Job ID = 2590954 sra ファイルのダウンロード中... Read layout: PAIRED fastq に変換中... spots read : 18,748,518 reads read : 37,497,036 reads written : 37,497,036 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: 00:25:07 18748518 reads; of these: 18748518 (100.00%) were paired; of these: 10184243 (54.32%) aligned concordantly 0 times 6329860 (33.76%) aligned concordantly exactly 1 time 2234415 (11.92%) aligned concordantly >1 times ---- 10184243 pairs aligned concordantly 0 times; of these: 77925 (0.77%) aligned discordantly 1 time ---- 10106318 pairs aligned 0 times concordantly or discordantly; of these: 20212636 mates make up the pairs; of these: 19715179 (97.54%) aligned 0 times 287133 (1.42%) aligned exactly 1 time 210324 (1.04%) aligned >1 times 47.42% overall alignment rate Time searching: 00:25:07 Overall time: 00:25:07 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_sort_core] merging from 8 files... [bam_rmdup_core] processing reference chr2L... [bam_rmdup_core] processing reference chr2LHet... [bam_rmdup_core] processing reference chr2R... [bam_rmdup_core] processing reference chr2RHet... [bam_rmdup_core] processing reference chr3L... [bam_rmdup_core] processing reference chr3LHet... [bam_rmdup_core] processing reference chr3R... [bam_rmdup_core] processing reference chr3RHet... [bam_rmdup_core] processing reference chr4... [bam_rmdup_core] processing reference chrM... [bam_rmdup_core] processing reference chrU... [bam_rmdup_core] processing reference chrUextra... [bam_rmdup_core] processing reference chrX... [bam_rmdup_core] processing reference chrXHet... [bam_rmdup_core] processing reference chrYHet... [bam_rmdup_core] 1629035 / 8612652 = 0.1891 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 @ Tue, 13 Aug 2019 00:49:57: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.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 @ Tue, 13 Aug 2019 00:49:57: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:49:57: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:49:58: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.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 @ Tue, 13 Aug 2019 00:49:58: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:49:58: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:49:59: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.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 @ Tue, 13 Aug 2019 00:49:59: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:49:59: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:50:04: 1000000 INFO @ Tue, 13 Aug 2019 00:50:05: 1000000 INFO @ Tue, 13 Aug 2019 00:50:07: 1000000 INFO @ Tue, 13 Aug 2019 00:50:12: 2000000 INFO @ Tue, 13 Aug 2019 00:50:13: 2000000 INFO @ Tue, 13 Aug 2019 00:50:15: 2000000 INFO @ Tue, 13 Aug 2019 00:50:19: 3000000 INFO @ Tue, 13 Aug 2019 00:50:20: 3000000 INFO @ Tue, 13 Aug 2019 00:50:24: 3000000 INFO @ Tue, 13 Aug 2019 00:50:26: 4000000 INFO @ Tue, 13 Aug 2019 00:50:27: 4000000 INFO @ Tue, 13 Aug 2019 00:50:32: 4000000 INFO @ Tue, 13 Aug 2019 00:50:33: 5000000 INFO @ Tue, 13 Aug 2019 00:50:34: 5000000 INFO @ Tue, 13 Aug 2019 00:50:40: 5000000 INFO @ Tue, 13 Aug 2019 00:50:41: 6000000 INFO @ Tue, 13 Aug 2019 00:50:42: 6000000 INFO @ Tue, 13 Aug 2019 00:50:48: 7000000 INFO @ Tue, 13 Aug 2019 00:50:48: 6000000 INFO @ Tue, 13 Aug 2019 00:50:49: 7000000 INFO @ Tue, 13 Aug 2019 00:50:55: 8000000 INFO @ Tue, 13 Aug 2019 00:50:56: 7000000 INFO @ Tue, 13 Aug 2019 00:50:56: 8000000 INFO @ Tue, 13 Aug 2019 00:51:02: 9000000 INFO @ Tue, 13 Aug 2019 00:51:04: 9000000 INFO @ Tue, 13 Aug 2019 00:51:04: 8000000 INFO @ Tue, 13 Aug 2019 00:51:10: 10000000 INFO @ Tue, 13 Aug 2019 00:51:11: 10000000 INFO @ Tue, 13 Aug 2019 00:51:12: 9000000 INFO @ Tue, 13 Aug 2019 00:51:17: 11000000 INFO @ Tue, 13 Aug 2019 00:51:18: 11000000 INFO @ Tue, 13 Aug 2019 00:51:20: 10000000 INFO @ Tue, 13 Aug 2019 00:51:24: 12000000 INFO @ Tue, 13 Aug 2019 00:51:25: 12000000 INFO @ Tue, 13 Aug 2019 00:51:28: 11000000 INFO @ Tue, 13 Aug 2019 00:51:31: 13000000 INFO @ Tue, 13 Aug 2019 00:51:32: 13000000 INFO @ Tue, 13 Aug 2019 00:51:36: 12000000 INFO @ Tue, 13 Aug 2019 00:51:38: 14000000 INFO @ Tue, 13 Aug 2019 00:51:39: 14000000 INFO @ Tue, 13 Aug 2019 00:51:42: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:51:42: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:51:42: #1 total tags in treatment: 6946239 INFO @ Tue, 13 Aug 2019 00:51:42: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:51:42: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:51:42: #1 tags after filtering in treatment: 6362332 INFO @ Tue, 13 Aug 2019 00:51:42: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 13 Aug 2019 00:51:42: #1 finished! INFO @ Tue, 13 Aug 2019 00:51:42: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:51:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:51:43: #2 number of paired peaks: 113 WARNING @ Tue, 13 Aug 2019 00:51:43: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 13 Aug 2019 00:51:43: start model_add_line... INFO @ Tue, 13 Aug 2019 00:51:43: start X-correlation... INFO @ Tue, 13 Aug 2019 00:51:43: end of X-cor INFO @ Tue, 13 Aug 2019 00:51:43: #2 finished! INFO @ Tue, 13 Aug 2019 00:51:43: #2 predicted fragment length is 77 bps INFO @ Tue, 13 Aug 2019 