Job ID = 2590994 sra ファイルのダウンロード中... Read layout: SINGLE fastq に変換中... spots read : 18,164,520 reads read : 18,164,520 reads written : 18,164,520 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: 00:09:25 18164520 reads; of these: 18164520 (100.00%) were unpaired; of these: 8420240 (46.36%) aligned 0 times 6901314 (37.99%) aligned exactly 1 time 2842966 (15.65%) aligned >1 times 53.64% overall alignment rate Time searching: 00:09:25 Overall time: 00:09:25 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] 1507670 / 9744280 = 0.1547 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 00:49:23: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.05 -q 1e-05 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.05 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.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 00:49:23: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:49:23: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:49:25: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.10 -q 1e-10 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.10 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.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 00:49:25: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:49:25: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:49:27: # Command line: callpeak -t /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.bam -f BAM -g dm -n /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.20 -q 1e-20 # ARGUMENTS LIST: # name = /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.20 # format = BAM # ChIP-seq file = ['/home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.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 00:49:27: #1 read tag files... INFO @ Tue, 13 Aug 2019 00:49:27: #1 read treatment tags... INFO @ Tue, 13 Aug 2019 00:49:36: 1000000 INFO @ Tue, 13 Aug 2019 00:49:38: 1000000 INFO @ Tue, 13 Aug 2019 00:49:39: 1000000 INFO @ Tue, 13 Aug 2019 00:49:46: 2000000 INFO @ Tue, 13 Aug 2019 00:49:48: 2000000 INFO @ Tue, 13 Aug 2019 00:49:49: 2000000 INFO @ Tue, 13 Aug 2019 00:49:55: 3000000 INFO @ Tue, 13 Aug 2019 00:49:56: 3000000 INFO @ Tue, 13 Aug 2019 00:49:59: 3000000 INFO @ Tue, 13 Aug 2019 00:50:04: 4000000 INFO @ Tue, 13 Aug 2019 00:50:05: 4000000 INFO @ Tue, 13 Aug 2019 00:50:09: 4000000 INFO @ Tue, 13 Aug 2019 00:50:13: 5000000 INFO @ Tue, 13 Aug 2019 00:50:14: 5000000 INFO @ Tue, 13 Aug 2019 00:50:18: 5000000 INFO @ Tue, 13 Aug 2019 00:50:22: 6000000 INFO @ Tue, 13 Aug 2019 00:50:23: 6000000 INFO @ Tue, 13 Aug 2019 00:50:28: 6000000 INFO @ Tue, 13 Aug 2019 00:50:31: 7000000 INFO @ Tue, 13 Aug 2019 00:50:32: 7000000 INFO @ Tue, 13 Aug 2019 00:50:38: 7000000 INFO @ Tue, 13 Aug 2019 00:50:39: 8000000 INFO @ Tue, 13 Aug 2019 00:50:41: 8000000 INFO @ Tue, 13 Aug 2019 00:50:41: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 00:50:42: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 00:50:42: #1 total tags in treatment: 8236610 INFO @ Tue, 13 Aug 2019 00:50:42: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:50:42: #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 00:50:42: #1 tags after filtering in treatment: 8236610 INFO @ Tue, 13 Aug 2019 00:50:42: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:50:42: #1 finished! INFO @ Tue, 13 Aug 2019 00:50:42: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:50:42: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:50:42: #2 number of paired peaks: 116 WARNING @ Tue, 13 Aug 2019 00:50:42: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 13 Aug 2019 00:50:42: start model_add_line... INFO @ Tue, 13 Aug 2019 00:50:42: start X-correlation... INFO @ Tue, 13 Aug 2019 00:50:43: end of X-cor INFO @ Tue, 13 Aug 2019 00:50:43: #2 finished! INFO @ Tue, 13 Aug 2019 00:50:43: #2 predicted fragment length is 92 bps INFO @ Tue, 13 Aug 2019 00:50:43: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 13 Aug 2019 00:50:43: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.05_model.r WARNING @ Tue, 13 Aug 2019 00:50:43: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:50:43: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 13 Aug 2019 00:50:43: #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 00:50:43: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:50:43: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:50:43: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 00:50:43: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 00:50:43: #1 total tags in treatment: 8236610 INFO @ Tue, 13 Aug 2019 00:50:43: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:50:43: #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 00:50:43: #1 tags after filtering in treatment: 8236610 INFO @ Tue, 13 Aug 2019 00:50:43: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:50:43: #1 finished! INFO @ Tue, 13 Aug 2019 00:50:43: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:50:43: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:50:44: #2 number of paired peaks: 116 WARNING @ Tue, 13 Aug 2019 00:50:44: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 13 Aug 2019 00:50:44: start model_add_line... INFO @ Tue, 13 Aug 2019 00:50:44: start X-correlation... INFO @ Tue, 13 Aug 2019 00:50:44: end of X-cor INFO @ Tue, 13 Aug 2019 00:50:44: #2 finished! INFO @ Tue, 13 Aug 2019 00:50:44: #2 predicted fragment length is 92 bps INFO @ Tue, 13 Aug 2019 00:50:44: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 13 Aug 2019 00:50:44: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.10_model.r WARNING @ Tue, 13 Aug 2019 00:50:44: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:50:44: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 13 Aug 2019 00:50:44: #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 00:50:44: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:50:44: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:50:47: 8000000 INFO @ Tue, 13 Aug 2019 00:50:50: #1 tag size is determined as 100 bps INFO @ Tue, 13 Aug 2019 00:50:50: #1 tag size = 100 INFO @ Tue, 13 Aug 2019 00:50:50: #1 total tags in treatment: 8236610 INFO @ Tue, 13 Aug 2019 00:50:50: #1 user defined the maximum tags... INFO @ Tue, 13 Aug 2019 00:50:50: #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 00:50:51: #1 tags after filtering in treatment: 8236610 INFO @ Tue, 13 Aug 2019 00:50:51: #1 Redundant rate of treatment: 0.00 INFO @ Tue, 13 Aug 2019 00:50:51: #1 finished! INFO @ Tue, 13 Aug 2019 00:50:51: #2 Build Peak Model... INFO @ Tue, 13 Aug 2019 00:50:51: #2 looking for paired plus/minus strand peaks... INFO @ Tue, 13 Aug 2019 00:50:51: #2 number of paired peaks: 116 WARNING @ Tue, 13 Aug 2019 00:50:51: Fewer paired peaks (116) than 1000! Model may not be build well! Lower your MFOLD parameter may erase this warning. Now I will use 116 pairs to build model! INFO @ Tue, 13 Aug 2019 00:50:51: start model_add_line... INFO @ Tue, 13 Aug 2019 00:50:51: start X-correlation... INFO @ Tue, 13 Aug 2019 00:50:51: end of X-cor INFO @ Tue, 13 Aug 2019 00:50:51: #2 finished! INFO @ Tue, 13 Aug 2019 00:50:51: #2 predicted fragment length is 92 bps INFO @ Tue, 13 Aug 2019 00:50:51: #2 alternative fragment length(s) may be 92 bps INFO @ Tue, 13 Aug 2019 00:50:51: #2.2 Generate R script for model : /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.20_model.r WARNING @ Tue, 13 Aug 2019 00:50:51: #2 Since the d (92) calculated from paired-peaks are smaller than 2*tag length, it may be influenced by unknown sequencing problem! WARNING @ Tue, 13 Aug 2019 00:50:51: #2 You may need to consider one of the other alternative d(s): 92 WARNING @ Tue, 13 Aug 2019 00:50:51: #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 00:50:51: #3 Call peaks... INFO @ Tue, 13 Aug 2019 00:50:51: #3 Pre-compute pvalue-qvalue table... INFO @ Tue, 13 Aug 2019 00:51:06: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:51:07: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:51:15: #3 Call peaks for each chromosome... INFO @ Tue, 13 Aug 2019 00:51:18: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.05_peaks.xls INFO @ Tue, 13 Aug 2019 00:51:18: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.05_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:51:18: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.05_summits.bed INFO @ Tue, 13 Aug 2019 00:51:18: Done! pass1 - making usageList (14 chroms): 2 millis pass2 - checking and writing primary data (1309 records, 4 fields): 8 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:51:19: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.10_peaks.xls INFO @ Tue, 13 Aug 2019 00:51:19: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.10_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:51:19: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.10_summits.bed INFO @ Tue, 13 Aug 2019 00:51:19: Done! pass1 - making usageList (13 chroms): 1 millis pass2 - checking and writing primary data (842 records, 4 fields): 5 millis CompletedMACS2peakCalling INFO @ Tue, 13 Aug 2019 00:51:28: #4 Write output xls file... /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.20_peaks.xls INFO @ Tue, 13 Aug 2019 00:51:28: #4 Write peak in narrowPeak format file... /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.20_peaks.narrowPeak INFO @ Tue, 13 Aug 2019 00:51:28: #4 Write summits bed file... /home/okishinya/chipatlas/results/dm3/SRX645099/SRX645099.20_summits.bed INFO @ Tue, 13 Aug 2019 00:51:28: Done! pass1 - making usageList (8 chroms): 1 millis pass2 - checking and writing primary data (553 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。