Job ID = 2589382 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 8,331,974 reads read : 8,331,974 reads written : 8,331,974 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: 00:01:32 8331974 reads; of these: 8331974 (100.00%) were unpaired; of these: 385859 (4.63%) aligned 0 times 6698140 (80.39%) aligned exactly 1 time 1247975 (14.98%) aligned >1 times 95.37% overall alignment rate Time searching: 00:01:32 Overall time: 00:01:32 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] 668048 / 7946115 = 0.0841 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 17:37:38: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.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 17:37:38: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:37:38: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:37:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.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 17:37:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:37:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:37:40: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.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 17:37:40: #1 read tag files... INFO @ Mon, 12 Aug 2019 17:37:40: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 17:37:45: 1000000 INFO @ Mon, 12 Aug 2019 17:37:46: 1000000 INFO @ Mon, 12 Aug 2019 17:37:47: 1000000 INFO @ Mon, 12 Aug 2019 17:37:52: 2000000 INFO @ Mon, 12 Aug 2019 17:37:54: 2000000 INFO @ Mon, 12 Aug 2019 17:37:55: 2000000 INFO @ Mon, 12 Aug 2019 17:38:00: 3000000 INFO @ Mon, 12 Aug 2019 17:38:01: 3000000 INFO @ Mon, 12 Aug 2019 17:38:02: 3000000 INFO @ Mon, 12 Aug 2019 17:38:07: 4000000 INFO @ Mon, 12 Aug 2019 17:38:08: 4000000 INFO @ Mon, 12 Aug 2019 17:38:09: 4000000 INFO @ Mon, 12 Aug 2019 17:38:14: 5000000 INFO @ Mon, 12 Aug 2019 17:38:15: 5000000 INFO @ Mon, 12 Aug 2019 17:38:16: 5000000 INFO @ Mon, 12 Aug 2019 17:38:21: 6000000 INFO @ Mon, 12 Aug 2019 17:38:22: 6000000 INFO @ Mon, 12 Aug 2019 17:38:24: 6000000 INFO @ Mon, 12 Aug 2019 17:38:28: 7000000 INFO @ Mon, 12 Aug 2019 17:38:30: 7000000 INFO @ Mon, 12 Aug 2019 17:38:30: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:38:30: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:38:30: #1 total tags in treatment: 7278067 INFO @ Mon, 12 Aug 2019 17:38:30: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:38:30: #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 17:38:30: #1 tags after filtering in treatment: 7278067 INFO @ Mon, 12 Aug 2019 17:38:30: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:38:30: #1 finished! INFO @ Mon, 12 Aug 2019 17:38:30: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:38:30: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:38:31: 7000000 INFO @ Mon, 12 Aug 2019 17:38:31: #2 number of paired peaks: 333 WARNING @ Mon, 12 Aug 2019 17:38:31: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Mon, 12 Aug 2019 17:38:31: start model_add_line... INFO @ Mon, 12 Aug 2019 17:38:31: start X-correlation... INFO @ Mon, 12 Aug 2019 17:38:31: end of X-cor INFO @ Mon, 12 Aug 2019 17:38:31: #2 finished! INFO @ Mon, 12 Aug 2019 17:38:31: #2 predicted fragment length is 36 bps INFO @ Mon, 12 Aug 2019 17:38:31: #2 alternative fragment length(s) may be 3,36 bps INFO @ Mon, 12 Aug 2019 17:38:31: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.05_model.r WARNING @ Mon, 12 Aug 2019 17:38:31: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:38:31: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Mon, 12 Aug 2019 17:38:31: #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 17:38:31: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:38:31: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:38:31: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:38:31: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:38:31: #1 total tags in treatment: 7278067 INFO @ Mon, 12 Aug 2019 17:38:31: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:38:31: #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 17:38:32: #1 tags after filtering in treatment: 7278067 INFO @ Mon, 12 Aug 2019 17:38:32: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:38:32: #1 finished! INFO @ Mon, 12 Aug 2019 17:38:32: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:38:32: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:38:32: #2 number of paired peaks: 333 WARNING @ Mon, 12 Aug 2019 17:38:32: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Mon, 12 Aug 2019 17:38:32: start model_add_line... INFO @ Mon, 12 Aug 2019 17:38:32: start X-correlation... INFO @ Mon, 12 Aug 2019 17:38:32: end of X-cor INFO @ Mon, 12 Aug 2019 17:38:32: #2 finished! INFO @ Mon, 12 Aug 2019 17:38:32: #2 predicted fragment length is 36 bps INFO @ Mon, 12 Aug 2019 17:38:32: #2 alternative fragment length(s) may be 3,36 bps INFO @ Mon, 12 Aug 2019 17:38:32: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.10_model.r WARNING @ Mon, 12 Aug 2019 17:38:32: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:38:32: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Mon, 12 Aug 2019 17:38:32: #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 17:38:32: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:38:32: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:38:33: #1 tag size is determined as 32 bps INFO @ Mon, 12 Aug 2019 17:38:33: #1 tag size = 32 INFO @ Mon, 12 Aug 2019 17:38:33: #1 total tags in treatment: 7278067 INFO @ Mon, 12 Aug 2019 17:38:33: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 17:38:33: #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 17:38:33: #1 tags after filtering in treatment: 7278067 INFO @ Mon, 12 Aug 2019 17:38:33: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 17:38:33: #1 finished! INFO @ Mon, 12 Aug 2019 17:38:33: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 17:38:33: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 17:38:33: #2 number of paired peaks: 333 WARNING @ Mon, 12 Aug 2019 17:38:33: Fewer paired peaks (333) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 333 pairs to build model! INFO @ Mon, 12 Aug 2019 17:38:33: start model_add_line... INFO @ Mon, 12 Aug 2019 17:38:33: start X-correlation... INFO @ Mon, 12 Aug 2019 17:38:33: end of X-cor INFO @ Mon, 12 Aug 2019 17:38:33: #2 finished! INFO @ Mon, 12 Aug 2019 17:38:33: #2 predicted fragment length is 36 bps INFO @ Mon, 12 Aug 2019 17:38:33: #2 alternative fragment length(s) may be 3,36 bps INFO @ Mon, 12 Aug 2019 17:38:33: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.20_model.r WARNING @ Mon, 12 Aug 2019 17:38:33: #2 Since the d (36) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 17:38:33: #2 You may need to consider one of the other alternative d(s): 3,36 WARNING @ Mon, 12 Aug 2019 17:38:33: #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 17:38:33: #3 Call peaks... INFO @ Mon, 12 Aug 2019 17:38:33: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 17:38:51: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:38:52: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:38:53: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 17:39:00: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.05_peaks.xls INFO @ Mon, 12 Aug 2019 17:39:00: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:39:00: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.05_summits.bed INFO @ Mon, 12 Aug 2019 17:39:00: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (469 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:39:02: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.10_peaks.xls INFO @ Mon, 12 Aug 2019 17:39:02: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:39:02: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.10_summits.bed INFO @ Mon, 12 Aug 2019 17:39:02: Done! pass1 - making usageList (7 chroms): 1 millis pass2 - checking and writing primary data (230 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 17:39:03: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.20_peaks.xls INFO @ Mon, 12 Aug 2019 17:39:03: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 17:39:03: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX118219/SRX118219.20_summits.bed INFO @ Mon, 12 Aug 2019 17:39:03: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (74 records, 4 fields): 2 millis CompletedMACS2peakCalling BedGraph に変換しました。 BigWig に変換中... BigWig に変換しました。