Job ID = 4303114 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... 2019-12-11T15:45:27 fasterq-dump.2.9.6 int: no error - skipping the cache-tee completely spots read : 7,237,878 reads read : 7,237,878 reads written : 7,237,878 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: 00:03:00 7237878 reads; of these: 7237878 (100.00%) were unpaired; of these: 248169 (3.43%) aligned 0 times 4486208 (61.98%) aligned exactly 1 time 2503501 (34.59%) aligned >1 times 96.57% overall alignment rate Time searching: 00:03:00 Overall time: 00:03:00 マッピングが完了しました。 samtools でBAM に変換中... [samopen] SAM header is present: 15 sequences. [bam_rmdupse_core] 196846 / 6989709 = 0.0282 in library ' ' BAM に変換しました。 Bed ファイルを作成中... INFO @ Thu, 12 Dec 2019 00:54:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 12 Dec 2019 00:54:54: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:54:54: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:55:00: 1000000 INFO @ Thu, 12 Dec 2019 00:55:05: 2000000 INFO @ Thu, 12 Dec 2019 00:55:10: 3000000 INFO @ Thu, 12 Dec 2019 00:55:15: 4000000 INFO @ Thu, 12 Dec 2019 00:55:20: 5000000 INFO @ Thu, 12 Dec 2019 00:55:24: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 12 Dec 2019 00:55:24: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:55:24: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:55:25: 6000000 INFO @ Thu, 12 Dec 2019 00:55:29: 1000000 INFO @ Thu, 12 Dec 2019 00:55:30: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 00:55:30: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 00:55:30: #1 total tags in treatment: 6792863 INFO @ Thu, 12 Dec 2019 00:55:30: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:55:30: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:55:30: #1 tags after filtering in treatment: 6792863 INFO @ Thu, 12 Dec 2019 00:55:30: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:55:30: #1 finished! INFO @ Thu, 12 Dec 2019 00:55:30: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:55:30: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:55:30: #2 number of paired peaks: 204 WARNING @ Thu, 12 Dec 2019 00:55:30: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Thu, 12 Dec 2019 00:55:30: start model_add_line... INFO @ Thu, 12 Dec 2019 00:55:30: start X-correlation... INFO @ Thu, 12 Dec 2019 00:55:30: end of X-cor INFO @ Thu, 12 Dec 2019 00:55:30: #2 finished! INFO @ Thu, 12 Dec 2019 00:55:30: #2 predicted fragment length is 63 bps INFO @ Thu, 12 Dec 2019 00:55:30: #2 alternative fragment length(s) may be 63,546 bps INFO @ Thu, 12 Dec 2019 00:55:30: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.05_model.r WARNING @ Thu, 12 Dec 2019 00:55:30: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:55:30: #2 You may need to consider one of the other alternative d(s): 63,546 WARNING @ Thu, 12 Dec 2019 00:55:30: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:55:30: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:55:30: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:55:34: 2000000 INFO @ Thu, 12 Dec 2019 00:55:40: 3000000 INFO @ Thu, 12 Dec 2019 00:55:43: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:55:45: 4000000 INFO @ Thu, 12 Dec 2019 00:55:50: 5000000 INFO @ Thu, 12 Dec 2019 00:55:50: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.05_peaks.xls INFO @ Thu, 12 Dec 2019 00:55:50: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.05_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:55:50: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.05_summits.bed INFO @ Thu, 12 Dec 2019 00:55:50: Done! pass1 - making usageList (15 chroms): 1 millis pass2 - checking and writing primary data (2111 records, 4 fields): 148 millis CompletedMACS2peakCalling BedGraph に変換中... INFO @ Thu, 12 Dec 2019 00:55:54: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.bam'] # control file = None # effective genome size = 1.20e+08 # 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 @ Thu, 12 Dec 2019 00:55:54: #1 read tag files... INFO @ Thu, 12 Dec 2019 00:55:54: #1 read treatment tags... INFO @ Thu, 12 Dec 2019 00:55:55: 6000000 INFO @ Thu, 12 Dec 2019 00:55:59: 1000000 INFO @ Thu, 12 Dec 2019 00:55:59: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 00:55:59: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 00:55:59: #1 total tags in treatment: 6792863 INFO @ Thu, 12 Dec 2019 