Job ID = 2590230 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 17,075,468 reads read : 17,075,468 reads written : 17,075,468 rm: cannot remove ‘[DSE]RR*’: 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: 00:05:37 17075468 reads; of these: 17075468 (100.00%) were unpaired; of these: 601847 (3.52%) aligned 0 times 14708602 (86.14%) aligned exactly 1 time 1765019 (10.34%) aligned >1 times 96.48% overall alignment rate Time searching: 00:05:37 Overall time: 00:05:37 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] 2644820 / 16473621 = 0.1605 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 @ Mon, 12 Aug 2019 20:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.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 @ Mon, 12 Aug 2019 20:33:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:33:17: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.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 @ Mon, 12 Aug 2019 20:33:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:33:17: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:33:17: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:33:18: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.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 @ Mon, 12 Aug 2019 20:33:18: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:33:18: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:33:28: 1000000 INFO @ Mon, 12 Aug 2019 20:33:28: 1000000 INFO @ Mon, 12 Aug 2019 20:33:28: 1000000 INFO @ Mon, 12 Aug 2019 20:33:37: 2000000 INFO @ Mon, 12 Aug 2019 20:33:37: 2000000 INFO @ Mon, 12 Aug 2019 20:33:38: 2000000 INFO @ Mon, 12 Aug 2019 20:33:46: 3000000 INFO @ Mon, 12 Aug 2019 20:33:46: 3000000 INFO @ Mon, 12 Aug 2019 20:33:47: 3000000 INFO @ Mon, 12 Aug 2019 20:33:56: 4000000 INFO @ Mon, 12 Aug 2019 20:33:56: 4000000 INFO @ Mon, 12 Aug 2019 20:33:57: 4000000 INFO @ Mon, 12 Aug 2019 20:34:05: 5000000 INFO @ Mon, 12 Aug 2019 20:34:05: 5000000 INFO @ Mon, 12 Aug 2019 20:34:07: 5000000 INFO @ Mon, 12 Aug 2019 20:34:14: 6000000 INFO @ Mon, 12 Aug 2019 20:34:14: 6000000 INFO @ Mon, 12 Aug 2019 20:34:16: 6000000 INFO @ Mon, 12 Aug 2019 20:34:23: 7000000 INFO @ Mon, 12 Aug 2019 20:34:23: 7000000 INFO @ Mon, 12 Aug 2019 20:34:26: 7000000 INFO @ Mon, 12 Aug 2019 20:34:33: 8000000 INFO @ Mon, 12 Aug 2019 20:34:33: 8000000 INFO @ Mon, 12 Aug 2019 20:34:35: 8000000 INFO @ Mon, 12 Aug 2019 20:34:42: 9000000 INFO @ Mon, 12 Aug 2019 20:34:42: 9000000 INFO @ Mon, 12 Aug 2019 20:34:45: 9000000 INFO @ Mon, 12 Aug 2019 20:34:52: 10000000 INFO @ Mon, 12 Aug 2019 20:34:52: 10000000 INFO @ Mon, 12 Aug 2019 20:34:55: 10000000 INFO @ Mon, 12 Aug 2019 20:35:01: 11000000 INFO @ Mon, 12 Aug 2019 20:35:01: 11000000 INFO @ Mon, 12 Aug 2019 20:35:04: 11000000 INFO @ Mon, 12 Aug 2019 20:35:10: 12000000 INFO @ Mon, 12 Aug 2019 20:35:10: 12000000 INFO @ Mon, 12 Aug 2019 20:35:14: 12000000 INFO @ Mon, 12 Aug 2019 20:35:19: 13000000 INFO @ Mon, 12 Aug 2019 20:35:20: 13000000 INFO @ Mon, 12 Aug 2019 20:35:24: 13000000 INFO @ Mon, 12 Aug 2019 20:35:27: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:35:27: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:35:27: #1 total tags in treatment: 13828801 INFO @ Mon, 12 Aug 2019 20:35:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:35:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:35:27: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:35:27: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:35:27: #1 total tags in treatment: 13828801 INFO @ Mon, 12 Aug 2019 20:35:27: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:35:27: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:35:27: #1 tags after filtering in treatment: 13828801 INFO @ Mon, 12 Aug 2019 20:35:27: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:35:27: #1 finished! INFO @ Mon, 12 Aug 2019 20:35:27: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:35:27: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:35:28: #1 tags after filtering in treatment: 13828801 INFO @ Mon, 12 Aug 2019 20:35:28: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:35:28: #1 finished! INFO @ Mon, 12 Aug 2019 20:35:28: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:35:28: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:35:29: #2 number of paired peaks: 1355 INFO @ Mon, 12 Aug 2019 20:35:29: start model_add_line... INFO @ Mon, 12 Aug 2019 20:35:29: #2 number of paired peaks: 1355 INFO @ Mon, 12 Aug 2019 20:35:29: start model_add_line... INFO @ Mon, 12 Aug 2019 20:35:29: start X-correlation... INFO @ Mon, 12 Aug 2019 20:35:29: end of X-cor INFO @ Mon, 12 Aug 2019 20:35:29: #2 finished! INFO @ Mon, 12 Aug 2019 20:35:29: #2 predicted fragment length is 123 bps INFO @ Mon, 12 Aug 2019 20:35:29: #2 alternative fragment length(s) may be 4,123 bps INFO @ Mon, 12 Aug 2019 20:35:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.10_model.r WARNING @ Mon, 12 Aug 2019 20:35:29: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:35:29: #2 You may need to consider one of the other alternative d(s): 4,123 WARNING @ Mon, 12 Aug 2019 20:35:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:35:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:35:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:35:29: start X-correlation... INFO @ Mon, 12 Aug 2019 20:35:29: end of X-cor INFO @ Mon, 12 Aug 2019 20:35:29: #2 finished! INFO @ Mon, 12 Aug 2019 20:35:29: #2 predicted fragment length is 123 bps INFO @ Mon, 12 Aug 2019 20:35:29: #2 alternative fragment length(s) may be 4,123 bps INFO @ Mon, 12 Aug 2019 20:35:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.05_model.r WARNING @ Mon, 12 Aug 2019 20:35:29: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:35:29: #2 You may need to consider one of the other alternative d(s): 4,123 WARNING @ Mon, 12 Aug 2019 20:35:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:35:29: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:35:29: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:35:32: #1 tag size is determined as 76 bps INFO @ Mon, 12 Aug 2019 20:35:32: #1 tag size = 76 INFO @ Mon, 12 Aug 2019 20:35:32: #1 total tags in treatment: 13828801 INFO @ Mon, 12 Aug 2019 20:35:32: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:35:32: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Mon, 12 Aug 2019 20:35:32: #1 tags after filtering in treatment: 13828801 INFO @ Mon, 12 Aug 2019 20:35:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:35:32: #1 finished! INFO @ Mon, 12 Aug 2019 20:35:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:35:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:35:33: #2 number of paired peaks: 1355 INFO @ Mon, 12 Aug 2019 20:35:33: start model_add_line... INFO @ Mon, 12 Aug 2019 20:35:34: start X-correlation... INFO @ Mon, 12 Aug 2019 20:35:34: end of X-cor INFO @ Mon, 12 Aug 2019 20:35:34: #2 finished! INFO @ Mon, 12 Aug 2019 20:35:34: #2 predicted fragment length is 123 bps INFO @ Mon, 12 Aug 2019 20:35:34: #2 alternative fragment length(s) may be 4,123 bps INFO @ Mon, 12 Aug 2019 20:35:34: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.20_model.r WARNING @ Mon, 12 Aug 2019 20:35:34: #2 Since the d (123) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:35:34: #2 You may need to consider one of the other alternative d(s): 4,123 WARNING @ Mon, 12 Aug 2019 20:35:34: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Mon, 12 Aug 2019 20:35:34: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:35:34: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:36:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:36:09: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:36:13: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:36:30: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.10_summits.bed INFO @ Mon, 12 Aug 2019 20:36:30: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:36:30: Done! INFO @ Mon, 12 Aug 2019 20:36:30: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.05_summits.bed INFO @ Mon, 12 Aug 2019 20:36:30: Done! pass1 - making usageList (7 chroms): 2 millis pass1 - making usageList (7 chroms): 4 millis pass2 - checking and writing primary data (3200 records, 4 fields): 13 millis pass2 - checking and writing primary data (5642 records, 4 fields): 13 millis CompletedMACS2peakCalling CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:36:31: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:36:31: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:36:31: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX5985664/SRX5985664.20_summits.bed INFO @ Mon, 12 Aug 2019 20:36:31: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (1364 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。