00:51:43: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 13 Aug 2019 00:51:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.05_model.r WARNING @ Tue, 13 Aug 2019 00:51:43: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:51:43: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 13 Aug 2019 00:51:43: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:51:43: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:51:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:51:43: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:51:43: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:51:43: #1 total tags in treatment: 6946239 INFO @ Tue, 13 Aug 2019 00:51:43: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:51:43: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:51:43: #1 tags after filtering in treatment: 6362332 INFO @ Tue, 13 Aug 2019 00:51:43: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 13 Aug 2019 00:51:43: #1 finished! INFO @ Tue, 13 Aug 2019 00:51:43: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:51:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:51:44: #2 number of paired peaks: 113 WARNING @ Tue, 13 Aug 2019 00:51:44: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 13 Aug 2019 00:51:44: start model_add_line... INFO @ Tue, 13 Aug 2019 00:51:44: start X-correlation... INFO @ Tue, 13 Aug 2019 00:51:44: end of X-cor INFO @ Tue, 13 Aug 2019 00:51:44: #2 finished! INFO @ Tue, 13 Aug 2019 00:51:44: #2 predicted fragment length is 77 bps INFO @ Tue, 13 Aug 2019 00:51:44: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 13 Aug 2019 00:51:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.10_model.r WARNING @ Tue, 13 Aug 2019 00:51:44: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:51:44: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 13 Aug 2019 00:51:44: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:51:44: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:51:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:51:44: 13000000 INFO @ Tue, 13 Aug 2019 00:51:52: 14000000 INFO @ Tue, 13 Aug 2019 00:51:56: #1 tag size is determined as 50 bps INFO @ Tue, 13 Aug 2019 00:51:56: #1 tag size = 50 INFO @ Tue, 13 Aug 2019 00:51:56: #1 total tags in treatment: 6946239 INFO @ Tue, 13 Aug 2019 00:51:56: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:51:56: #1 filter out redundant tags at the same location and the same strand by allowing at most 1 tag(s) INFO @ Tue, 13 Aug 2019 00:51:56: #1 tags after filtering in treatment: 6362332 INFO @ Tue, 13 Aug 2019 00:51:56: #1 Redundant rate of treatment: 0.08 INFO @ Tue, 13 Aug 2019 00:51:56: #1 finished! INFO @ Tue, 13 Aug 2019 00:51:56: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:51:56: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:51:57: #2 number of paired peaks: 113 WARNING @ Tue, 13 Aug 2019 00:51:57: Fewer paired peaks (113) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 113 pairs to build model! INFO @ Tue, 13 Aug 2019 00:51:57: start model_add_line... INFO @ Tue, 13 Aug 2019 00:51:57: start X-correlation... INFO @ Tue, 13 Aug 2019 00:51:57: end of X-cor INFO @ Tue, 13 Aug 2019 00:51:57: #2 finished! INFO @ Tue, 13 Aug 2019 00:51:57: #2 predicted fragment length is 77 bps INFO @ Tue, 13 Aug 2019 00:51:57: #2 alternative fragment length(s) may be 77 bps INFO @ Tue, 13 Aug 2019 00:51:57: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.20_model.r WARNING @ Tue, 13 Aug 2019 00:51:57: #2 Since the d (77) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:51:57: #2 You may need to consider one of the other alternative d(s): 77 WARNING @ Tue, 13 Aug 2019 00:51:57: #2 You can restart the process with --nomodel --extsize XXX with your choice or an arbitrary number. Nontheless, MACS will continute computing. INFO @ Tue, 13 Aug 2019 00:51:57: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:51:57: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:52:01: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:52:02: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:52:09: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:52:09: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:52:10: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.05_summits.bed INFO @ Tue, 13 Aug 2019 00:52:10: Done! pass1 - making usageList (9 chroms): 1 millis pass2 - checking and writing primary data (402 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:52:11: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:52:11: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:52:11: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.10_summits.bed INFO @ Tue, 13 Aug 2019 00:52:11: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (208 records, 4 fields): 2 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:52:15: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:52:24: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:52:24: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:52:24: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX5865770/SRX5865770.20_summits.bed INFO @ Tue, 13 Aug 2019 00:52:24: Done! pass1 - making usageList (4 chroms): 1 millis pass2 - checking and writing primary data (115 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。