00:55:59: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:55:59: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:55:59: #1 tags after filtering in treatment: 6792863 INFO @ Thu, 12 Dec 2019 00:55:59: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:55:59: #1 finished! INFO @ Thu, 12 Dec 2019 00:55:59: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:55:59: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:56:00: #2 number of paired peaks: 204 WARNING @ Thu, 12 Dec 2019 00:56:00: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Thu, 12 Dec 2019 00:56:00: start model_add_line... INFO @ Thu, 12 Dec 2019 00:56:00: start X-correlation... INFO @ Thu, 12 Dec 2019 00:56:00: end of X-cor INFO @ Thu, 12 Dec 2019 00:56:00: #2 finished! INFO @ Thu, 12 Dec 2019 00:56:00: #2 predicted fragment length is 63 bps INFO @ Thu, 12 Dec 2019 00:56:00: #2 alternative fragment length(s) may be 63,546 bps INFO @ Thu, 12 Dec 2019 00:56:00: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.10_model.r WARNING @ Thu, 12 Dec 2019 00:56:00: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:56:00: #2 You may need to consider one of the other alternative d(s): 63,546 WARNING @ Thu, 12 Dec 2019 00:56:00: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:56:00: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:56:00: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:56:04: 2000000 INFO @ Thu, 12 Dec 2019 00:56:09: 3000000 INFO @ Thu, 12 Dec 2019 00:56:12: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:56:14: 4000000 INFO @ Thu, 12 Dec 2019 00:56:19: 5000000 INFO @ Thu, 12 Dec 2019 00:56:20: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.10_peaks.xls INFO @ Thu, 12 Dec 2019 00:56:20: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.10_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:56:20: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.10_summits.bed INFO @ Thu, 12 Dec 2019 00:56:20: Done! pass1 - making usageList (14 chroms): 1 millis pass2 - checking and writing primary data (1080 records, 4 fields): 3 millis CompletedMACS2peakCalling INFO @ Thu, 12 Dec 2019 00:56:25: 6000000 INFO @ Thu, 12 Dec 2019 00:56:29: #1 tag size is determined as 51 bps INFO @ Thu, 12 Dec 2019 00:56:29: #1 tag size = 51 INFO @ Thu, 12 Dec 2019 00:56:29: #1 total tags in treatment: 6792863 INFO @ Thu, 12 Dec 2019 00:56:29: #1 user defined the maximum tags... INFO @ Thu, 12 Dec 2019 00:56:29: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Thu, 12 Dec 2019 00:56:29: #1 tags after filtering in treatment: 6792863 INFO @ Thu, 12 Dec 2019 00:56:29: #1 Redundant rate of treatment: 0.00 INFO @ Thu, 12 Dec 2019 00:56:29: #1 finished! INFO @ Thu, 12 Dec 2019 00:56:29: #2 Build Peak Model... INFO @ Thu, 12 Dec 2019 00:56:29: #2 looking for paired plus/minus strand peaks... INFO @ Thu, 12 Dec 2019 00:56:29: #2 number of paired peaks: 204 WARNING @ Thu, 12 Dec 2019 00:56:29: Fewer paired peaks (204) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 204 pairs to build model! INFO @ Thu, 12 Dec 2019 00:56:29: start model_add_line... INFO @ Thu, 12 Dec 2019 00:56:29: start X-correlation... INFO @ Thu, 12 Dec 2019 00:56:29: end of X-cor INFO @ Thu, 12 Dec 2019 00:56:29: #2 finished! INFO @ Thu, 12 Dec 2019 00:56:29: #2 predicted fragment length is 63 bps INFO @ Thu, 12 Dec 2019 00:56:29: #2 alternative fragment length(s) may be 63,546 bps INFO @ Thu, 12 Dec 2019 00:56:29: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.20_model.r WARNING @ Thu, 12 Dec 2019 00:56:29: #2 Since the d (63) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Thu, 12 Dec 2019 00:56:29: #2 You may need to consider one of the other alternative d(s): 63,546 WARNING @ Thu, 12 Dec 2019 00:56:29: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Thu, 12 Dec 2019 00:56:29: #3 Call peaks... INFO @ Thu, 12 Dec 2019 00:56:29: #3 Pre-compute pvalue-qvalue table... INFO @ Thu, 12 Dec 2019 00:56:42: #3 Call peaks for each chromosome... INFO @ Thu, 12 Dec 2019 00:56:49: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.20_peaks.xls INFO @ Thu, 12 Dec 2019 00:56:49: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.20_peaks.narrowPeak INFO @ Thu, 12 Dec 2019 00:56:49: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX474524/SRX474524.20_summits.bed INFO @ Thu, 12 Dec 2019 00:56:49: Done! pass1 - making usageList (10 chroms): 0 millis pass2 - checking and writing primary data (351 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。