ Sun, 02 Jun 2019 22:39:45: #2 finished! INFO @ Sun, 02 Jun 2019 22:39:45: #2 predicted fragment length is 98 bps INFO @ Sun, 02 Jun 2019 22:39:45: #2 alternative fragment length(s) may be 4,98 bps INFO @ Sun, 02 Jun 2019 22:39:45: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.10_model.r WARNING @ Sun, 02 Jun 2019 22:39:45: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:39:45: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Sun, 02 Jun 2019 22:39:45: #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 22:39:45: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:39:45: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:39:47: 13000000 INFO @ Sun, 02 Jun 2019 22:39:51: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:39:51: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:39:51: #1 total tags in treatment: 14892117 INFO @ Sun, 02 Jun 2019 22:39:51: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:39:51: #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 22:39:51: #1 tags after filtering in treatment: 14892117 INFO @ Sun, 02 Jun 2019 22:39:51: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:39:51: #1 finished! INFO @ Sun, 02 Jun 2019 22:39:51: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:39:51: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:39:53: #2 number of paired peaks: 2095 INFO @ Sun, 02 Jun 2019 22:39:53: start model_add_line... INFO @ Sun, 02 Jun 2019 22:39:53: start X-correlation... INFO @ Sun, 02 Jun 2019 22:39:53: end of X-cor INFO @ Sun, 02 Jun 2019 22:39:53: #2 finished! INFO @ Sun, 02 Jun 2019 22:39:53: #2 predicted fragment length is 98 bps INFO @ Sun, 02 Jun 2019 22:39:53: #2 alternative fragment length(s) may be 4,98 bps INFO @ Sun, 02 Jun 2019 22:39:53: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.20_model.r WARNING @ Sun, 02 Jun 2019 22:39:53: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:39:53: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Sun, 02 Jun 2019 22:39:53: #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 22:39:53: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:39:53: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:39:57: 14000000 INFO @ Sun, 02 Jun 2019 22:40:05: #1 tag size is determined as 50 bps INFO @ Sun, 02 Jun 2019 22:40:05: #1 tag size = 50 INFO @ Sun, 02 Jun 2019 22:40:05: #1 total tags in treatment: 14892117 INFO @ Sun, 02 Jun 2019 22:40:05: #1 user defined the maximum tags... INFO @ Sun, 02 Jun 2019 22:40:05: #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 22:40:05: #1 tags after filtering in treatment: 14892117 INFO @ Sun, 02 Jun 2019 22:40:05: #1 Redundant rate of treatment: 0.00 INFO @ Sun, 02 Jun 2019 22:40:05: #1 finished! INFO @ Sun, 02 Jun 2019 22:40:05: #2 Build Peak Model... INFO @ Sun, 02 Jun 2019 22:40:05: #2 looking for paired plus/minus strand peaks... INFO @ Sun, 02 Jun 2019 22:40:07: #2 number of paired peaks: 2095 INFO @ Sun, 02 Jun 2019 22:40:07: start model_add_line... INFO @ Sun, 02 Jun 2019 22:40:07: start X-correlation... INFO @ Sun, 02 Jun 2019 22:40:07: end of X-cor INFO @ Sun, 02 Jun 2019 22:40:07: #2 finished! INFO @ Sun, 02 Jun 2019 22:40:07: #2 predicted fragment length is 98 bps INFO @ Sun, 02 Jun 2019 22:40:07: #2 alternative fragment length(s) may be 4,98 bps INFO @ Sun, 02 Jun 2019 22:40:07: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.05_model.r WARNING @ Sun, 02 Jun 2019 22:40:07: #2 Since the d (98) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Sun, 02 Jun 2019 22:40:07: #2 You may need to consider one of the other alternative d(s): 4,98 WARNING @ Sun, 02 Jun 2019 22:40:07: #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 22:40:07: #3 Call peaks... INFO @ Sun, 02 Jun 2019 22:40:07: #3 Pre-compute pvalue-qvalue table... INFO @ Sun, 02 Jun 2019 22:40:28: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:40:36: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:40:49: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.10_peaks.xls INFO @ Sun, 02 Jun 2019 22:40:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.10_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:40:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.10_summits.bed INFO @ Sun, 02 Jun 2019 22:40:49: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (6706 records, 4 fields): 10 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:40:50: #3 Call peaks for each chromosome... INFO @ Sun, 02 Jun 2019 22:40:56: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.20_peaks.xls INFO @ Sun, 02 Jun 2019 22:40:56: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.20_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:40:56: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.20_summits.bed INFO @ Sun, 02 Jun 2019 22:40:56: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (3376 records, 4 fields): 6 millis CompletedMACS2peakCalling INFO @ Sun, 02 Jun 2019 22:41:11: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.05_peaks.xls INFO @ Sun, 02 Jun 2019 22:41:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.05_peaks.narrowPeak INFO @ Sun, 02 Jun 2019 22:41:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5402754/SRX5402754.05_summits.bed INFO @ Sun, 02 Jun 2019 22:41:11: Done! pass1 - making usageList (7 chroms): 2 millis pass2 - checking and writing primary data (10212 records, 4 fields): 14 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。