Job ID = 2590188 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 13,181,807 reads read : 13,181,807 reads written : 13,181,807 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: 00:03:03 13181807 reads; of these: 13181807 (100.00%) were unpaired; of these: 576960 (4.38%) aligned 0 times 11022655 (83.62%) aligned exactly 1 time 1582192 (12.00%) aligned >1 times 95.62% overall alignment rate Time searching: 00:03:03 Overall time: 00:03:03 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] 2240040 / 12604847 = 0.1777 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 20:08:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.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 20:08:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:08:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:08:37: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.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 20:08:37: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:08:37: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:08:39: # Command line: callpeak -t /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.bam -f BAM -g ce -n /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.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 20:08:39: #1 read tag files... INFO @ Mon, 12 Aug 2019 20:08:39: #1 read treatment tags... INFO @ Mon, 12 Aug 2019 20:08:45: 1000000 INFO @ Mon, 12 Aug 2019 20:08:46: 1000000 INFO @ Mon, 12 Aug 2019 20:08:48: 1000000 INFO @ Mon, 12 Aug 2019 20:08:53: 2000000 INFO @ Mon, 12 Aug 2019 20:08:54: 2000000 INFO @ Mon, 12 Aug 2019 20:08:56: 2000000 INFO @ Mon, 12 Aug 2019 20:09:01: 3000000 INFO @ Mon, 12 Aug 2019 20:09:02: 3000000 INFO @ Mon, 12 Aug 2019 20:09:04: 3000000 INFO @ Mon, 12 Aug 2019 20:09:09: 4000000 INFO @ Mon, 12 Aug 2019 20:09:11: 4000000 INFO @ Mon, 12 Aug 2019 20:09:13: 4000000 INFO @ Mon, 12 Aug 2019 20:09:17: 5000000 INFO @ Mon, 12 Aug 2019 20:09:19: 5000000 INFO @ Mon, 12 Aug 2019 20:09:21: 5000000 INFO @ Mon, 12 Aug 2019 20:09:25: 6000000 INFO @ Mon, 12 Aug 2019 20:09:27: 6000000 INFO @ Mon, 12 Aug 2019 20:09:29: 6000000 INFO @ Mon, 12 Aug 2019 20:09:32: 7000000 INFO @ Mon, 12 Aug 2019 20:09:36: 7000000 INFO @ Mon, 12 Aug 2019 20:09:37: 7000000 INFO @ Mon, 12 Aug 2019 20:09:40: 8000000 INFO @ Mon, 12 Aug 2019 20:09:44: 8000000 INFO @ Mon, 12 Aug 2019 20:09:45: 8000000 INFO @ Mon, 12 Aug 2019 20:09:48: 9000000 INFO @ Mon, 12 Aug 2019 20:09:52: 9000000 INFO @ Mon, 12 Aug 2019 20:09:54: 9000000 INFO @ Mon, 12 Aug 2019 20:09:56: 10000000 INFO @ Mon, 12 Aug 2019 20:09:59: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:09:59: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:09:59: #1 total tags in treatment: 10364807 INFO @ Mon, 12 Aug 2019 20:09:59: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:09:59: #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 20:09:59: #1 tags after filtering in treatment: 10364807 INFO @ Mon, 12 Aug 2019 20:09:59: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:09:59: #1 finished! INFO @ Mon, 12 Aug 2019 20:09:59: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:09:59: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:10:00: #2 number of paired peaks: 267 WARNING @ Mon, 12 Aug 2019 20:10:00: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Mon, 12 Aug 2019 20:10:00: start model_add_line... INFO @ Mon, 12 Aug 2019 20:10:00: start X-correlation... INFO @ Mon, 12 Aug 2019 20:10:00: end of X-cor INFO @ Mon, 12 Aug 2019 20:10:00: #2 finished! INFO @ Mon, 12 Aug 2019 20:10:00: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 20:10:00: #2 alternative fragment length(s) may be 3,50,573,592 bps INFO @ Mon, 12 Aug 2019 20:10:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.05_model.r WARNING @ Mon, 12 Aug 2019 20:10:00: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:10:00: #2 You may need to consider one of the other alternative d(s): 3,50,573,592 WARNING @ Mon, 12 Aug 2019 20:10:00: #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 20:10:00: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:10:00: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:10:00: 10000000 INFO @ Mon, 12 Aug 2019 20:10:02: 10000000 INFO @ Mon, 12 Aug 2019 20:10:03: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:10:03: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:10:03: #1 total tags in treatment: 10364807 INFO @ Mon, 12 Aug 2019 20:10:03: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:10:03: #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 20:10:03: #1 tags after filtering in treatment: 10364807 INFO @ Mon, 12 Aug 2019 20:10:03: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:10:03: #1 finished! INFO @ Mon, 12 Aug 2019 20:10:03: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:10:03: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:10:04: #2 number of paired peaks: 267 WARNING @ Mon, 12 Aug 2019 20:10:04: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Mon, 12 Aug 2019 20:10:04: start model_add_line... INFO @ Mon, 12 Aug 2019 20:10:04: start X-correlation... INFO @ Mon, 12 Aug 2019 20:10:04: end of X-cor INFO @ Mon, 12 Aug 2019 20:10:04: #2 finished! INFO @ Mon, 12 Aug 2019 20:10:04: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 20:10:04: #2 alternative fragment length(s) may be 3,50,573,592 bps INFO @ Mon, 12 Aug 2019 20:10:04: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.10_model.r WARNING @ Mon, 12 Aug 2019 20:10:04: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:10:04: #2 You may need to consider one of the other alternative d(s): 3,50,573,592 WARNING @ Mon, 12 Aug 2019 20:10:04: #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 20:10:04: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:10:04: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:10:05: #1 tag size is determined as 50 bps INFO @ Mon, 12 Aug 2019 20:10:05: #1 tag size = 50 INFO @ Mon, 12 Aug 2019 20:10:05: #1 total tags in treatment: 10364807 INFO @ Mon, 12 Aug 2019 20:10:05: #1 user defined the maximum tags... INFO @ Mon, 12 Aug 2019 20:10:05: #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 20:10:05: #1 tags after filtering in treatment: 10364807 INFO @ Mon, 12 Aug 2019 20:10:05: #1 Redundant rate of treatment: 0.00 INFO @ Mon, 12 Aug 2019 20:10:05: #1 finished! INFO @ Mon, 12 Aug 2019 20:10:05: #2 Build Peak Model... INFO @ Mon, 12 Aug 2019 20:10:05: #2 looking for paired plus/minus strand peaks... INFO @ Mon, 12 Aug 2019 20:10:06: #2 number of paired peaks: 267 WARNING @ Mon, 12 Aug 2019 20:10:06: Fewer paired peaks (267) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 267 pairs to build model! INFO @ Mon, 12 Aug 2019 20:10:06: start model_add_line... INFO @ Mon, 12 Aug 2019 20:10:06: start X-correlation... INFO @ Mon, 12 Aug 2019 20:10:06: end of X-cor INFO @ Mon, 12 Aug 2019 20:10:06: #2 finished! INFO @ Mon, 12 Aug 2019 20:10:06: #2 predicted fragment length is 50 bps INFO @ Mon, 12 Aug 2019 20:10:06: #2 alternative fragment length(s) may be 3,50,573,592 bps INFO @ Mon, 12 Aug 2019 20:10:06: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.20_model.r WARNING @ Mon, 12 Aug 2019 20:10:06: #2 Since the d (50) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Mon, 12 Aug 2019 20:10:06: #2 You may need to consider one of the other alternative d(s): 3,50,573,592 WARNING @ Mon, 12 Aug 2019 20:10:06: #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 20:10:06: #3 Call peaks... INFO @ Mon, 12 Aug 2019 20:10:06: #3 Pre-compute pvalue-qvalue table... INFO @ Mon, 12 Aug 2019 20:10:28: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:10:32: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:10:34: #3 Call peaks for each chromosome... INFO @ Mon, 12 Aug 2019 20:10:42: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.05_peaks.xls INFO @ Mon, 12 Aug 2019 20:10:42: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.05_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:10:42: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.05_summits.bed INFO @ Mon, 12 Aug 2019 20:10:42: Done! pass1 - making usageList (6 chroms): 0 millis pass2 - checking and writing primary data (529 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:10:45: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.10_peaks.xls INFO @ Mon, 12 Aug 2019 20:10:45: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.10_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:10:45: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.10_summits.bed INFO @ Mon, 12 Aug 2019 20:10:45: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (300 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Mon, 12 Aug 2019 20:10:48: #4 Write output xls file... /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.20_peaks.xls INFO @ Mon, 12 Aug 2019 20:10:48: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.20_peaks.narrowPeak INFO @ Mon, 12 Aug 2019 20:10:48: #4 Write summits bed file... /home/okishinya/chipatlas/results/ce10/SRX495080/SRX495080.20_summits.bed INFO @ Mon, 12 Aug 2019 20:10:48: Done! pass1 - making usageList (6 chroms): 1 millis pass2 - checking and writing primary data (120 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。